PI | Yashar Ahmadian |
---|---|
Organization | University of Oregon |
Department | Institute of Neuroscience |
Field of Science | Neuroscience |
Sponsor | CG OSG Connect |
Date Registered | 09/27/2017 |
Abstract of work | We investigate how synchronous population activity arise in spiking dynamics of the sensory and other cortical areas. We especially focus on how primary auditory cortex modulate dynamical timescales during spontaneous bump dynamics in quiet wake condition and up and down states in anesthetized and sleep conditions. |
PI | Trevor Santarra |
---|---|
Organization | University of California Santa Cruz |
Department | Computer Science |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 01/26/2017 |
Abstract of work | We are evaluating heuristic approaches from active learning for communicating partial policy information in ad hoc teamwork scenarios. |
PI | Rob Quick |
---|---|
Organization | Indiana University |
Department | UITS |
Field of Science | Education |
Sponsor | CG OSG Connect |
Date Registered | 06/10/2016 |
Abstract of work | A project for teaching the grid computing component of the African School of Physics. |
PI | David Minh |
---|---|
Organization | Illinois Institute of Technology |
Department | Chemistry |
Field of Science | Chemistry |
Sponsor | CG OSG Connect |
Date Registered | 05/06/2014 |
Abstract of work | Binding Potential of Mean Force Calculations with Alchemical Interaction Grids Standard binding free energies are frequently sought in drug design. According to implicit ligand theory, standard binding free energies can be determined from binding potential of mean force (PMF) calculations from different receptor structures. Binding PMFs are a special type of binding free energy in which the receptor is rigid. The purpose of this project is to develop methods for estimating binding PMFs. |
PI | John Carlstrom |
---|---|
Organization | University of Chicago |
Department | Physics |
Field of Science | Astrophysics |
Sponsor | CG SPT Connect |
Date Registered | 10/24/2016 |
Abstract of work | The South Pole Telescope (or SPT) is a new telescope deployed at the South Pole that is designed to study the Cosmic Microwave background. Constructed between November 2006 and February 2007, the SPT is the largest telescope ever deployed at the South Pole. This telescope provides astronomers a powerful new tool to explore dark energy, the mysterious phenomena that may be causing the universe to accelerate. SPT members from various institutions are all added into this group. This group utilize the OSG opportunistic cycles. |
PI | Ian Foster |
---|---|
Organization | University of Chicago |
Department | Computer Science |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 11/27/2013 |
Abstract of work | Amfora is a POSIX-compatible parallel scripting framework that lets users run existing programs in parallel with data stored in RAM on distributed platforms: e.g. clouds, clusters, supercomputers. |
PI | Patrick Charbonneau |
---|---|
Organization | Duke University |
Department | Chemistry |
Field of Science | Chemistry |
Sponsor | CG OSG Connect |
Date Registered | 01/11/2016 |
Abstract of work | Glass-forming liquids exhibit dramatical slowdown upon cooling, which may be controlled by the growing amorphous order that emerges due to the rarefaction of metastable states in the rugged free-energy landscape. The amorphous order is well captured by point-to-set correlations, and their measurements are indispensable in testing ideas surrounding this new order parameter. To attain good statistics on point-to-set observables, however, requires a huge number of independent simulations. Exploration of many parameter ranges -- such as temperature or confinement parameters -- further increases the need for parallel computing. The high throughout computing thus provides an ideal tool for investigating the notion of the growing amorphous order in glassy systems. |
PI | Baosong Shan |
---|---|
Organization | MIT |
Department | LNS |
Field of Science | Particle Physics |
Sponsor | VO OSG |
Date Registered | 02/16/2016 |
Abstract of work | Monte Carlo simulation for the AMS experiment |
PI | Erol Akcay |
---|---|
Organization | University of Pennsylvania |
Department | Biology |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 11/30/2015 |
Abstract of work | Project Name: Animal Social Networks Short Project Name: AnimalSocialNetworks Field of Science: Ecology Field of Science (if Other): PI Name: Erol Akcay PI Email: eakcay@sas.upenn.edu PI Organization: University of Pennsylvania PI Department: Biology Join Date: Nov 30th 2015 Sponsor: OSG Connect OSG Sponsor Contact: Bala Project Contact: Amiyaal Ilany Project Contact Email: amiyaal@sas.upenn.edu Telephone Number: Project Description: Modeling the formation and dynamics of animal social networks, and how these dynamics affect phenomena at the individual and population levels |
PI | Jan Balewski |
---|---|
Organization | MIT |
Department | LNS |
Field of Science | Nuclear Physics |
Sponsor | CG OSG Connect |
Date Registered | 04/08/2014 |
Abstract of work | DarkLight experiment planned to run at Jefferson LAB in the upcoming years will search for a massive photon possibly produced in interaction of an electron with electric filed of a proton. Monte-Carlo simulations are needed design and optimize the Darklight experiment. The initial OSG-Connect resources of few CPU years will be sufficient. The simulation will use CERN libraries, namely: Geant4.10, root5.34, compiled on Scientific Linux 6.5. |
PI | Joe Boyd |
---|---|
Organization | Fermilab |
Department | N/A |
Field of Science | High Energy Physics |
Sponsor | VO Fermilab |
Date Registered | 03/15/2018 |
Abstract of work | Project entry corresponding to the Argoneut VO. |
PI | ilyoup kwak |
---|---|
Organization | University of Minnesota |
Department | Division of Biostatistics |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 05/01/2015 |
Abstract of work | developing genetic association tests using GWAS data |
PI | Jay Etchings |
---|---|
Organization | Arizona State University |
Department | Research Computing |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 07/10/2017 |
Abstract of work | Testing OSG integration with ASU HPC |
PI | Robert William Gardner Jr |
---|---|
Organization | State University of New York — Albany |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for SUNY Albany |
PI | Robert William Gardner Jr |
---|---|
Organization | Argonne National Laboratory |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Argonne National Laboratory |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Arizona |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for University of Arizona |
PI | Robert William Gardner Jr |
---|---|
Organization | Brookhaven National Laboratory |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Brookhaven National Laboratory |
PI | Robert William Gardner Jr |
---|---|
Organization | Brandeis University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Brandeis University |
PI | Robert William Gardner Jr |
---|---|
Organization | Boston University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Boston University |
PI | Robert William Gardner Jr |
---|---|
Organization | Columbia University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Columbia University |
PI | Doug Benjamin |
---|---|
Organization | Duke University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 06/05/2014 |
Abstract of work | Duke University's Tier 2 ATLAS group in ATLAS Connect. |
PI | Harinder Singh Bawa |
---|---|
Organization | Fresno State University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 06/05/2014 |
Abstract of work | Fresno State University's Tier 3 ATLAS group in ATLAS Connect. |
PI | Robert William Gardner Jr |
---|---|
Organization | Hampton University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Hampton University |
PI | Robert William Gardner Jr |
---|---|
Organization | Harvard University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Harvard University |
PI | Robert William Gardner Jr |
---|---|
Organization | Iowa State University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Iowa State University |
PI | Mark Neubauer |
---|---|
Organization | University of Illinois |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 06/05/2014 |
Abstract of work | University of Illinois Urbana/Champaign Tier 3 ATLAS group. |
PI | Frederick Luehring |
---|---|
Organization | Indiana University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 06/05/2014 |
Abstract of work | Indiana University Tier 3 ATLAS group. |
PI | Robert William Gardner Jr |
---|---|
Organization | US ATLAS |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Jet EtMiss |
PI | Robert William Gardner Jr |
---|---|
Organization | Louisiana Tech University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Louisiana Tech University |
PI | Robert William Gardner Jr |
---|---|
Organization | Lawrence Berkeley National Laboratory |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Lawrence Berkeley National Laboratory |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Louisville |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | University of Louisville |
PI | Robert William Gardner Jr |
---|---|
Organization | MIT |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for MIT |
PI | Robert William Gardner Jr |
---|---|
Organization | Michigan State University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Michigan State University |
PI | Robert William Gardner Jr |
---|---|
Organization | Northern Illinois University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Northern Illinois University |
PI | Robert William Gardner Jr |
---|---|
Organization | New York University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for New York University |
PI | Robert William Gardner Jr |
---|---|
Organization | Oklahoma State University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Oklahoma State University |
PI | Robert William Gardner Jr |
---|---|
Organization | The Ohio State University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for The Ohio State University |
PI | Robert William Gardner Jr |
---|---|
Organization | Oklahoma University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Oklahoma University |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Pittsburgh |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for University of Pittsburgh |
PI | Robert William Gardner Jr |
---|---|
Organization | University of South Carolina |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for University of South Carolina |
PI | Robert William Gardner Jr |
---|---|
Organization | SLAC National Accelerator Laboratory |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for SLAC National Accelerator Laboratory |
PI | Robert William Gardner Jr |
---|---|
Organization | Southern Methodist University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Southern Methodist University |
PI | Robert William Gardner Jr |
---|---|
Organization | State University of New York — Stony Brook |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for State University of New York — Stony Brook |
PI | Robert William Gardner Jr |
---|---|
Organization | US ATLAS |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Tau |
PI | Robert William Gardner Jr |
---|---|
Organization | Tufts University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Tufts University |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Chicago |
Department | High Energy Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 03/07/2014 |
Abstract of work | Tier3 computing for the UChicago ATLAS group via the ATLAS Connect service |
PI | Robert William Gardner Jr |
---|---|
Organization | University of California — Irvine |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for University of California — Irvine |
PI | Robert William Gardner Jr |
---|---|
Organization | University of California — Santa Cruz |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for University of California — Santa Cruz |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Iowa |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for University of Iowa |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Massachusetts |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for University of Massachusetts |
PI | Robert William Gardner Jr |
---|---|
Organization | University of New Mexico |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for University of New Mexico |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Oregon |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for University of Oregon |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Pennsylvania |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for University of Pennsylvania |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Texas - Arlington |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for University of Texas - Arlington |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Texas - Dallas |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect Team for University of Texas - Dallas |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Texas-Austin |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for University of Texas-Austin |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Washington |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for University of Washington |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Wisconsin |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for University of Wisconsin |
PI | Robert William Gardner Jr |
---|---|
Organization | Yale University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Yale University |
PI | Robert William Gardner Jr |
---|---|
Organization | US ATLAS |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for B Physics |
PI | Robert William Gardner Jr |
---|---|
Organization | US ATLAS |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Combined Muon |
PI | Robert William Gardner Jr |
---|---|
Organization | US ATLAS |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for E Gamma |
PI | Robert William Gardner Jr |
---|---|
Organization | ATLAS |
Department | ATLAS |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 10/29/2015 |
Abstract of work | We study exotics. |
PI | Robert William Gardner Jr |
---|---|
Organization | US ATLAS |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Flavour Tagging |
PI | Robert William Gardner Jr |
---|---|
Organization | US ATLAS |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Heavy Ions |
PI | Robert William Gardner Jr |
---|---|
Organization | US ATLAS |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Higgs |
PI | Robert William Gardner Jr |
---|---|
Organization | US ATLAS |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Inner Tracking |
PI | Robert William Gardner Jr |
---|---|
Organization | US ATLAS |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Monte Carlo |
PI | Robert William Gardner Jr |
---|---|
Organization | US ATLAS |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Standard Model |
PI | Robert William Gardner Jr |
---|---|
Organization | US ATLAS |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for SUSY |
PI | Robert William Gardner Jr |
---|---|
Organization | US ATLAS |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 11/10/2015 |
Abstract of work | ATLAS Connect team for Top |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | High Energy Physics |
Sponsor | CG ATLAS Connect |
Date Registered | 03/08/2016 |
Abstract of work | Atlas Connect training project |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Chicago |
Department | Computation and Enrico Fermi Institutes |
Field of Science | High Energy Physics |
Sponsor | CG OSG Connect |
Date Registered | 09/25/2013 |
Abstract of work | To support ATLAS Tier 3 flocking into Tier 1 and Tier 2 centers and to support an OSG Connect-like service dedicated to the US ATLAS Collaboration. The ATLAS detector studies physics at the energy frontier at the Large Hadron Collider in Geneva, Switzerland. |
PI | David Baker |
---|---|
Organization | University of Washington |
Department | Molecular Engineering and Sciences |
Field of Science | Molecular and Structural Biosciences |
Sponsor | VO OSG |
Date Registered | 02/26/2016 |
Abstract of work | Protein folding |
PI | Eric Jankowski |
---|---|
Organization | Boise State University |
Department | Material Science and Engineering |
Field of Science | Computational Condensed Matter Physics |
Sponsor | CG OSG Connect |
Date Registered | 01/10/2018 |
Abstract of work | We will utilize the Open Science Grid to conduct quantum chemical calculations and kinetic Monte Carlo simulations of organic photovoltaic morphologies. We have a simulation pipeline that enables high throughput material screening for chemistires and processing conditions relevent for organic photovoltaic devices. We will use molecular configurations from previously simulated morphologies, generated with molecular dynamics code accelerated by GPUs. |
PI | Liang Yang |
---|---|
Organization | University of Illinois at Urbana-Champaign |
Department | Physics |
Field of Science | Physics |
Sponsor | CG OSG Connect |
Date Registered | 10/18/2017 |
Abstract of work | Neutrinoless Double Beta Decay |
PI | Sucheta Tripathy |
---|---|
Organization | Indian Institute of Chemical Biology |
Department | Structural Biology and Bioinformatics division |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 08/03/2015 |
Abstract of work | This is a cyanobacteria genomics program |
PI | Natasha Pavlovikj |
---|---|
Organization | University of Nebraska - Lincoln |
Department | Computer Science |
Field of Science | Bioinformatics |
Sponsor | VO HCC |
Date Registered | 04/27/2017 |
Abstract of work | Algorithmic development for Bioinformatics |
PI | Martin Morgan |
---|---|
Organization | Roswell Park Cancer Institute |
Department | Biostatistics and Bioinformatics |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 09/06/2017 |
Abstract of work | Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. |
PI | Alex Feltus |
---|---|
Organization | Clemson University |
Department | Genetics & Biochemistry |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 07/06/2015 |
Abstract of work | Constructing gene interaction graphs at high scale |
PI | Erik Wright |
---|---|
Organization | University of Pittsburgh |
Department | Bioinformatics |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 11/22/2017 |
Abstract of work | Development and application of software tools for performing large-scale biomedical informatics on microbial genome sequence data. |
PI | Puja Goyal |
---|---|
Organization | State University of New York at Binghamton |
Department | Chemistry |
Field of Science | Chemistry |
Sponsor | CG OSG Connect |
Date Registered | 08/10/2017 |
Abstract of work | The project involves studies of substrate binding, electron and proton transport pathways and substrate release in enzymes that can catalyze the synthesis of fuels in photoelectrochemical cells. The insights obtained will guide the design of small molecule electrocatalysts in collaboration with experimentalists. |
PI | Benoit Roux |
---|---|
Organization | University of Chicago |
Department | Biology |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG Connect |
Date Registered | 07/07/2014 |
Abstract of work | The molecular machines associated with biological membranes are particularly remarkable. Membrane-associated proteins play an essential role in controlling the bidirectional flow of material and information, and as such, they are truly devices able to accomplish complex tasks. These include ion channels, transporters, pumps, receptors, kinases, and phosphatases. These proteins, like any machine, need to change shape and visit many conformational states to perform their function. Our project is aimed at gaining a deep mechanistic perspective of such protein function, linking structure to dynamics, by characterizing the free energy landscape that governs the key functional motions. |
PI | Janice McCarthy |
---|---|
Organization | Duke University |
Department | Medical Center |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 09/25/2013 |
Abstract of work | Bioinformatics and biostatistics for genetic risk factors at the Duke Medical Center. |
PI | Matthew Snowball |
---|---|
Organization | Brookhaven National Laboratory |
Department | Physics Department |
Field of Science | Nuclear Physics |
Sponsor | VO OSG |
Date Registered | 11/25/2014 |
Abstract of work | Running HEP/NP Monte Carlo simulations for the collaboration of the PHENIX detector at Relativistic Heavy Ion Collider (RHIC) at BNL. |
PI | Martin Purschke |
---|---|
Organization | Brookhaven National Laboratory |
Department | Physics Department |
Field of Science | Medical Sciences |
Sponsor | VO OSG |
Date Registered | 08/20/2013 |
Abstract of work | Positron Emission Tomography (PET) at BNL: Develop the efficient and easily parallelizable 3D image reconstruction algorithms for Positron Emission Tomography detectors developed by the BNL PET group. Use OSG XSEDE resources for reconstructing the images obtained by the group while doing a biomedical and biochemistry research. http://www.bnl.gov/pet/ . |
PI | David Wilkins Miller |
---|---|
Organization | University of Chicago |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG OSG Connect |
Date Registered | 11/14/2014 |
Abstract of work | Project for data sharing and analysis of boosted object physics and jet phenomenology for topics discussed in the BOOST Conference Series |
PI | XUETONG ZHAI |
---|---|
Organization | University of Pittsburgh |
Department | Bioengineering |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 10/10/2017 |
Abstract of work | This project is about simulation validation of a continuous data binning algorithm. |
PI | Joe Boyd |
---|---|
Organization | CDMS |
Department | CDMS |
Field of Science | High Energy Physics |
Sponsor | VO Fermilab |
Date Registered | 02/06/2018 |
Abstract of work | CDMS Experiment Cryogenic Dark Matter Search |
PI | Nathan Kaib |
---|---|
Organization | Northwestern University |
Department | Physics and Astronomy |
Field of Science | Astrophysics |
Sponsor | CG OSG Connect |
Date Registered | 08/14/2014 |
Abstract of work | Centaurs are icy objects in the outer solar system whose orbits cross those of the giant planets. It is thought that most Centaurs originate from the solar system's Kuiper Belt, a reservoir of icy bodies orbiting just beyond Neptune. However, a few Centaurs with very large orbital inclinations and/or mean orbital distances cannot be well-explained with a Kuiper Belt origin. Alternatively, it has been proposed that these outlier Cenaturs may come from the Oort Cloud, a spherical halo of icy objects that extends over halfway to the nearest star. In this project we will simulate the production of Centaurs from the Oort Cloud using numerical orbital integrations. Following this, we will run our simulated orbits/objects through a sky survey simulator to compare our simulated "detections" with the real sample of known objects. Thus, we will be able to evaluate whether the Oort Cloud is a potential source of Centaurs with extreme orbits. |
PI | Juan J de Pablo |
---|---|
Organization | University of Chicago |
Department | Institute of Molecular Engineering |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG Connect |
Date Registered | 04/08/2015 |
Abstract of work | Molecular-level information of DNA at nanometer length scales is of fundamental interest to many aspects of nanotechnology and biology. Molecular models provide a powerful tool to interrogate these systems by providing detailed thermodynamic and kinetic information. Towards this end, this project involves developing highly-accurate coarse-grained models of DNA and using them to study complex nano-scale phenomena. |
PI | Jason H. Moore |
---|---|
Organization | University of pennsylvania |
Department | Biostatistics and Epidemiology |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 05/11/2015 |
Abstract of work | We use machine learning to look for complex epistatic interactions associated with disease risk. Website: http://www.epistasis.org |
PI | Panthea Sepehrband |
---|---|
Organization | Santa Clara University |
Department | Mechanical Engineering |
Field of Science | Materials Science |
Sponsor | CG OSG Connect |
Date Registered | 11/18/2015 |
Abstract of work | Project Name: grian growth simulation Short Project Name: GGS Field of Science: Materials Science Field of Science (if Other): PI Name: Panthea Sepehrband PI Email: psepehrband@scu.edu PI Organization: Santa Clara Univeristy PI Department: Mechanical Engineering Join Date: Sponsor: OSG Sponsor Contact: Project Contact: Panthea Sepehrband Project Contact Email: psepehrband@scu.edu Telephone Number: 4088338665 Project Description: Simulation of grain growth using the LAMMPS package. |
PI | Konstantin Mischaikow |
---|---|
Organization | Rutgers, The State University of New Jersey |
Department | Mathematics |
Field of Science | Mathematical Sciences |
Sponsor | CG OSG Connect |
Date Registered | 05/12/2015 |
Abstract of work | Our group studies dynamical systems using methods from computational topology. A current focus is the study of gene regulatory networks via switching system models and the computation of Conley-Morse databases. |
PI | Marcin Ziolkowski |
---|---|
Organization | Clemson University |
Department | Computational Science |
Field of Science | Multi-Science Community |
Sponsor | CG OSG Connect |
Date Registered | 03/11/2016 |
Abstract of work | HTC training for the computational scientist at Clemson University. |
PI | Hatef Monajemi |
---|---|
Organization | Stanford University |
Department | Statistics |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 03/14/2017 |
Abstract of work | ClusterJob is a project for 'painless massive computational experiments'. Visit www.clusterjob.org |
PI | Kenichi Hatakeyama |
---|---|
Organization | Baylor University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Baylor University |
PI | Achille Petrilli |
---|---|
Organization | CERN |
Department | Physics |
Field of Science | Particle Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/11/2016 |
Abstract of work | CMS Connect group for CERN |
PI | Kevin Lannon |
---|---|
Organization | University of Notre Dame |
Department | High Energy Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 01/05/2015 |
Abstract of work | CMS Connect at Notre Dame |
PI | Kenichi Hatakeyama |
---|---|
Organization | Baylor University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 11/06/2017 |
Abstract of work | CMS Connect at Baylor University |
PI | Meenakshi Narain |
---|---|
Organization | Brown University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Brown University |
PI | Jim Rohlf |
---|---|
Organization | Boston University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Boston University |
PI | Avto Kharchilava |
---|---|
Organization | SUNY Buffalo |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at State University of New York at Buffalo |
PI | Harvey Newman |
---|---|
Organization | Caltech |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Caltech |
PI | Achille Petrilli |
---|---|
Organization | CERN |
Department | Physics |
Field of Science | Particle Physics |
Sponsor | CG CMS Connect |
Date Registered | 11/04/2017 |
Abstract of work | CMS Connect group for CERN |
PI | Manfred Paulini |
---|---|
Organization | Carnegie-Mellon University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Carnegie-Mellon University |
PI | Douglas Johnson |
---|---|
Organization | University of Colorado Boulder |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 02/25/2015 |
Abstract of work | CMS Connect project for University of Colorado |
PI | Jim Alexander |
---|---|
Organization | Cornell University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Cornell University |
PI | Dave Winn |
---|---|
Organization | Fairfield |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Fairfield |
PI | Marc Baarmand |
---|---|
Organization | Florida Institute of Technology |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Florida Institute of Technology |
PI | Pete Markowitz |
---|---|
Organization | Florida International University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Florida International University |
PI | Lothar Bauerdick |
---|---|
Organization | Fermi National Accelerator Laboratory |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 02/25/2015 |
Abstract of work | CMS Connect group for FNAL |
PI | Todd Adams |
---|---|
Organization | Florida State University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Florida State University |
PI | Morris Swartz |
---|---|
Organization | Johns Hopkins University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Johns Hopkins University |
PI | Yurii Maravin |
---|---|
Organization | Kansas State University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Kansas State University |
PI | Alice Bean |
---|---|
Organization | The University of Kansas |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at The University of Kansas |
PI | Doug Wright |
---|---|
Organization | Lawrence Livermore National Laboratory |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Lawrence Livermore National Laboratory |
PI | Christoph Paus |
---|---|
Organization | Massachusetts Institute of Technology |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Massachusetts Institute of Technology |
PI | Kevin Lannon |
---|---|
Organization | University of Notre Dame |
Department | High Energy Physics |
Field of Science | Particle Physics |
Sponsor | CG CMS Connect |
Date Registered | 11/04/2017 |
Abstract of work | CMS Connect at Notre Dame |
PI | Emanuela Barbaris |
---|---|
Organization | Northeastern University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Northeastern University |
PI | Mayda Velasco |
---|---|
Organization | Northwestern University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Northwestern University |
PI | Stan Durkin |
---|---|
Organization | Ohio State University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS connect at Ohio State University |
PI | Lucien Cremaldi |
---|---|
Organization | University of Mississipi |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at University of Mississipi |
PI | Dan Marlow |
---|---|
Organization | Princeton University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Princeton University |
PI | Norbert Neumeister |
---|---|
Organization | Purdue University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Purdue University |
PI | Neeti Parashar |
---|---|
Organization | Purdue University Calumet |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Purdue University Calumet |
PI | Jay Roberts |
---|---|
Organization | Rice University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Rice University |
PI | Regina Demina |
---|---|
Organization | University of Rochester |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at University of Rochester |
PI | Dino Goulianos |
---|---|
Organization | Rockefeller University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Rockefeller University |
PI | Amit Lath |
---|---|
Organization | Rutgers University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Rutgers University |
PI | Alexei Safonov |
---|---|
Organization | Texas A&M University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Texas A&M University |
PI | Nural Akchurin |
---|---|
Organization | Texas Tech University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Texas Tech University |
PI | Conor Henderson |
---|---|
Organization | University of Alabama |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at University of Alabama |
PI | John Conway |
---|---|
Organization | UC Davis |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at University of California, Davis |
PI | Jay Hauser |
---|---|
Organization | UCLA |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Universify of California, Los Angeles |
PI | Gail Hanson |
---|---|
Organization | UCR |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at University of California, Riverside |
PI | Joe Incandela |
---|---|
Organization | UCSB |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at University of California, Santa Barbara |
PI | Frank Wuerthwein |
---|---|
Organization | University of California, San Diego |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 02/25/2015 |
Abstract of work | CMS Connect group for UCSD |
PI | Gena Mitselmakher |
---|---|
Organization | University of Florida |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at University of Florida |
PI | Nikos Varelas |
---|---|
Organization | University of Illinois at Chicago |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at University of Illinois at Chicago |
PI | Yasar Onel |
---|---|
Organization | University of Iowa |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at University of Iowa |
PI | Andris Skuja |
---|---|
Organization | University of Maryland |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at University of Maryland |
PI | Roger Rusack |
---|---|
Organization | University of Minnesota |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at University of Minnesota |
PI | Kenneth Bloom |
---|---|
Organization | University of Nebraska-Lincoln |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 02/25/2015 |
Abstract of work | CMS Connect group for UNL |
PI | Malik Sudhir |
---|---|
Organization | University of Puerto Rico |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at University of Puerto Rico |
PI | Stefan Spanier |
---|---|
Organization | University of Tennessee |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at University of Tennessee |
PI | Will Johns |
---|---|
Organization | Vanderbilt University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at Vanderbilt University |
PI | Brad Cox |
---|---|
Organization | University of Virginia |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at University of Virginia |
PI | Paul Karchin |
---|---|
Organization | Wayne State University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | Wayne State University |
PI | Wesley Smith |
---|---|
Organization | University of Wisconsin |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG CMS Connect |
Date Registered | 10/22/2015 |
Abstract of work | CMS Connect at University of Wisconsin |
PI | Joshua B. Plotkin |
---|---|
Organization | University of Pennsylvania |
Department | Biology |
Field of Science | Evolutionary Sciences |
Sponsor | CG OSG Connect |
Date Registered | 08/18/2017 |
Abstract of work | Different languages divide the visible light spectrum into words (e.g. "red," "green," "blue" ... in English) in different ways. However, despite the apparent freedom in assigning colors to different categories, there are clear universal patterns across languages in how they divide color space according to the number of color terms in the language. This pattern has now been empirically well established, however there remains a confusion of theories for why this pattern should exist at all. In fact, a simple, evolutionary model in tandem with a model of perceptual color space and color saliency, completely accounts for the observed universal patterns. We will use the open science grid to explore the parameter space of this model via many parallel, independent runs of the dynamics to find the best fit parameter values to the language data available. |
PI | Ozkan Celik |
---|---|
Organization | Colorado School of Mines |
Department | Mechanical Engineering |
Field of Science | Biological and Critical Systems |
Sponsor | CG OSG Connect |
Date Registered | 01/04/2017 |
Abstract of work | Design and control of exoskeletons (and prostheses) thus far has been primarily carried out following heuristic methods and exhaustive experimental (design and test) procedures. This approach significantly slows down design iterations and increases project costs. A predictive simulation framework for combined human and device dynamics is a valuable tool that can significantly accelerate optimal device and controller design. We are building predictive models of combined muscuoloskeletal and exoskeleton dynamics for walking, where design parameters for the exoskeleton (such as actuation torque profiles) and various objective functions (such as metabolic cost) can be optimized simultaneously. |
PI | Javier Diaz-Montes |
---|---|
Organization | Rutgers |
Department | Electrical and Computer Engineering |
Field of Science | Computer and Information Science and Engineering |
Sponsor | VO OSG |
Date Registered | 11/27/2013 |
Abstract of work | CometCloud is an autonomic framework for enabling real-world applications on dynamically federated, hybrid infrastructure integrating (public & private) clouds, data-centers and Grids. Specifically, CometCloud provides abstractions and mechanisms to support a range of programming paradigms and real-world applications on such an infrastructure. Furthermore, it enables policy-based autonomic cloud-bridging and cloud-bursting. Autonomic cloud-bridging enables on-the-fly integration of local computational environments (data-centers, grids) and public cloud services (such as Amazon EC2), and autonomic cloud-bursting enables dynamic application scale-out to address dynamic workloads, spikes in demands, and other extreme requirements. Currently, we support various applications as part of our collaborations in multiple domains such as medical diagnostics, material sciences, biology, and engineering. |
PI | Chaoren Liu |
---|---|
Organization | Duke University |
Department | Chemistry |
Field of Science | Chemistry |
Sponsor | CG OSG Connect |
Date Registered | 09/25/2013 |
Abstract of work | Modeling and simulation of molecules. |
PI | Derrick Stolee |
---|---|
Organization | Iowa State University |
Department | Mathematics |
Field of Science | Mathematical Sciences |
Sponsor | VO HCC |
Date Registered | 06/27/2014 |
Abstract of work | Computational Combinatorics uses significant computational resources to solve problems in combinatorics, graph theory, and discrete mathematics. |
PI | Po-He Tseng |
---|---|
Organization | Duke University |
Department | Neurobiology |
Field of Science | Neuroscience |
Sponsor | CG OSG Connect |
Date Registered | 09/25/2013 |
Abstract of work | To give you a brief idea, I am trying to identify the information flow among several brain regions in rats in the neuronal level. The rats were actively doing a aperture discrimination task (whether a gate opened wide or narrow). I wish to find not only the static neuronal circuitry of the sensory input, but also the dynamics of the flow across time. |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Chicago |
Department | Computation and Enrico Fermi Institutes |
Field of Science | Training |
Sponsor | CG OSG Connect |
Date Registered | 09/25/2013 |
Abstract of work | OSG Connect training activity. |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | Technology |
Sponsor | CG OSG Connect |
Date Registered | 07/16/2014 |
Abstract of work | Provides continuous build and test services for OSG Connect via Jenkins. |
PI | Edward O'Brien |
---|---|
Organization | The Pennsylvania State University |
Department | Chemistry |
Field of Science | Biophysics |
Sponsor | VO OSG |
Date Registered | 07/25/2014 |
Abstract of work | There is now a large body of experimental evidence that the ability of many proteins to reach full functionality in a cell depends strongly on the rate at which individual codons are translated by the ribosome during protein synthesis. This project aims to demonstrate that, counter to conventional wisdom, fast-translating codons can help coordinate co-translational protein folding by minimizing misfolding [O’Brien, Nature Comm. 2014]. To do this we will use a two-step approach: First (Aim 1), we will utilize coarse-grained molecular dynamics simulations in combination with a genetic algorithm to find the optimal codon translation rate profile that maximizes the co-translational folding of a protein. And then (Aim 2) mutate, in silico, fast-translating codon positions to slower rates to test, if as predicted, we observe a concomitant decrease in the amount of co-translational folding. The results of this study will provide a new computational tool for the rational design of mRNA sequences to control nascent proten behavior. |
PI | Christoph Paus |
---|---|
Organization | MIT |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | VO OSG |
Date Registered | 03/10/2016 |
Abstract of work | Generate a grid of Monte Carlo samples to be used in collider-based searches for dark matter |
PI | Nirav Merchant |
---|---|
Organization | University of Arizona |
Department | Biology |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 03/29/2018 |
Abstract of work | CyVerse is a cyberinfrastructure project (formerly iPlant Collaborative). This project will be an umbrella for initial testing of OSG integration, with the hope that eventually we will instead ask users for their own projects to submit with jobs. |
PI | Joe Boyd |
---|---|
Organization | Darkside |
Department | N/A |
Field of Science | High Energy Physics |
Sponsor | VO Darkside |
Date Registered | 02/19/2018 |
Abstract of work | Project entry for the Darkside VO. http://darkside.lngs.infn.it/ |
PI | Rob Quick |
---|---|
Organization | Indiana University |
Department | UITS |
Field of Science | Education |
Sponsor | CG OSG Connect |
Date Registered | 11/29/2017 |
Abstract of work | A project for teaching the grid computing component at Sao Paulo, Brazil |
PI | Rob Quick |
---|---|
Organization | International Center for Theoretical Physics |
Department | Education |
Field of Science | Multi-Science Community |
Sponsor | VO OSG |
Date Registered | 08/04/2016 |
Abstract of work | CODATA/RDA Summer School on Research Data Science |
PI | Richard Jean So |
---|---|
Organization | University of Chicago |
Department | Interdisciplinary |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 02/05/2014 |
Abstract of work | We're conducting a network analysis of a 10% sample (1.6TB; 3.6m files) of the Google Books corpus. |
PI | Noah Fahlgren |
---|---|
Organization | Donald Danforth Plant Science Center |
Department | Bioinformatics |
Field of Science | Plant Biology |
Sponsor | CG OSG Connect |
Date Registered | 06/05/2017 |
Abstract of work | The Donald Danforth Plant Science Center Bioinformatics project tracks Open Science Grid computing usage by Danforth Center researchers. Bioinformatics research at the Danforth Center largely focuses on plant genomics (genome sequencing, genetic analysis, transcript profiling, etc.) and high-throughput phenotyping (image analysis, genotype-phenotype association analysis, etc.). |
PI | Micheal Marasco |
---|---|
Organization | Northwestern University |
Department | Farley Center for Entrepreneurship and Innovation |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 04/27/2017 |
Abstract of work | To develop a contextual search technique on a given text corpus. The idea is to develop a search model using Deep Learning techniques and Natural Language Processing. More specifically, we are currently exploring Word Embedding techniques in NLP and Neural Network models like Word2Vec. The model would first train itself on the existing email corpus of a given user and then be able to provide search results based on contextual queries. |
PI | Lene Jung Kjaer |
---|---|
Organization | Southern Illinois University |
Department | Department of Zoology |
Field of Science | Biological Sciences |
Sponsor | VO OSG |
Date Registered | 12/04/2013 |
Abstract of work | I have created an individual-based computer model simulating disease spread in deer populations. The population in the model is represented by deer agents that all follow rules and behaviors. I am using Repast Simphony 1.0 and the code is written in java. |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | Physics |
Sponsor | CG OSG Connect |
Date Registered | 03/10/2015 |
Abstract of work | Workshop at Delhi |
PI | Fernando Luco |
---|---|
Organization | Texas A&M University, University of Illinois at Urbana-Champaign |
Department | Economics |
Field of Science | Economics |
Sponsor | CG OSG Connect |
Date Registered | 08/03/2015 |
Abstract of work | We estimate switching costs with aggregate data in the context of price wars and collusion to study how mergers and changes to market structure affect welfare under the different competitive scenarios |
PI | Nikolay Kuropatkin |
---|---|
Organization | Fermilab |
Department | N/A |
Field of Science | Astrophysics |
Sponsor | VO Fermilab |
Date Registered | 02/19/2018 |
Abstract of work | Project entry corresponding to the Dark Energy Survey (DES) VO. |
PI | John Strologas |
---|---|
Organization | University of New Mexico |
Department | Physics and Astronomy |
Field of Science | Medical Sciences |
Sponsor | VO OSG |
Date Registered | 08/15/2013 |
Abstract of work | Investigate how different simulated SPECT system geometries can affect reconstructed images. |
PI | Jacek Herbrych |
---|---|
Organization | University of Tennessee |
Department | Department of Physics and Astronomy |
Field of Science | Computational Condensed Matter Physics |
Sponsor | CG OSG Connect |
Date Registered | 04/13/2018 |
Abstract of work | Dynamics of electrons with different degree of correlations |
PI | Franco Pestilli |
---|---|
Organization | Indiana University |
Department | Neuroscience |
Field of Science | Neuroscience |
Sponsor | CG OSG Connect |
Date Registered | 11/07/2017 |
Abstract of work | Modelling and simulation of diffusion magnetic resonance images (dMRI) using white matter tract mapping information |
PI | Soichi Hayashi |
---|---|
Organization | Indiana University |
Department | Brain Science |
Field of Science | Neuroscience |
Sponsor | VO OSG |
Date Registered | 11/06/2017 |
Abstract of work | Diffusion predictor from IU Brain Science |
PI | Ann Arthur |
---|---|
Organization | University of Nebraska-Lincoln |
Department | Educational Psychology |
Field of Science | Educational Psychology |
Sponsor | CG OSG Connect |
Date Registered | 01/18/2018 |
Abstract of work | This study involves the use of Monte Carlo simulation methods to test the use of mixture models to improve the estimation of a latent ability. |
PI | Rob Quick |
---|---|
Organization | DOSAR |
Department | HEP |
Field of Science | Education |
Sponsor | VO OSG |
Date Registered | 08/23/2016 |
Abstract of work | Distributed Organization for Scientific Academic Research. International outreach projects sponsored by the DOSAR Virtual Organization. Students that would like to maintain accounts on OSG. |
PI | Luke Remage-Healey |
---|---|
Organization | University of Massachusetts Amherst |
Department | Psychological and Brain Sciences |
Field of Science | Neuroscience |
Sponsor | CG OSG Connect |
Date Registered | 07/05/2017 |
Abstract of work | Pattern classifier of neuronal responses with dynamic time warping as a distance measure. |
PI | Shailesh Chandrasekharan |
---|---|
Organization | Duke University |
Department | Physics Department |
Field of Science | High Energy Physics |
Sponsor | CG Duke |
Date Registered | 01/13/2014 |
Abstract of work | We are performing a lattice field theory calculation of a 2 flavor fermion model with a four fermion interaction. We look for critical behavior at strong coupling. |
PI | Hai Yan |
---|---|
Organization | Duke University |
Department | Pathology |
Field of Science | Bioinformatics |
Sponsor | CG Duke |
Date Registered | 12/15/2016 |
Abstract of work | To study the genomic and genetic aspects of brainstem gliomas |
PI | Daniel Gauthier |
---|---|
Organization | Duke University |
Department | Physics |
Field of Science | Physics |
Sponsor | CG Duke |
Date Registered | 02/09/2016 |
Abstract of work | Experimental Boolean networks built on FPGAs, with the purpose of studying the fundamental dynamical properties of complex |
PI | Tom Milledge |
---|---|
Organization | Duke University |
Department | Scalable Computing Suport Center-OIT |
Field of Science | Community Grid |
Sponsor | CG Duke |
Date Registered | 01/30/2014 |
Abstract of work | Default project for new Duke users |
PI | Harold U. Baranger |
---|---|
Organization | Duke University |
Department | Physics |
Field of Science | Computational Condensed Matter Physics |
Sponsor | CG Duke |
Date Registered | 08/16/2016 |
Abstract of work | We are condensed-matter theorists at Duke. We study the onset of strong correlation in various setups, such as qubits coupled to a 1D waveguide and impurities immersed in an electromagnetic environment. With the aid of the OSG distributive environment, we are able to solve problems using a variety of numerical approaches, including but not limited to quantum Monte Carlo, quantum jumps, etc. |
PI | Konosuke Iwamoto |
---|---|
Organization | Duke University |
Department | Biostatistics |
Field of Science | Statistics |
Sponsor | CG Duke |
Date Registered | 02/01/2017 |
Abstract of work | We will benchmark various algorithms to benchmark the efficient score. |
PI | Steffen A. Bass |
---|---|
Organization | Duke University |
Department | Physics |
Field of Science | Nuclear Physics |
Sponsor | VO OSG |
Date Registered | 08/28/2013 |
Abstract of work | Event-by-event simulations of relativistic heavy-ion collisions. QGP characterization via model-to-data comparison. |
PI | Tom Milledge |
---|---|
Organization | Duke University |
Department | IT |
Field of Science | Community Grid |
Sponsor | CG Duke |
Date Registered | 02/01/2017 |
Abstract of work | campus project |
PI | Mark R. DeLong |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | Multi-Science Community |
Sponsor | CG Duke |
Date Registered | 01/08/2016 |
Abstract of work | Training Workshop |
PI | Mark R. DeLong |
---|---|
Organization | Duke University |
Department | Office of Information Technology |
Field of Science | Multi-Science Community |
Sponsor | CG Duke |
Date Registered | 09/29/2015 |
Abstract of work | Duke Software Carpentry Workshop from Oct 27th to Oct 29th 2015 http://swc-osg-workshop.github.io/2015-10-27-duke/index.html |
PI | Patrick Charbonneau |
---|---|
Organization | Duke University |
Department | Chemistry |
Field of Science | Biochemistry |
Sponsor | CG Duke |
Date Registered | 07/16/2014 |
Abstract of work | Water structure in protein crystals |
PI | Thomas Robert Junk |
---|---|
Organization | DUNE |
Department | N/A |
Field of Science | High Energy Physics |
Sponsor | VO Fermilab |
Date Registered | 02/19/2018 |
Abstract of work | Project entry corresponding to the DUNE VO. |
PI | Ewa Deelman |
---|---|
Organization | University of Southern California |
Department | Information Sciences Institute |
Field of Science | Computer and Information Science and Engineering |
Sponsor | VO OSG |
Date Registered | 06/06/2014 |
Abstract of work | The main goal of the project is to design a computational framework that enables computational experimentation at scale while supporting the model of “submit locally, compute globally”. The project focuses on estimating application resource needs, finding the appropriate computing resources, acquiring those resources, deploying the applications and data on the resources, managing applications and resources during run. The project also aims to advance the understanding of resource management within a collaboration in the areas of: trust, planning for resource provisioning, and workload, computer, data, and network resource management. |
PI | Asher Wasserman |
---|---|
Organization | University of California, Santa Cruz |
Department | Astronomy and Astrophysics |
Field of Science | Astrophysics |
Sponsor | CG OSG Connect |
Date Registered | 02/26/2018 |
Abstract of work | Equilibrium dynamical models are useful tools for inferring the mass distribution of galaxies and determining the amount and structure of their dark matter halos. The goal of this work is to explore degeneracies in the modeling of elliptical galaxies to evaluate how well we can understand properties such as their dark matter density distribution, the mass-to-light ratio of their stellar populations, and the orbital anisotropy of various tracer populations. |
PI | Meenakshi Narain |
---|---|
Organization | Brown University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | VO OSG |
Date Registered | 08/16/2013 |
Abstract of work | Simulate hundreds of millions of high-energy proton proton collisions, which mimic the collisions expected at the LHC in the coming years. This simulated data is used to assess the physics potential of potential detector upgrades, allowing decision makers and funding agencies to plan for the future. |
PI | Jianghao Chu |
---|---|
Organization | UC Riverside |
Department | Economics |
Field of Science | Economics |
Sponsor | CG OSG Connect |
Date Registered | 08/26/2016 |
Abstract of work | The project looks into the use of heteroskedasticity consistent variance-covariance estimators for conducting hypothesis testing. It uses Monte Carlo and bootstrap techniques to find the distribution of t-statistics using heteroskedasticity consistent variance-covariance estimator under normality and nonnormality. Comparison between using different heteroskedasticity consistent estimators are included and possible corrections are proposed and will be examined. |
PI | Chuck Kaspar |
---|---|
Organization | University of Wisconsin-Madison |
Department | Bacteriology |
Field of Science | Microbiology |
Sponsor | CG OSG Connect |
Date Registered | 09/23/2015 |
Abstract of work | Project Description: Our research is primarily focused on the transmission and evolution of two zoonotic pathogens, enterohemorrhagic Escherichia coli (EHEC) and Salmonella. These pathogens reside in the intestinal tracts of animal hosts where they encounter diverse microbial communities, fluctuating nutrient levels, and myriad host factors. Transmission between hosts requires these pathogens to survive varied environmental conditions. The general stress protection system (regulated by the alternative sigma factor, σs) is known to play a central role in environmental persistence and transmission. Acid and desiccation tolerance are two transmission-associated phenotypes that are dependent upon σs –regulated genes. We are also investigating the role of prophage in fitness. EHEC harbor multiple lambda-like prophage and cryptic phage remnants in their genome that facilitate genomic rearrangements, gene duplications, and deletions by homologous recombination. We are investigating how these phage-mediated genomic rearrangements influence the persistence of EHEC in its bovine host and the environment. The goals of our research are to use results from these fundamental studies in the development of strategies to reduce pathogen transmission. |
PI | Tobias Toll |
---|---|
Organization | Brookhaven National Laboratory |
Department | Physics Department |
Field of Science | High Energy Physics |
Sponsor | VO OSG |
Date Registered | 08/20/2013 |
Abstract of work | Electron Ion Collider (EIC) at BNL: Modeling the performance and optimizing the design of the prospected future Electron Ion Collider (EIC) at BNL. https://wiki.bnl.gov/eic/index.php/Main_Page |
PI | Jesse McDaniel |
---|---|
Organization | Georgia Institute of Technology |
Department | Chemistry and Biochemistry |
Field of Science | Chemistry |
Sponsor | CG OSG Connect |
Date Registered | 06/29/2017 |
Abstract of work | Molecular Dynamics simulations of concentrated electrolyte mixtures both in bulk and at interfaces, and spectroscopic characterization of these systems. Electronic Structure calculations used to investigate specific interactions between liquid components |
PI | Dayne Broderson |
---|---|
Organization | University of Alaska Fairbanks |
Department | Geographic Information Network of Alaska |
Field of Science | Geographic Information Science |
Sponsor | CG OSG Connect |
Date Registered | 08/04/2017 |
Abstract of work | processing EMODIS NDVI using HTC |
PI | Ashley Vissing |
---|---|
Organization | University of Chicago |
Department | Economics |
Field of Science | Economics |
Sponsor | CG OSG Connect |
Date Registered | 09/27/2016 |
Abstract of work | I study the privately negotiated outcomes of the natural gas leasing market for mineral rights using a one-to-many matching model that allows for the presence of complementary preferences among firms negotiating bundles of land leases. |
PI | David Mogul |
---|---|
Organization | Illinois Institute of Technology |
Department | Biomedical Engineering |
Field of Science | Neuroscience |
Sponsor | CG OSG Connect |
Date Registered | 10/27/2017 |
Abstract of work | We are trying to better understand how networks evolve in the brain of animals and humans with epilepsy. We hope to leverage this information in the design of more effective electrical stimulation paradigms. |
PI | Christopher Richards |
---|---|
Organization | USDA Agricultural Research Service |
Department | National Center for Genetic Resources Preservation |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG Connect |
Date Registered | 11/14/2014 |
Abstract of work | Missing data and genotyping errors are common features of microsatellite data sets used to infer the genetic structure of natural populations. We used simulated data to quantify the effect of these data aberrations on the accuracy of population structure inference. Data sets were simulated under the coalescent and ranged from panmictic to highly subdivided with complex, randomly generated, population histories. Models describing the characteristic patterns of missing data and genotyping error in real microsatellite data sets were developed, and used to modify the simulated data sets. Performance of an ordination, a tree based, and a model based Bayesian method of population structure inference was evaluated before and after data set modifications. The ability to recover correct population clusters decreased as missing data increased. The rate of decrease was similar among analytical procedures, thus no single analytical approach was preferable when faced with incomplete data. Researchers should expect to retrieve 3–4% fewer correct clusters for every 1% of a data matrix made up of missing data using these methods. For every 1% of a matrix that contained erroneous genotypes, approximately 1–2% fewer correct clusters were recovered using ordination and tree based methods. A Bayesian procedure that minimizes the deviation from Hardy Weinberg equilibrium in order to assign individuals to clusters performed better as genotyping error increased. We attribute this surprising result to the inbreeding like nature of microsatellite genotyping error, and recommend the use of related analytical methods that explicitly account for inbreeding, as a means to mitigate the effect of genotyping error. |
PI | Fabricia Nascimento |
---|---|
Organization | University of Oxford |
Department | Department of Zoology |
Field of Science | Zoology |
Sponsor | CG OSG Connect |
Date Registered | 10/06/2015 |
Abstract of work | Project Description: Endogenous retroviruses (ERVs) are viewed as ancient retroviral infections in vertebrate genomes and are commonly referred to as viral fossils, accounting for approximately 8% of the human genome. In order to increase our understanding of these viruses in host genomes, I am developing more complex models that describe the evolution of ERVs in host genomes. Specifically, I am interested in understanding evolutionary patterns of ERVs that have intact genes and are theoretically able to re-infect when compared to those that lost this ability. |
PI | Davorka Gulisija |
---|---|
Organization | University of Pennsylvania |
Department | Biology |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 06/28/2017 |
Abstract of work | Multi-locus simulations under periodic environments. |
PI | Erik Sotka |
---|---|
Organization | College of Charleston |
Department | Department of Biology |
Field of Science | Evolutionary Sciences |
Sponsor | CG OSG Connect |
Date Registered | 03/20/2017 |
Abstract of work | Our group uses genomic tools to understand the evolutionary process of marine invasions. |
PI | Oana Carja |
---|---|
Organization | University of Pennsylvania |
Department | Biology |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 06/26/2015 |
Abstract of work | Evolutionary simulation tracking gene frequencies under a variety of environmental conditions. |
PI | Jeff Clune |
---|---|
Organization | University of Wyoming |
Department | Computer Science |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 08/11/2015 |
Abstract of work | Modern day software and robotics are notorious for lacking robustness and adaptability, often breaking down when encountering unexpected situations. Natural animals, on the other hand, are well known for their robustness and their ability to adapt to new environments. The Evolving Artificial Intelligence project aims to study how the robustness and adaptability of natural animals evolved, both to learn more about natural evolution, and to increase the robustness and adaptability of modern software and robotics systems. |
PI | Milo Lin |
---|---|
Organization | UT Southwestern |
Department | Green Center for Systems Biology |
Field of Science | Biophysics |
Sponsor | CG OSG Connect |
Date Registered | 08/22/2016 |
Abstract of work | Little is known about the evolutionary pathways enabling a protein to change its function to changing environmental needs, especially in regards to metabolism and toxicity. Evolution simulations that explicitly model the three-dimensional interaction of mutated proteins with their targets is a new approach that complements the ongoing explosion of directed evolution experiments. In this project, the evolutionary dynamics of a lattice representation of antibiotic resistance protein (beta lactamase) is studied by enhanced-sampling folding-binding simulations for an initial protein undergoing selection-dependent mutation to bind a new antibiotic. The goals of this work are to understand the fundamental physical bottlenecks and dynamical behavior of protein evolution. Important questions include the extent of dominant pathways (convergent evolution) and phase transitions in evolutionary rates (punctuated equilibrium). These principals and their structural underpinnings can also be used to inform rational design of antibiotics that exploit bottlenecks in pathogen mutational response. |
PI | Christina Burch |
---|---|
Organization | University of North Carolina at Chapel Hill |
Department | Biology |
Field of Science | Evolutionary Sciences |
Sponsor | CG OSG Connect |
Date Registered | 09/25/2013 |
Abstract of work | Linkage disequilibrium's contribution to the maintenance of sexual reproduction Though sexual reproduction is nearly ubiquitous in nature, its costs are substantial. Foremost among these costs are the twofold cost of males and the cost of destroying successful genetic associations. Understanding the paradox of the persistence of sex despite these detriments is a central question in evolutionary theory. In order to persist regardless of these disadvantages, the benefits of sexual reproduction must be substantial - offspring of sexual reproduction must have at least twice the fitness of asexual clones. The most generalizable hypotheses addressing the benefits of sex propose that genetic drift increases linkage disequilibrium, creating a surfeit of genomes with intermediate fitness. Sexual recombination eliminates linkage disequilibrium, thereby increasing genetic variation for fitness and improving the efficiency of natural selection. However, previous research using this framework has failed to address the biological reality of interactions between genes. Because the cost of destroying beneficial genetic interactions is one of the major costs of sex, this cannot be overlooked. In this work, I use a computational gene network model in which genes interact and genetic interactions evolve to investigate the hypothesis that linkage disequilibrium decreases the fitness and adaptability of asexual populations. I test this both by evolving artificial organisms in conditions that will increase linkage disequilibrium, and by evolving them in an environment with a shifting optimum, which will make linkage disequilibrium more costly. I am running a python script that runs populations of artificial gene networks (numerical matrices) through repeated rounds (on the order of 10s of thousands) of mutation, selection and reproduction, analyzing the evolutionary dynamics of these populations, and storing the data generated by this in text files. |
PI | Sam Volchenboum |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 03/28/2014 |
Abstract of work | ExhaustiveSearch (or ExSearch) is a machine learning application tuned to analyze class-labeled data using n-tuple feature vectors. |
PI | Shripad Tuljapurkar |
---|---|
Organization | Stanford University |
Department | Biology |
Field of Science | Ecological and Environmental Sciences |
Sponsor | CG OSG Connect |
Date Registered | 10/06/2017 |
Abstract of work | Population dynamics simulations in R and Python will be used to understand how increasing environmental variability due to climate change and habitat degradation interact and affect a species' time to extinction. |
PI | Joe Boyd |
---|---|
Organization | Fermilab |
Department | N/A |
Field of Science | High Energy Physics |
Sponsor | VO Fermilab |
Date Registered | 02/19/2018 |
Abstract of work | Project entry corresponding to Fermilab VO. |
PI | Vijay Pande |
---|---|
Organization | Stanford University |
Department | Department of Chemistry |
Field of Science | Chemistry |
Sponsor | CG OSG Connect |
Date Registered | 06/25/2014 |
Abstract of work | This project will involve running molecular dynamics simulations to validate new protein force fields. We will be comparing the results of the simulations to experimental protein crystal structures and nuclear magnetic resonance (NMR) measurements. |
PI | Erkan Tuzel |
---|---|
Organization | Worcester Polytechnic Institute |
Department | Physics |
Field of Science | Physics |
Sponsor | CG OSG Connect |
Date Registered | 03/09/2016 |
Abstract of work | In this project we study fluid/structure interactions using a novel particle-based fluid simulation technique. |
PI | Sunil Chitra |
---|---|
Organization | Brookhaven National Laboratory |
Department | Physics |
Field of Science | Physics |
Sponsor | CG OSG Connect |
Date Registered | 12/11/2017 |
Abstract of work | FLUKA Monte Carlo calculations |
PI | Donald Krieger |
---|---|
Organization | University of Pittsburgh |
Department | Department of Neurological Surgery |
Field of Science | Neuroscience |
Sponsor | CG OSG Connect |
Date Registered | 11/06/2015 |
Abstract of work | Brain image analysis with free surfer software |
PI | Chuck Kaspar |
---|---|
Organization | University of Wisconsin Madison |
Department | Microbiology |
Field of Science | Microbiology |
Sponsor | CG OSG Connect |
Date Registered | 09/19/2016 |
Abstract of work | We are using the Mothur pipeline to clean and analyze 16S rRNA gene sequences collected from sous vide vegetables that were held under refrigeration until the onset of spoilage. (Goal- To identify microorganisms responsible for spoilage in sous vide processed vegetables) |
PI | Sergei Chekanov |
---|---|
Organization | Argonne National Lab |
Department | High Energy Physics |
Field of Science | High Energy Physics |
Sponsor | CG OSG Connect |
Date Registered | 08/27/2015 |
Abstract of work | Studies of physics potential of future high-energy experiments (VLHC, FCC) with performance significantly beyond the Large Hadron Collider. The project will focus on Monte Carlo simulations for future energy fronter at DOE |
PI | Wolfgang Lorenzon |
---|---|
Organization | University of Michigan |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG OSG Connect |
Date Registered | 09/22/2017 |
Abstract of work | MUSE is an experiment to measure the proton radius using muon and electron scattering. I work on simulations of the experiment using GEANT4, a particle physics simulation toolkit. |
PI | Xin Li |
---|---|
Organization | Duke Unversity |
Department | Electrical and Computer Engineering |
Field of Science | Engineering |
Sponsor | CG OSG Connect |
Date Registered | 10/03/2017 |
Abstract of work | Test Case Generation For ADAS Validation Via Cycle GAN Today’s automobile is equipped with a large amount of electronic circuits to achieve intelligent functions, such as collision avoidance, traffic sign detection, etc., for autonomous driving. To meet the safety standard, ensuring extremely small failure probability over all possible operation conditions is one of the critical tasks for an autonomous driving system. However, physically observing all these corner cases over a long time is almost impossible in practice. In this project, we use machine learning algorithms to efficiently generate corner cases that are not easy to observe. |
PI | Dean Tullsen |
---|---|
Organization | University of California San Diego |
Department | Computer Science and Engineering |
Field of Science | Multi-Science Community |
Sponsor | CG OSG Connect |
Date Registered | 02/23/2015 |
Abstract of work | The work is looking into microarchitectural details utilizing gem5 to do cycle-accurate simulation of an O3 processor. The work additionally uses McPAT and Hotspot to flush out the research framework. |
PI | Gabriel Nathan Perdue |
---|---|
Organization | Fermilab |
Department | Scientific Computing Simulation |
Field of Science | High Energy Physics |
Sponsor | VO Fermilab |
Date Registered | 12/16/2014 |
Abstract of work | Generates Events for Neutrino Interaction Experiments(GENIE) is a universal object-oriented neutrino MC generator supported and developed by an international collaboration of scientists whose expertise covers a very broad range of neutrino physics aspects, both phenomenological and experimental. GENIE is currently being used by T2K, NOvA, MINERvA, MicroBooNE, ArgoNEUT, LAGUNA-LBNO, LBNE, INO, IceCUBE, NESSiE and others. |
PI | Casey Greene |
---|---|
Organization | Dartmouth College |
Department | Genetics |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 05/13/2015 |
Abstract of work | Integration of publicly available large-scale genomic data. |
PI | Elena Guardincerri |
---|---|
Organization | Las Alamos National Lab |
Department | Physics |
Field of Science | Nuclear Physics |
Sponsor | CG OSG Connect |
Date Registered | 06/16/2016 |
Abstract of work | Analyzing muon data to obtain information about the objects they traversed. |
PI | Patrick Charbonneau |
---|---|
Organization | Duke University |
Department | Chemistry |
Field of Science | Computational Condensed Matter Physics |
Sponsor | CG Duke |
Date Registered | 10/13/2017 |
Abstract of work | Glass problem is one of the outstanding unsolved problems in condensed matter physics. The exact solution of a model glass former in the limit of infinite spatial dimension exhibit a dynamical critical point. It is important to check the robustness of the resulting description under changing d for fundamental understanding. In this project we aim to take a closer look at this dynamical criticality as a function of spatial dimensions, using models of polydisperse hard sphere fluids. Computer simulation is an essential tool to pursue this study. |
PI | David Reichman |
---|---|
Organization | Columbia University |
Department | Chemistry |
Field of Science | Chemistry |
Sponsor | CG OSG Connect |
Date Registered | 09/25/2013 |
Abstract of work | Studies of static and dynamic properties of glassy systems. See also: http://www.columbia.edu/cu/chemistry/groups/reichman/ The dynamics and static properties of glassy systems can be studied in great detail by simple model systems, either those on a lattice or those consisting of mixtures of spherical particles. In order to do that, one can use any many techniques generally under the umbrella of Monte Carlo Sampling or Molecular Dynamics. In order to get detailed properties, is is often advantageous or necessary to run a large number of independent simulations, and to calculate properties averaged over these simulations. It may also be necessary to study these systems with a range of parameter values, e.g. temperature or system size. Hence, this problem lends itself well to high throughput computing, at least for cases where the individual simulations comprising a workflow are not too long. |
PI | Kang Wang |
---|---|
Organization | UNIVERSITY of COLORADO at BOULDER |
Department | INSTAAR |
Field of Science | Earth Sciences |
Sponsor | CG OSG Connect |
Date Registered | 04/20/2018 |
Abstract of work | Test a tool to deal with global data sets. |
PI | Kurt Johann Strosahl |
---|---|
Organization | JLAB |
Department | Physics |
Field of Science | Nuclear Physics |
Sponsor | VO JLab |
Date Registered | 03/23/2017 |
Abstract of work | GlueX project |
PI | Joe Boyd |
---|---|
Organization | Fermilab |
Department | N/A |
Field of Science | High Energy Physics |
Sponsor | VO Fermilab |
Date Registered | 02/19/2018 |
Abstract of work | Project entry corresponding to the gm2 VO (Muon g-2 at Fermilab). |
PI | Christopher Bahl |
---|---|
Organization | Institute for Protein Innovation |
Department | Biology |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 02/07/2018 |
Abstract of work | Computational design of protein-based affinity reagents capable of binding to GPCRs and inducing an agonized or antagonize state, or binding in a function-independent manner. |
PI | Richard Irving |
---|---|
Organization | University of Toledo |
Department | Physics |
Field of Science | Physics and astronomy |
Sponsor | CG OSG Connect |
Date Registered | 07/01/2014 |
Abstract of work | Atomic structure calculations based on multiconfiguration Dirac–Hartree–Fock theory utilizing Grasp2k, a general-purpose relativistic atomic structure package. |
PI | David Rhee |
---|---|
Organization | Albert Einstein College of Medicine |
Department | Genetics |
Field of Science | Biological Sciences |
Sponsor | VO OSG |
Date Registered | 11/25/2013 |
Abstract of work | The use of methylation-specific restriction enzymes to preferentially cleave 5'-CCGG-3' sites in conjunction with Next Generation Sequencing platforms has formed the basis for the widely used Methyl-seq and HELP-tagging assays. The recent development of an R package using a Bayesian hierarchical model approach, msBayes, offered a statistically rigorous alternative to the basic tag-counting/geometric mapping previously used for these two techniques. Its dependence on the WinBUGS package however, severely limited its performance and usage by the community. We have re-implemented msBayes to make use of both OpenBUGS and OpenMP, and have integrated this new core module, msBayes2.0, into a web-based platform and subsequent deployment and processing on a diversity of computing platforms. |
PI | Eric Halgren |
---|---|
Organization | University of California San Diego |
Department | School of Medicine |
Field of Science | Neuroscience |
Sponsor | CG OSG Connect |
Date Registered | 01/06/2017 |
Abstract of work | Define spatio-temporal High Gamma activity patterns in the human neocortex during waking, and compare them to the observed activity in preceding/subsequent sleeps to see whether specific waking patterns recur during sleep. |
PI | Daniel J. Katz |
---|---|
Organization | California State University, Northridge |
Department | Mathematics |
Field of Science | Mathematical Sciences |
Sponsor | CG OSG Connect |
Date Registered | 10/23/2017 |
Abstract of work | We calculate the autocorrelation merit factors for Golay-Shapiro-Rudin-like sequences and the crosscorrelation merit factors for pairs of such sequences. Each of the 2^n seed sequences of length n gives rise to an infinite family of sequences, and we have asymptotic formulas (see our preprint at arXiv: 1702.07697 [math.NT]) for the merit factors based on calculations involving only the seeds. The number of seeds grows exponentially, thus making this a project that is well-suited to distributed computing. We would like to extend Table 2 of our paper (minimum combined measure of autocorrelation and crosscorrelation, unconstrained search) to seeds of length 28. And we would like to extend Tables 1 and 3 of our paper (minimum autocorrelation and minimum combined measure among those sequences of minimum autocorrelation) to seeds of length 52, because we have a conjectue that something interesting may happen at length 52. We expect that the extension of T! ables 1 and 3 will require about 130,000 runs, each of which would take about an hour each on a single thread of a typical workstation. And we expect that the extension of Table 2 will require about 45,000 runs taking about 45 minutes each in a similar situation. |
PI | Mehmet Belgin |
---|---|
Organization | Georgia Tech |
Department | Advanced Research Computing |
Field of Science | Multi-Science Community |
Sponsor | CG OSG Connect |
Date Registered | 07/20/2016 |
Abstract of work | help GT researchers convert their existing projects into HTC workloads |
PI | Yvonne Chan |
---|---|
Organization | Iolani School |
Department | Biology |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 11/27/2015 |
Abstract of work | Hierarchical Approximate Bayesian Computation to Detect Community Response to Sea Level Change in the Hawaiian Archipelago. Methods that integrate population sampling from multiple taxa into a single analysis are a much needed addition to the comparative phylogeographic toolkit. Here we present a statistical framework for multi-species analysis based on hierarchical approximate Bayesian computation (hABC) for inferring community dynamics and concerted demographic response. Detecting community response to climate change is an important issue with regards to how species have and will react to past and future events. Furthermore, whether species responded individualistically or in concert is at the center of related questions about the abiotic and biotic determinants of community assembly. This method combines multi-taxon genetic datasets into a single analysis to determine the proportion of a contemporary community that historically expanded in a temporally clustered pulse as well as when the pulse occurred. We will apply this method to 59 species in the Hawaiian Archip ela! go in order to examine community response of coral reef taxa to sea-level change in Hawaii. The method can accommodate dataset heterogeneity such as variability in effective population size, mutation rates, and sample sizes across species and utilizes borrowing strength from the simultaneous analysis of multiple species. This hABC framework used in a multi-taxa demographic context can increase our understanding of the impact of historical climate change by determining what proportion of the community responded in concert or independently, and can be used with a wide variety of comparative phylogeographic datasets as biota-wide DNA barcoding data sets accumulate. |
PI | Brian Cheda |
---|---|
Organization | Arcadia university |
Department | Biology |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 12/07/2017 |
Abstract of work | Program uses NCBI’s Entrez.efetch on the nucleotide database to take in large number of sequences and searches the sequences for palindromes ranging in size from 4 to 20 and appends the results to a list. The program then takes each palindrome and checks for its occurrence on the 11 genes of the influenza A virus’s and outputs every match of the palindrome with relevant sequence Information. |
PI | Brad Minnery |
---|---|
Organization | Wright State Research Institute |
Department | Wright State Research Institute |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 03/14/2018 |
Abstract of work | The project aims to achieve explainable machine learning (ML) through the integration of structured semantic data with the inputs, outputs and hidden layers of deep learning systems. The proliferation of explicitly structured semantic data has occurred in parallel with the emergence of powerful ML algorithms, particularly deep neural networks (DNNs), whose internal layers encode information implicitly. This research attempts to bridge the gap between explicit, easy-to-understand semantic information and implicit, difficult-to-understand features of a deep learning system to achieve transparency and trust in an algorithm's reasoning across multiple layers. |
PI | David Swanson |
---|---|
Organization | University of Nebraska |
Department | Holland Computing Center |
Field of Science | Community Grid |
Sponsor | VO HCC |
Date Registered | 09/12/2016 |
Abstract of work | Jobs from our clusters that flock to the OSG |
PI | Karl Jablonowski |
---|---|
Organization | University of Washington |
Department | Biomedical and Health Informatics |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 08/24/2016 |
Abstract of work | My research focuses on detecting patterns in physiological data of patients in an Intensive Care Unit setting, with the aim of constructing an early warning system. The approach I am taking includes machine learning algorithms such as Artificial Neural Networks, Hidden Markov Models, and Support Vector Machines. I presently have limited computational resources for which to conduct this research. The data I am using for training and validation is both static and time based information on 32,000 patients and includes approximately 30GB of raw data. Additionally I have extremely high resolution data on 2,600 patient. The search-space is prohibitively large for a single computer and even some of the smaller clusters. I am employing an optimization methodology which allows for a differential evolution approach to incrementally improve a structurally adaptive model. The methodology allows for parallel programming which is of course a necessity for distributed computing. |
PI | Meenakshi Narain |
---|---|
Organization | Brown University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | VO OSG |
Date Registered | 03/12/2014 |
Abstract of work | Simulate hundreds of millions of high-energy proton proton collisions, which mimic the collisions expected at a potential High Luminosity LHC. This simulated data will be used to assess the performance of potential CMS detector upgrades, for inclusion in a Technical Proposal. |
PI | Allan Strand |
---|---|
Organization | College of Charleston |
Department | Biology |
Field of Science | Evolutionary Sciences |
Sponsor | CG OSG Connect |
Date Registered | 01/23/2017 |
Abstract of work | simulations of population genetics in 2d landscapes |
PI | Brian Blaylock |
---|---|
Organization | University of Utah |
Department | Atmospheric Sciences |
Field of Science | Earth Sciences |
Sponsor | CG OSG Connect |
Date Registered | 06/28/2017 |
Abstract of work | I have archived about 30TB (and growing) of output from NOAA's operational High Resolution Rapid Refresh model on an object storage archive system at Utah's Center for High Performance Computing. The challenge is to mine data from such a large data set. Open Science Grid may be a solution for processing this voluminous data set, if questions and data mining objectives can be broken into serial tasks. |
PI | Rob Quick |
---|---|
Organization | Indiana University |
Department | Research Technologies |
Field of Science | Community Grid |
Sponsor | VO OSG |
Date Registered | 04/01/2014 |
Abstract of work | This project will be used for the OSG AHM HTC Challenge. It may also be the home of future challenges. |
PI | Sarah Lynne Behrens |
---|---|
Organization | University of Nebraska - Lincoln |
Department | Mathematics |
Field of Science | Mathematical Sciences |
Sponsor | VO HCC |
Date Registered | 02/26/2015 |
Abstract of work | A degree sequence of a hypergraph is a list of numbers that gives the total number of edges each vertex is in and multiple hypergraphs can have the same degree sequence. I'm trying to determine a minimal set of moves that connects all of the realizations. I need to use parallel programming as there are many degree sequences to investigate. |
PI | Donald Krieger |
---|---|
Organization | University of Pittsburgh |
Department | Neurosurgery |
Field of Science | Neuroscience |
Sponsor | CG OSG-XSEDE |
Date Registered | 01/25/2016 |
Abstract of work | Child project of TG-IBN130001 |
PI | Francis Halzen |
---|---|
Organization | University of Wisconsin |
Department | Physics |
Field of Science | Astrophysics |
Sponsor | CG OSG Connect |
Date Registered | 06/02/2014 |
Abstract of work | IceCube is the world's largest neutrino detector. It is located at the South Pole and includes a cubic kilometer of instrumented ice. IceCube searches for neutrinos from the most violent astrophysical sources: events like exploding stars, gamma ray bursts, and cataclysmic phenomena involving black holes and neutron stars. The IceCube telescope is a powerful tool to search for dark matter, and could reveal the new physical processes associated with the enigmatic origin of the highest energy particles in nature. In addition, exploring the background of neutrinos produced in the atmosphere, IceCube studies the neutrinos themselves; their energies far exceed those produced by accelerator beams. |
PI | Andrew Ruether |
---|---|
Organization | Swarthmore College |
Department | ITS |
Field of Science | Evolutionary Sciences |
Sponsor | CG OSG Connect |
Date Registered | 09/22/2016 |
Abstract of work | Running the idTracker software (http://www.idtracker.es/) in parallel on OSG. |
PI | Bryce Littlejohn |
---|---|
Organization | Illinois Institute of Technology |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG OSG Connect |
Date Registered | 06/26/2017 |
Abstract of work | Monte Carlo generation and data analysis for the PROSPECT experiment. |
PI | Thomas A. Kursar |
---|---|
Organization | University of Utah |
Department | Biology |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 03/01/2017 |
Abstract of work | We study how interactions between plants and their insect herbivores lead to the evolution of plant defenses, including plant's chemical defenses. In order to identify some of the many unknown compounds we have isolated via LC-MS from the tropical tree genus Inga (Fabaceae), we use in silico fragmentation to predict the ms/ms spectra for a given chemical structure using Competitive Fragmentation Modeling for Metabolite Identification (CFM-ID) (http://cfmid.wishartlab.com). This allows us to match observed ms/ms spectra with a theoretical library of known and predicted chemical structures. |
PI | Mats Rynge |
---|---|
Organization | University of Southern Caliornia |
Department | ISI |
Field of Science | Bioinformatics |
Sponsor | CG ISI |
Date Registered | 05/11/2016 |
Abstract of work | Collaboration with the Rice3k IRRI project |
PI | Rob Quick |
---|---|
Organization | Indiana University |
Department | Bioinformatics |
Field of Science | Bioinformatics |
Sponsor | VO CSIU |
Date Registered | 08/20/2013 |
Abstract of work | Submitting blast queries via Galaxy portal on OSG resources. |
PI | Hao Xu |
---|---|
Organization | University of California Riverside |
Department | Econimics |
Field of Science | Economics |
Sponsor | CG OSG Connect |
Date Registered | 10/06/2016 |
Abstract of work | We could like to preform instruments selection in the IV model by Machine Learning technique, and estimated the structure parameters by GMM method. |
PI | Bradley Voytek |
---|---|
Organization | University of California San Diego |
Department | Neuroscience |
Field of Science | Neuroscience |
Sponsor | CG OSG Connect |
Date Registered | 04/04/2017 |
Abstract of work | Training recurrent neural nets on various tasks; discretizing the dynamics of the networks and observing changes in network stability, performance and topology. |
PI | Feng Bill Shi |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | Statistics |
Sponsor | CG OSG Connect |
Date Registered | 05/07/2015 |
Abstract of work | Project Description: Over the past five years, there has been a boom in technology startups that continues to attract more and more talent. While everyone starts with a million-dollar idea, only a few manage to transfer into real innovations and impact our lives. What makes those ideas successful? Can you imagine an app that tells you how innovative your idea is? This project will take a computational approach to the understanding of innovation and develop a machinery to learn from real data to evaluate the creativity of new ideas. Innovation is a broad topic, constantly discussed in business, economics, sociology, etc. It is such a complex phenomenon that there is no thorough theory about it. Here we will take a combinatorial perspective: an idea is a combination of existing and new knowledge. Hence, the goal is to understand why certain combinations are more interesting than others. Specifically, the first step is to map out our idea space with data from kickstarter, US Patents, and possibly other knowledge databases. The second step is to find interesting patterns, associations and dynamics in this map of knowledge. And finally computational methods will be developed to evaluate the fitness of any idea in a given environment. |
PI | James Evans |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | Other |
Sponsor | CG OSG Connect |
Date Registered | 03/26/2014 |
Abstract of work | Knowledge Lab / CI |
PI | Michael J. Culbertson |
---|---|
Organization | University of Illinois, Urbana-Champaign |
Department | Psychology |
Field of Science | Educational Psychology |
Sponsor | CG OSG Connect |
Date Registered | 09/25/2013 |
Abstract of work | In educational assessment, several questions must be answered when constructing a test, such as “How many items are necessary for adequate knowledge measurement precision?”, “How many field-test students are needed to adequately calibrate model parameters?”, or “Which computerized adaptive testing (CAT) algorithm performs best?” For complex non-linear models, these questions are typically approached by simulation: Model parameters are calibrated (as if unknown) from simulated student item responses, or the emergent properties of particular CAT algorithms are investigated with a large number of simulated test takers. Since the design space grows quickly, many simulations are necessary to understand general trends. Match-for-OSG: Simulations throughout the test design space can be run independently, requiring little coordination between cores. Computations generally do not have high memory requirements or unusual library/code dependencies, and computations can be recovered from checkpoints easily. The large number of simulations suggests parallel computing, but the independence allows an asynchronous, distributed environment, such as OSG. |
PI | David Toth |
---|---|
Organization | Centre College |
Department | Chemistry |
Field of Science | Chemistry |
Sponsor | CG OSG Connect |
Date Registered | 04/18/2017 |
Abstract of work | It has been shown that deregulation of the Kappa Opioid Receptor (KOR) can contribute to drug abuse and other psychiatric disorders. Therefore, KOR agonists/antagonists have become a target for the development of pharmacotherapies for the treatment of addiction and other CNS disorders. Unfortunately, few chemical scaffolds have been shown to bind selectively to the KOR. Through the use of computational methods, we will screen a variety of chemical scaffolds to see how well they bind to the active pocket of the KOR and Mu Opioid Receptor. From these results, we will identify targets with high binding affinity to Kappa and low binding affinity to Mu. The identified compounds will then be screened for in vitro binding affinity to identify novel KOR selective ligands. |
PI | Joe Boyd |
---|---|
Organization | Fermilab |
Department | N/A |
Field of Science | High Energy Physics |
Sponsor | VO Fermilab |
Date Registered | 02/19/2018 |
Abstract of work | Project entry corresponding to Lariat VO. |
PI | Erica Snider |
---|---|
Organization | Fermilab |
Department | Scientific Computing Division |
Field of Science | High Energy Physics |
Sponsor | VO Fermilab |
Date Registered | 02/06/2018 |
Abstract of work | The Liquid Argon Software (LArSoft) Collaboration develops and supports a shared base of physics software across Liquid Argon (LAr) Time Projection Chamber (TPC) experiments. |
PI | Jozsef Balogh |
---|---|
Organization | University of Illinois Urbana-Champaign |
Department | Mathematics |
Field of Science | Mathematical Sciences |
Sponsor | CG OSG Connect |
Date Registered | 04/04/2017 |
Abstract of work | Leader-Milicevic-Tan asked how many products of complete bipartite graphs are needed to decompose the edge set of K_3 x K_n. Doing this with 2*(n-1) is trivial, here we use simulated annealing to search for a better construction. |
PI | Joel Giedt |
---|---|
Organization | Rensselaer Polytechnic Institute |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG OSG Connect |
Date Registered | 10/04/2016 |
Abstract of work | We are simulating quantum field theory and many particle systems using lattice field theory techniques. Although some of our work involves lattice QCD, much of it does not. It encompasses supersymmetric systems and phase transitions in nonrelativisting systems. |
PI | Andrea C Gallegos |
---|---|
Organization | New Mexico State University |
Department | Earth Sciences |
Field of Science | Earth Sciences |
Sponsor | CG OSG Connect |
Date Registered | 03/02/2016 |
Abstract of work | Determine the attenuation of the regional shear wave Lg for NE China and the contiguous United States using broadband seismograms. |
PI | Debashis Ghosh |
---|---|
Organization | University of Colorado Denver |
Department | Biostatistics |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 11/13/2017 |
Abstract of work | Simulations for developing a kernel based statistical methodology. |
PI | Peter F. Couvares |
---|---|
Organization | Syracuse University |
Department | Physics |
Field of Science | Gravitational Physics |
Sponsor | CG OSG Connect |
Date Registered | 10/03/2014 |
Abstract of work | Gravitational Wave Astronomy |
PI | Kevin Jensen Liu |
---|---|
Organization | Michigan State University |
Department | Computer Science and Engineering |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 07/07/2016 |
Abstract of work | The project goal is to create new computational methodologies for large-scale phylogenomic analyses involving complex evolutionary histories. |
PI | James P. Howard, II |
---|---|
Organization | Johns Hopkins University |
Department | Mathematics |
Field of Science | Mathematical Sciences |
Sponsor | CG OSG Connect |
Date Registered | 12/18/2017 |
Abstract of work | This project will search for and perform limited verification of potential Lychrel numbers. A Lychrel number is a natural number that through reversing its digits and adding them together, repeatedly, does not form a palindrome. |
PI | Vivek Farias |
---|---|
Organization | Massachusetts Institute of Technology |
Department | Sloan School of Management |
Field of Science | Information Theory |
Sponsor | CG OSG Connect |
Date Registered | 09/21/2015 |
Abstract of work | Developing new policies for the (classical) Multi-Armed Bandit problem. |
PI | Ariella Gladstein |
---|---|
Organization | University of Arizona |
Department | Ecology and Evolutionary Biology |
Field of Science | Evolutionary Sciences |
Sponsor | CG OSG Connect |
Date Registered | 03/14/2017 |
Abstract of work | Every individual’s genome carries within it the history of all the ancestors of that individual. Thus, by analyzing a small number of genomes, we can accurately infer the demographic history of entire human populations. This demographic history helps establish a baseline that is needed for research and discovery in medical genomics. We are using a process to more accurately infer the demographic history of human populations by comparing genomic statistics from millions of genome simulations to real population genomic data. While other researchers have worked with this process using only a few individuals or a portion of a chromosome, we are pushing the limit of computing capabilities by simulating whole chromosomes of hundreds of individuals. Using the whole chromosome allows us to look at more recent demographic history, which is particularly helpful in finding genetic links to disease processes. After publication, we will make our pipeline available so other researchers can apply it to other populations. This project pushes the frontier of genomic research in that it uses new methods, simulates a larger part of the genome, and is being applied to populations not yet thoroughly studied. |
PI | Timothy M Beissinger |
---|---|
Organization | University of Missouri |
Department | Divison of Plant Sciences |
Field of Science | Evolutionary Sciences |
Sponsor | CG OSG Connect |
Date Registered | 03/20/2017 |
Abstract of work | The amino acid content in maize kernels is critically important for human and animal nutrition. However, the genetic basis underpinning amino acids is not fully understood. We are performing Genome Wide Association Studies and Genomic prediction in a panel of several thousand maize plants genotyped at tens of millions of loci to finely dissect amino acid traits in maize. |
PI | Liang Shi |
---|---|
Organization | UC Merced |
Department | Chemistry |
Field of Science | Chemistry |
Sponsor | CG OSG Connect |
Date Registered | 02/09/2018 |
Abstract of work | Spectroscopic maps are widely used in condensed-phase vibrational spectroscopic simulations. We aim to develop ab-initio-based maps for water, and more complex systems. |
PI | Jessica Mar |
---|---|
Organization | Albert Einstein College of Medicine |
Department | Systems and Computational Biology |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 09/25/2017 |
Abstract of work | Doing RNA-seq analysis to understand biomolecular systems. |
PI | Joe Boyd |
---|---|
Organization | Fermilab |
Department | N/A |
Field of Science | High Energy Physics |
Sponsor | VO Fermilab |
Date Registered | 03/15/2018 |
Abstract of work | Dummy project corresponding to the mars VO. |
PI | C. S. Raman |
---|---|
Organization | University of Maryland Baltimore |
Department | Pharmaceutical Sciences |
Field of Science | Biochemistry |
Sponsor | CG OSG Connect |
Date Registered | 07/16/2015 |
Abstract of work | We wish to use the Condor grid for running the program ARCIMBOLDO, which is geared for finding HT molecular replacement solutions. Because we have a recalcitrant system in our hands, we really need this system to solve our problem. |
PI | John McGreevy |
---|---|
Organization | University of California San Diego |
Department | Physics |
Field of Science | Physics |
Sponsor | CG OSG Connect |
Date Registered | 04/17/2017 |
Abstract of work | Perform monte carlo simulation on spin liquid systems |
PI | Alex Langerman |
---|---|
Organization | The University of Chicago |
Department | Otolaryngology |
Field of Science | Medical Sciences |
Sponsor | CG OSG Connect |
Date Registered | 08/24/2016 |
Abstract of work | Analysis of modern surgery presents many interesting computational challenges. The problems of access to data, data analysis, and interpretation of said analysis all present fundamental, unsolved difficulties to those in medical informatics. The focus of this project primarily involves data analysis where operations are still typically thought of holistically and conceptually, rather than algorithmically. This work is an attempt to change that by properly defining surgical procedures in a manner conducive to both education and analysis. |
PI | Humberto Ortiz-Zuazaga |
---|---|
Organization | University of Puerto Rico |
Department | Computer Science |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 10/13/2014 |
Abstract of work | high performance sequence analysis |
PI | Joe Boyd |
---|---|
Organization | Fermilab |
Department | N/A |
Field of Science | High Energy Physics |
Sponsor | VO Fermilab |
Date Registered | 02/19/2018 |
Abstract of work | Project entry corresponding to the MicroBooNE VO. |
PI | Patrick Charbonneau |
---|---|
Organization | Duke University |
Department | Chemistry |
Field of Science | Chemistry |
Sponsor | CG OSG Connect |
Date Registered | 11/04/2015 |
Abstract of work | Periodic microphases universally emerge in systems for which short-range inter-particle attraction is frustrated by long-range repulsion. The morphological richness of these phases makes them desirable material targets, but our relatively coarse understanding of even simple models limits our grasp of their assembly. The OSG computing resources will enable us to explore more solutions of the equilibrium phase behavior of a family of similar microscopic microphase formers through specialized Monte Carlo simulations. |
PI | Gabriel Nathan Perdue |
---|---|
Organization | Fermilab |
Department | N/A |
Field of Science | High Energy Physics |
Sponsor | VO Fermilab |
Date Registered | 02/19/2018 |
Abstract of work | Project entry corresponding to the Minerva VO. |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 04/08/2015 |
Abstract of work | Open Science Grid Mini-Workshop at University of Chicago on April 9th 2015 |
PI | Joe Boyd |
---|---|
Organization | Fermilab |
Department | N/A |
Field of Science | High Energy Physics |
Sponsor | VO Fermilab |
Date Registered | 03/15/2018 |
Abstract of work | Project entry corresponding to the Minos VO. |
PI | Ikuo Takei |
---|---|
Organization | University of Wisconsin Madison |
Department | Economics |
Field of Science | Economics |
Sponsor | CG OSG Connect |
Date Registered | 10/07/2016 |
Abstract of work | The project aim is to estimate structural parameters of dynamic heterogeneous agent model to investigate the optimal design of monetary and financial policies. In particular, we need to find numerical solutions for stochastic dynamic programming problems with many state variables. |
PI | Olexandr Isayev |
---|---|
Organization | University of North Carolina at Chapel Hill |
Department | Chemistry |
Field of Science | Chemistry |
Sponsor | CG OSG Connect |
Date Registered | 10/26/2016 |
Abstract of work | Quantum chemical and machine learning insights into supra-molecular organization of molecular crystals. |
PI | Wouter Deconinck |
---|---|
Organization | Jefferson Lab |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG OSG Connect |
Date Registered | 10/09/2017 |
Abstract of work | The MOLLER experiment at Jefferson Lab is a Department of Energy supported project (currently past CD-0 status) that aims to determine the electroweak mixing angle to the highest precision at low energies through elastic electron-electron scattering. |
PI | Maxene Meier |
---|---|
Organization | University of Colorado |
Department | School of Public Health |
Field of Science | Statistics |
Sponsor | CG OSG Connect |
Date Registered | 01/24/2018 |
Abstract of work | Looking at agreement of African triage data using Meier's Omega |
PI | Shripad Tuljapurkar |
---|---|
Organization | Stanford University |
Department | Biology |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 10/09/2017 |
Abstract of work | his project is about the mortality of developed countries in Human Fertility Database. |
PI | Jacob Pessin |
---|---|
Organization | Albert Einstein College of Medicine |
Department | Endocrinology |
Field of Science | Medical Sciences |
Sponsor | CG OSG Connect |
Date Registered | 12/23/2014 |
Abstract of work | For modeling and other computational projects of the Mt. Sinai-Einstein DRC and affiliates, primarily structurally related protein Modeling and Docking. |
PI | Joe Boyd |
---|---|
Organization | Fermilab |
Department | N/A |
Field of Science | High Energy Physics |
Sponsor | VO Fermilab |
Date Registered | 02/19/2018 |
Abstract of work | Project entry corresponding to the Mu2e VO. |
PI | Joel Bader |
---|---|
Organization | Johns Hopkins University |
Department | Department of Biomedical Engineering |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 10/29/2014 |
Abstract of work | Assembling the genome of a number of plant lines, and conducting RNASeq studies for the development of a transcriptome and differential expression analysis. |
PI | Alberto Otero de la Roza |
---|---|
Organization | National Research Council of Canada |
Department | National Institute for Nanotechnology |
Field of Science | Chemistry |
Sponsor | CG OSG Connect |
Date Registered | 09/09/2015 |
Abstract of work | Project Description: Density-Functional Theory (DFT) is the most successful method for the computation of quantum mechanical properties in molecules and solids. The aim of our project is to advance the DFT field by extending and improving the existing methods for modeling non-covalent interactions. Computational tasks for this project include DFT calculations on small molecules as well as periodic solids, and the use of home-made programs that implement our methodologies. |
PI | Michael Dinerstein |
---|---|
Organization | The University of Chicago |
Department | Economics |
Field of Science | Economics |
Sponsor | CG OSG Connect |
Date Registered | 02/28/2017 |
Abstract of work | Studying the effects of the North Carolina Opportunity Scholarship using a discrete choice model. The estimation recovers utility parameters for school choice using school enrollments. |
PI | Sandra Gesing |
---|---|
Organization | Notre Dame |
Department | Computer Science and Engineering |
Field of Science | Bioinformatics |
Sponsor | VO CSIU |
Date Registered | 09/18/2014 |
Abstract of work | Submitting blast queries via Notre Dame Galaxy portal on OSG resources. |
PI | Nick Dusek |
---|---|
Organization | North Dakota State University |
Department | Center for Computationally Assisted Science and Technology |
Field of Science | Multi-Science Community |
Sponsor | CG OSG Connect |
Date Registered | 02/06/2018 |
Abstract of work | As a new contributor of resources to OSG, we would like to introduce our users to the grid and help them transition some of their jobs to OSG resources, as appropriate. |
PI | Frank McKenna |
---|---|
Organization | UC Berkeley |
Department | Civil Engineering |
Field of Science | Civil Engineering |
Sponsor | VO OSG |
Date Registered | 05/20/2014 |
Abstract of work | Earthquake Engineering is moving towards performance based engineering. Performance based engineering will potentially require and exponentially increase the amount of computation required of engineers as engineers move to incorporate risk and uncertainty associated with hazard, modeling, cost, material, etc. into the simulations. Currently those in research mostly are using the OpenSees (http://opensees.berkeley.edu) application to perform these calculations. This project aims at providing these researchers with access to current versions of OpenSees by utilizing resources to build the application on OSG resources. |
PI | Petra Lenz |
---|---|
Organization | University of Hawaii at Manoa |
Department | Pacific Biosciences Research Center |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 09/22/2015 |
Abstract of work | Generation of a transcriptome for the copepod Neocalanus flamingeri in the gulf of Alaska. |
PI | Fabricia Nascimento |
---|---|
Organization | Duke University, The University of North Carolina at Chapel Hill, and North Carolina State University |
Department | NESCent Center |
Field of Science | Evolutionary Sciences |
Sponsor | CG OSG Connect |
Date Registered | 09/25/2013 |
Abstract of work | NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent achieves this by supporting research and education across disciplinary, institutional, geographic, and demographic boundaries. |
PI | James Saxon |
---|---|
Organization | University of Chicago |
Department | Harris School of Public Policy |
Field of Science | Earth Sciences |
Sponsor | CG OSG Connect |
Date Registered | 03/02/2018 |
Abstract of work | Measuring driving and walking times for very large matrices of points. |
PI | Bradley Voytek |
---|---|
Organization | University of California San Diego |
Department | Cognitive Science |
Field of Science | Neuroscience |
Sponsor | CG OSG Connect |
Date Registered | 07/28/2016 |
Abstract of work | Our lab studies the rhythms of the brain, recorded electrically as oscillations in voltage. These brain rhythms have been hypothesized to underlie functional communication between different brain regions, but the mechanism by which it does this is not clear. Additionally, it is not clear from a biophysical standpoint how these oscillations are generated. Our lab studies both noninvasive and clinical recordings from human subjects and patients in order to better understand these rhythms of the brain. For example, the project contact's personal research investigates the variations in the waveform shape of neural oscillations. Why are some oscillations nonsinusoidal (e.g. sawtooth), how does this impact neural communication, and how does this relate to high-level behaviors? |
PI | Raymond Tsang |
---|---|
Organization | Pacific Northwest National Laboratory |
Department | National Security Directorate |
Field of Science | High Energy Physics |
Sponsor | CG OSG Connect |
Date Registered | 09/05/2017 |
Abstract of work | The nEXO experiment aims to search for double beta decay of Xenon-136. |
PI | Caterina Stamoulis |
---|---|
Organization | Harvard Medical School |
Department | Medicine |
Field of Science | Medical Sciences |
Sponsor | CG OSG Connect |
Date Registered | 09/15/2017 |
Abstract of work | The goal of this project is to develop and deploy a novel computational platform for massive parallel analysis of high-dimensional brain networks. |
PI | Nathan Kaib |
---|---|
Organization | University of Oklahoma |
Department | Physics and Astronomy |
Field of Science | Physics and astronomy |
Sponsor | CG OSG Connect |
Date Registered | 11/23/2016 |
Abstract of work | The Nice Model, is an evolutionary model for the outer Solar System which has explained many puzzling observed qualities of the Solar System. As the newly formed planets cleared debris from the young Solar System, Saturn, Uranus, and Neptune tended to scatter objects inward, while Jupiter ejected these planetesimals out of the Solar System. To conserve angular momentum through this process, Jupiter slowly migrates inward while the other giant planets move outward. When Jupiter and Saturn cross a period of orbital resonance, the entire Solar System experiences a massive instability. We will run simulations to probe the affect of such an instability on an evolving system of inner planets. |
PI | Satrajit Ghosh |
---|---|
Organization | Massachusetts Institute of Technology |
Department | McGovern Institute for Brain Research |
Field of Science | Neuroscience |
Sponsor | CG OSG Connect |
Date Registered | 03/13/2017 |
Abstract of work | Regression testing of various brain imaging tools |
PI | Joe Boyd |
---|---|
Organization | Fermilab |
Department | N/A |
Field of Science | High Energy Physics |
Sponsor | VO Fermilab |
Date Registered | 02/19/2018 |
Abstract of work | Project entry corresponding to the Nova VO. |
PI | Peter Graf |
---|---|
Organization | NREL - National Renewable Energy Laboratory, Golden CO |
Department | Computational Science Center |
Field of Science | Materials Science |
Sponsor | CG OSG Connect |
Date Registered | 10/01/2013 |
Abstract of work | Ab initio calculation of the physical properties of 10^4 to 10^6 materials, database of results, and web site for access. |
PI | Nicholas Tatonetti |
---|---|
Organization | Columbia University |
Department | Biomedical Informatics |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 06/09/2017 |
Abstract of work | Using deep learning models to discover statistically significant drug effects using public drug surveillance datasets from the Federal Drug Administration. |
PI | Dean Andrew Hidas |
---|---|
Organization | Brookhaven National Laboratory |
Department | National Synchrotron Light Source II |
Field of Science | High Energy Physics |
Sponsor | CG OSG Connect |
Date Registered | 09/02/2015 |
Abstract of work | Using magnetic field measurements taken in the lab of undulators and wigglers we will compute the downstream photon spectrum and distributions for many configurations of many of the NSLS2 insertion devices, including wavefront propagation and beamline simulation where needed. |
PI | Vadim Apalkov |
---|---|
Organization | Georgia State University |
Department | Department of Physics and Astronomy |
Field of Science | Physics |
Sponsor | CG OSG Connect |
Date Registered | 01/04/2016 |
Abstract of work | This model uses Matlab parallel programming to predict noise sensitive neuronal model. |
PI | Jerry Tessendorf |
---|---|
Organization | Clemson University |
Department | Computer Science |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 08/03/2015 |
Abstract of work | We are developing a implementation of a Monte Carlo volume rendering method. The primary purpose is to impro ve the calculation of multiple scattering physics, with possible applications in computer graphics, nuclear physics, and remote s ensing. The project involves the numerical calculation of a Feynman path integral, which is what most of the computation is devot ed to, and the primary need for high throughput computing methods. |
PI | Manish Parashar |
---|---|
Organization | Rutgers University |
Department | Electrical & Computer Engineering |
Field of Science | Computer and Information Science and Engineering |
Sponsor | VO OSG |
Date Registered | 11/07/2013 |
Abstract of work | The goal of this work is to provide a federated heterogeneous infrastructure that can be federated on demand for scientists and scientific applications. The goal of this work is to integrate OSG as a part of the federated infrastructure cloud. The federation leverages the CometCloud software, currently being developed at Rutgers University. NWChem is the initial application to be used on OSG resources. A parallel in time algorithm will run multiple NWChem instances on the OSG resources, where each instance has different input parameters. The collective output of all instances is then gathered and analyzed. |
PI | Dave OConnor |
---|---|
Organization | University of Wisconsin |
Department | School of Medical and Public Health |
Field of Science | Medical Sciences |
Sponsor | CG OSG Connect |
Date Registered | 07/30/2015 |
Abstract of work | Immunology at OConner's lab |
PI | Anton Betten |
---|---|
Organization | Colorado State University |
Department | Department of Mathematics |
Field of Science | Mathematical Sciences |
Sponsor | CG OSG Connect |
Date Registered | 05/23/2014 |
Abstract of work | The goal of this project is to create farmed data in the form of classifications of discrete structures from mathematics. This data farm can be used to support discovery of new objects and constructions. |
PI | George Rudolph |
---|---|
Organization | The Citadel |
Department | Mathematics and Computer Science |
Field of Science | Computer and Information Science and Engineering |
Sponsor | VO OSG |
Date Registered | 08/14/2013 |
Abstract of work | Develop a metric that measures the real similarities and differences between machine learning algorithms (in this case classifiers) based on output behavior. Previous study included 17 representative algorithms and used 30 datasets from the UCI Machine Learning Repository. The main goal of the current effort is to extend the metric using semi-supervised learning techniques. I would also like, if possible, to experiment with more recent datasets beyond what is traditional from the UCI Repository; and to add more algorithms to the study. |
PI | Chander Sehgal |
---|---|
Organization | Fermilab |
Department | Computing Sector |
Field of Science | Computer and Information Science and Engineering |
Sponsor | VO OSG |
Date Registered | 08/15/2013 |
Abstract of work | Integration and testing of science applications for new users |
PI | Rob Quick |
---|---|
Organization | Open Science Grid |
Department | GOC |
Field of Science | Community Grid |
Sponsor | CG OSG Connect |
Date Registered | 06/05/2014 |
Abstract of work | Training project for OSG Operations staff. |
PI | Ulrich Heinz |
---|---|
Organization | Ohio State University |
Department | Physics Department |
Field of Science | Nuclear Physics |
Sponsor | CG OSG Connect |
Date Registered | 02/06/2018 |
Abstract of work | Experimentally calibrated event-by-event simulations of high-energy heavy-ion collisions. Numerical implementation of optimized dissipative relativistic fluid dynamics. |
PI | Henry Frisch |
---|---|
Organization | University of Chicago |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG OSG Connect |
Date Registered | 11/13/2017 |
Abstract of work | PSEC group at the University of Chicago is developing Large-Area Picosecond Photo-Detectors (LAPPDs). By reconstructing the arrival position and time of photons produced in water or liquid scintillator on highly segmented fast photo-detectors such as LAPPDs one can reconstruct tracks by using the `drift time' of photons, much as one does with electrons in a Time Projection Chamber. We are developing new event reconstruction techniques for large water and liquid scintillator detectors. For example see A. Elagin et al., “Separating Double-Beta Decay Events from Solar Neutrino Interactions in a Kiloton-Scale Liquid Scintillator Detector by Fast Timing”, Nucl. Instr. Meth. Phys. Res. A849 (2017) 102. |
PI | Maxim Potekhin |
---|---|
Organization | Brookhaven National Laboratory |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | VO OSG |
Date Registered | 02/03/2014 |
Abstract of work | LBNE will endeavor to perform precision measurements of key parameters pertaining to neutrino oscillations, advancing our understanding of some of the most fundamental issues in particle physics, such as neutrino mass hierarchy, nucleon decay and a few other others. The Software and Computing Organization of LBNE is tasked with providing core infrastructure for its Physics Tools development and data processing, which will need to accommodate the needs of a diverse and distributed research organization. |
PI | Pei Tang |
---|---|
Organization | University of Pittsburgh |
Department | Anesthesiology |
Field of Science | Medical Sciences |
Sponsor | CG OSG Connect |
Date Registered | 04/14/2015 |
Abstract of work | Virtual screening for novel anesthetic compounds. |
PI | Jacob Washburn |
---|---|
Organization | University of Missouri |
Department | Biological Sciences |
Field of Science | Evolutionary Sciences |
Sponsor | CG OSG Connect |
Date Registered | 10/16/2015 |
Abstract of work | Processing of Transcriptome data from many species across the grass tribe Paniceae |
PI | Georgios Papadimitriou |
---|---|
Organization | University of Southern California |
Department | Computer Science |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 01/11/2018 |
Abstract of work | Performance Data Capture and Analysis for End-to-end Scientific Workflows |
PI | Frank Pinski |
---|---|
Organization | University of Cincinnati |
Department | Physics |
Field of Science | Computational Condensed Matter Physics |
Sponsor | CG OSG Connect |
Date Registered | 09/25/2013 |
Abstract of work | The goal of this research is to develop a computational tool that can uncover the pathway and the transition states that exist when a molecule changes conformation or when it chemically changes. In many such circumstances, a process must overcome an energy barrier before proceeding to completion. If the size of the barrier is large compared to the available thermal energy, a process must rely on the occurrence of one or more rare events. For such circumstances, one would like to understand the reaction pathways so as to improve yields, or as in the case of protein folding, to understand the intermediate states. Many simple processes have been explored using theoretical tools such as molecular dynamics, where the movements of individual atoms are calculated. However, when the barrier is large, crossing the relevant barrier is indeed a very rare event. Although computer speeds have been doubling every 18 months (a consequence of Moore's law), the exponentially long waiting times necessary for barrier hopping pushes the required computational effort out of the feasibility range for all but the simplest models. To explore these barrier-limited processes, we are developing a novel computational technique to sample the paths themselves in a thermodynamically significant manner. |
PI | Yong Li |
---|---|
Organization | UC San Diego |
Department | Structural Engineering |
Field of Science | Civil Engineering |
Sponsor | CG OSG Connect |
Date Registered | 09/15/2016 |
Abstract of work | Probability-based structural design has now emerged as the most advanced methodology to design new and retrofit existing structures in the face of uncertainty. The focus of our research lies at the intersection of the areas of structural engineering and risk engineering against natural hazards (e.g., earthquakes). A large number of computationally-demanding Finite Element simulation jobs need to be run as part of our research using open source software (e.g., OpenSees, Dakota) and script languages (e.g., Matlab, Python). Thus, the used of high-throughput computing resources will be central for the success of our potentially high-impact research on probability-based optimum structural design against natural hazards. |
PI | Frank Wuerthwein |
---|---|
Organization | University of California San Diego |
Department | Physics Department |
Field of Science | Physics |
Sponsor | CG UCSD |
Date Registered | 10/03/2016 |
Abstract of work | Work submitted as part of the physics computing facility (PCF) at the physics department at UCSD |
PI | Jessica Sidler Folsom |
---|---|
Organization | Florida State University |
Department | Florida Center for Reading Research |
Field of Science | Ecological and Environmental Sciences |
Sponsor | CG OSG Connect |
Date Registered | 09/02/2015 |
Abstract of work | This is an analysis of statewide data for all students in grades K-2. The aim of the analysis is to examine the effects of peers' achievement and composition effects on individual student achievement. This analysis requires mixed-effect modeling and quantile regression. R, and qrLMM package, will be used for analysis, 19 instances of analysis (one for each quantile .05 to .95 in .05 increments) will be conducted for each grade (k, 1, and 2). Each data set is less than 1GB, but requires approximately 6gb to run. |
PI | Mats Rynge |
---|---|
Organization | USC |
Department | ISI |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG ISI |
Date Registered | 10/20/2015 |
Abstract of work | Project used for Pegasus tutorials and training |
PI | Justin M Hutchison |
---|---|
Organization | University of Illinois |
Department | Civil and Environmental Engineering |
Field of Science | Engineering |
Sponsor | CG OSG Connect |
Date Registered | 04/12/2016 |
Abstract of work | Assessment of costs and environmental impacts of drinking water technologies for the removal of perchlorate |
PI | Stefan Hoeche |
---|---|
Organization | SLAC |
Department | Theory Group |
Field of Science | High Energy Physics |
Sponsor | VO OSG |
Date Registered | 01/20/2014 |
Abstract of work | The goal of this project is to test and validate the Sherpa and Blackhat software for particle physics phenomenology at the Large Hadron Collider (LHC), and to perform studies which are directly applicable to physics analyses in the LHC experiments ATLAS and CMS. Sherpa is a complete Monte-Carlo event generation framework for collider experiments. Hard scattering events are simulated using perturbative QCD at the leading or the next-to-leading order with the help of BlackHat. QCD Resummation is implemented by an in-house parton shower model based on the dipole factorization approach. Hadronization is performed in a cluster model and a complete hadron decay simulation is included in the program. BlackHat is a program library to compute virtual corrections in perturbative QCD based on generalized unitarity methods. It is used to produce particle-level cross sections for phenomenologically relevant signal and background reactions of high particle multiplicity at the Large Hadron Collider. Recent progress achieved with the combination of BlackHat and Sherpa is described at https://twiki.grid.iu.edu/bin/view/Management/Nov2012Newsletter#Precision_Event_Simulation_for_t |
PI | Siavash Mirarab |
---|---|
Organization | UC San Diego |
Department | Electrical and Computer Engineering |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 08/28/2015 |
Abstract of work | In this project, we design, implement, and test new methods for phylogenomics analyses. The goal of phylogenomics, as used here, is to estimate a species tree from genomic data. The ultimate goal of this line of research is reconstructing the tree of life. |
PI | Nathan G Swenson |
---|---|
Organization | University of Maryland |
Department | Department of Biology |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 05/11/2015 |
Abstract of work | The project entails the sequencing and assembly of the transcriptomes of 100+ non-model tree species from the USA and China. This information is then used to infer a functional phylogenomic tree from which inferences regarding functional similarity and species co-existence and diversity are drawn. |
PI | Panthea Sepehrband |
---|---|
Organization | Santa Clara University |
Department | Mechanical |
Field of Science | Materials Science |
Sponsor | CG OSG Connect |
Date Registered | 11/03/2015 |
Abstract of work | A molecular dynamics study (LAMMPS) of diffusion along the core of a screw dislocation is to be studied. |
PI | Joy Bergleson |
---|---|
Organization | University of Chicago |
Department | Ecology and Evolution |
Field of Science | Plant Biology |
Sponsor | CG OSG Connect |
Date Registered | 10/01/2013 |
Abstract of work | Investigation of plant-pathogen interactions using genome-wide association mapping. |
PI | Karen McGinnis |
---|---|
Organization | Florida State University |
Department | Biological Science |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 03/08/2018 |
Abstract of work | With the emergence of massively parallel sequencing, genome-wide expression data production has reached an unprecedented level. This abundance of data has greatly facilitated maize research, but may not be amenable to traditional analysis techniques that were optimized for other data types. Using publicly available data, a Gene Co-expression Network (GCN) can be constructed and used for gene function prediction, candidate gene selection and improving understanding of regulatory pathways. Several GCN studies have been done in maize, mostly using microarray datasets. To build an optimal GCN from plant materials RNA-Seq data, parameters for expression data normalization and network inference were evaluated. We previously constructed an optimized gene coexpression network for maize. In this project, we want to build gene regulatory networks for Arabidopsis, rice maize, and sorghum. |
PI | Brian Keating |
---|---|
Organization | University of California - San Diego |
Department | Physics |
Field of Science | Astrophysics |
Sponsor | CG OSG Connect |
Date Registered | 04/14/2016 |
Abstract of work | The evolution of the universe is based on the idea of gravitational instability, whereby initial tiny fluctuations in the density of the Universe grew under the influence of gravity to form the large-scale gravitational structures we see around us today. These structures bend the trajectories of Cosmic Microwave Background photons through gravitational lensing, distorting its primordial polarization and converting divergent polarization patterns (E-modes) into curled polarization patterns (B-Modes). Imaging the lensing-generated B-modes, the POLARBEAR telescope will be able to shed light on all the components of the Universe influencing structure formation, such as neutrino mass and dark energy. |
PI | Gkikas Magiorkinis |
---|---|
Organization | University of Oxford |
Department | Zoology |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 02/01/2016 |
Abstract of work | Fine-mapping of human endogenous retrovirus polymorphisms |
PI | rajmohan muthaiah |
---|---|
Organization | University of Oklahoma |
Department | Mechanical Engineering |
Field of Science | Materials Science |
Sponsor | CG OSG Connect |
Date Registered | 04/13/2018 |
Abstract of work | Investigate the thermal conductivity of polymer and polymer composites using MD simulation |
PI | Benjamin Rose |
---|---|
Organization | University of Notre Dame |
Department | Physics |
Field of Science | Astrophysics |
Sponsor | CG OSG Connect |
Date Registered | 01/05/2018 |
Abstract of work | Using FSPS estimate the age of a stellar population from its SED. This will be applied to improving SN Ia distance measurements. |
PI | Shripad Tuljapurkar |
---|---|
Organization | Stanford University |
Department | Biology |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 10/09/2017 |
Abstract of work | Population dynamics across all species including human being. The life history, energy consumption, mortality pattern, and evolution paths and directions. |
PI | Stephen Moysey |
---|---|
Organization | Clemson University |
Department | Environmental Engineering and Earth Sciences |
Field of Science | Ecological and Environmental Sciences |
Sponsor | CG OSG Connect |
Date Registered | 06/02/2016 |
Abstract of work | In order to reduce carbon dioxide emissions, experts have proposed requiring major carbon dioxide emitters to modify their infrastructure to collect carbon dioxide exhaust and compress it into a super-critical fluid for injection into a well-sealed geologic structure such as an exhausted oil or natural gas reservoir. We are therefore developing a tool to assess and monitor potential carbon capture and storage sites. We use large-scale reservoir simulations to investigate the mechanical stresses that would effect a reservoir as it is injected with super-critical carbon dioxide. Since we will not know the precise geologic structure of a given field site, this requires us to run a very large number of computationally-intensive simulations (10$^4$-10$^7$) in order to adequately investigate every possible geologic structure. These simulations can then be compared to measurements from the surface and from wells drilled into the reservoir, allowing us to identify which proposed structures best explain the data. This will allow us to infer the structure and state of the subsurface. |
PI | J. Woods Halley |
---|---|
Organization | University of Minnesota |
Department | Physics |
Field of Science | Biophysics |
Sponsor | CG OSG Connect |
Date Registered | 02/11/2016 |
Abstract of work | We use simulations Kauffman-like model to study the probability of life forming on other planets. This project is supported by a NASA grant and is part of their Astrobiology mission. Reference: A. Wynveen, I. Fedorov, and J. W. Halley, Nonequilibrium steady states in a model for prebiotic evolution, Physical Review E 89 , 022725 (2014) We use simulations of a Kauffman-like model for prebiotic evolution to find the probabilities of lifelike steady states and study their properties. This project is supported by a NASA grant. References: A. Wynveen, I. Fedorov, and J. W. Halley, Nonequilibrium steady states in a model for prebiotic evolution, Physical Review E 89 , 022725 (2014) (https://doi.org/10.1103/PhysRevE.89.022725) B. F. Intoy, A. Wynveen, and J. W. Halley, Effects of spatial diffusion on nonequilibrium steady states in a model for prebiotic evolution, Physical Review E 94 , 042424 (2016) (https://doi.org/10.1103/PhysRevE.94.042424) |
PI | Dr. Bruce P. Hermann |
---|---|
Organization | University of Wisconsin |
Department | Department of Neurology |
Field of Science | Neuroscience |
Sponsor | CG OSG Connect |
Date Registered | 08/03/2015 |
Abstract of work | Graph theory analyses would be investigated on weighted undirected matrices based on the probability of white matter connectivity between 26 regions comprising both cortical and subcortical structures on children with epilepsy with and without anxiety disorders. This project aims at investigating if there are fundamental differences in structural connectivity in children with idiopathic epilepsy with and without anxiety comorbidity. The neuropsychological implications of potential differences between groups would also be investigated. |
PI | Sam Volchenboum |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 05/27/2014 |
Abstract of work | Bioinformatics methods for different proteomic applications in life sciences. Algorithm development for improving mass-spectrometry based proteomic techniques. |
PI | Premal Shah |
---|---|
Organization | University of Pennsylvania |
Department | Biology |
Field of Science | Evolutionary Sciences |
Sponsor | CG OSG Connect |
Date Registered | 02/23/2015 |
Abstract of work | How large a role does history play in evolution? Do later events depend critically on specific earlier events, or do all events occur more or less independently? If a change occurs early in evolution, does it become easier or harder to revert the change as time proceeds? We intend to explore these ideas in the context of protein evolution, by simulating sequence evolution under purifying selection and then systematically permuting the order of amino-acid substitutions. |
PI | Jinbo Xu |
---|---|
Organization | Toyota Technological Institute at Chicago |
Department | Computer Science |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 06/06/2014 |
Abstract of work | Study statistical machine learning and optimization algorithms for data-driven protein structure prediction, by learning sequence-structure relationship from existing protein sequence and structure data. |
PI | Endre Takacs |
---|---|
Organization | Clemson University |
Department | Astronomy and Physics |
Field of Science | Physics |
Sponsor | CG OSG Connect |
Date Registered | 04/28/2016 |
Abstract of work | Modeling of Monte Carlo simulations (Geant4) in order to test many different parameters (collimator and shielding size, irradiation angles...) to define the best design for new medical nuclear treatment devices |
PI | Paul Vaska |
---|---|
Organization | Stony Brook University |
Department | Biomedical Engineering |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 09/25/2017 |
Abstract of work | We need to use Monte-Carlo simulation to obtain the point spread function (PSF) kernels to be incorporated into our image reconstruction algorithm for more accurate image reconstruction |
PI | Joshua Elliott |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | Earth Sciences |
Sponsor | CG OSG Connect |
Date Registered | 10/21/2014 |
Abstract of work | A framework for massively parallel climate impact simulations: the parallel System for Integrating Impact Models and Sectors (pSIMS). This framework comprises a) tools for ingesting and converting large amounts of data to a versatile datatype based on a common geospatial grid; b) tools for translating this datatype into custom formats for site-based models; c) a scalable parallel framework for performing large ensemble simulations, using any one of a number of different impacts models, on clusters, supercomputers, distributed grids, or clouds; d) tools and data standards for reformatting outputs to common datatypes for analysis and visualization; and e) methodologies for aggregating these datatypes to arbitrary spatial scales such as administrative and environmental demarcations. By automating many time-consuming and error-prone aspects of large-scale climate impacts studies, pSIMS accelerates computational research, encourages model intercomparison, and enhances reproducibility of simulation results. |
PI | De Sa Nunes Correia Diogo |
---|---|
Organization | Northeastern University |
Department | College of Science |
Field of Science | Neuroscience |
Sponsor | CG OSG Connect |
Date Registered | 01/23/2018 |
Abstract of work | This project will make use of fMRI data of psychotic patients in order to parse heterogeneity in functional activity across multiple diagnosis. The need for computing power results from the need to preprocess the fMRI, from which we want to obtain a region level connectivity matrix for each of the approximately 1200 subjects that will be analyzed. |
PI | Derek Dolney |
---|---|
Organization | University of Pennsylvania |
Department | Radiation Oncology |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG Connect |
Date Registered | 01/04/2016 |
Abstract of work | We are applying Monte Carlo particle transport codes to proton therapy treatment planning with the goal of reducing the uncertainty in the proton beam range in patient. |
PI | Jeremy Van Cleve |
---|---|
Organization | University of Kentucky |
Department | Biology |
Field of Science | Biological and Critical Systems |
Sponsor | CG OSG Connect |
Date Registered | 09/22/2015 |
Abstract of work | Quantitative approaches to evolutionary biology including numerical analysis of mathematical models of evolutionary change and individually-based simulations of population dynamics, mutation, natural selection, and other evolutionary forces. |
PI | Patricia Carbajales-Dale |
---|---|
Organization | Clemson University |
Department | Clemson Center for Geospatial Technologies |
Field of Science | Geographic Information Science |
Sponsor | CG OSG Connect |
Date Registered | 08/03/2016 |
Abstract of work | This project is created to explore QGIS and analyze solar suitability in South Carolina. |
PI | Andrew Powell |
---|---|
Organization | Missouri University of Science and Technology |
Department | Chemistry |
Field of Science | Chemistry |
Sponsor | CG OSG Connect |
Date Registered | 08/24/2016 |
Abstract of work | Our project uses Quantum Monte Carlo (QMC) methods for energy calculations on molecular systems of interest. |
PI | Shripad Tuljapurkar |
---|---|
Organization | Stanford University |
Department | Biology |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 10/11/2017 |
Abstract of work | Simulations of evolution of quantitative characters in finite populations |
PI | Shantenu Jha |
---|---|
Organization | Rutgers University |
Department | Computer Science |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 11/26/2013 |
Abstract of work | RADICAL: SAGA / BigJob OSG / XSEDE interoperability and Python APIs for OSG / Condor / iRODS. |
PI | Xiaochun He |
---|---|
Organization | Georgia State University |
Department | Physics |
Field of Science | Physics |
Sponsor | CG OSG Connect |
Date Registered | 12/12/2017 |
Abstract of work | study of the real-time monitoring of space and earth weather, cosmic ray radiation and cancer formation, cosmic ray muon tomography, etc... |
PI | Ian Foster |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | Economics |
Sponsor | CG OSG Connect |
Date Registered | 09/25/2013 |
Abstract of work | Robust Decision Making on Climate and Energy Policy (RDCEP) The Center for Robust Decision Making on Climate and Energy Policy conducts research in four main areas: * Improving the fidelity of models used to forecast the impact of policies on future economic and climatic conditions. Many of the most decision-relevant aspects of climate and energy policy - for example, climate impacts and technological advances - are poorly or not at all represented in current policy analysis tools. The Center will build representations of the most important processes and increase model detail and resolution. * Quantifying sensitivities and uncertainties in the parameters, processes, and impacts in models. RDCEP will develop methods to characterize the dependence of model output on input, parameter, and model uncertainty; incorporate these uncertainties in models; and study how to communicate probabilistic model output to decision makers. * Identifying robust decisions in the face of uncertainty. The best policy is not necessarily that which produces the maximum return if all assumptions made are borne out, but the one that balances return and risk in the face of many uncertainties. The Center will develop models to identify robust strategies that perform well over a wide range of scenarios. * Developing improved computational methods and numerical methods required to achieve these goals. New parallel stochastic dynamic programming, robust optimal control, and numerical optimization methods able to make full use of modern supercomputers will allow tools developed at the Center to incorporate sectoral and process detail and explore uncertainty, in ways not previously possible. |
PI | Phil Duxbury |
---|---|
Organization | Michigan State University |
Department | Physics and Astronomy |
Field of Science | Physics and astronomy |
Sponsor | CG OSG Connect |
Date Registered | 12/11/2017 |
Abstract of work | Design of a pre-RFQ buncher ring for ReA at FRIB |
PI | Corrado Gatto |
---|---|
Organization | Fermi National Accelerator Lab |
Department | Particle Physics |
Field of Science | High Energy Physics |
Sponsor | CG OSG Connect |
Date Registered | 07/22/2016 |
Abstract of work | High intensity frontier experiment searching for physics beyond the Standard Model |
PI | Harkamal Walia |
---|---|
Organization | University of Nebraska Lincoln |
Department | Agronomy |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 05/28/2015 |
Abstract of work | Analysis of salinity tolerance in rice. |
PI | Stanisław P. Radziszowski |
---|---|
Organization | Rochester Institute of Technology |
Department | Computer Science |
Field of Science | Computer and Information Science and Engineering |
Sponsor | VO OSG |
Date Registered | 08/19/2013 |
Abstract of work | Ramsey theory studies the properties that combinatorial structures need in order to guarantee that desired substructures are contained within them. It is often seen as the study of the order that comes from randomness, and has applications in mathematics, computer science, finance, economics, and other areas. Our research involves a computational approach to establishing the values of various Ramsey numbers, whose role is to quantify the general existential theorems in Ramsey theory. |
PI | Dave Denlinger |
---|---|
Organization | Ohio State University |
Department | Department of Evolution, Ecology, and Organismal Biology |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 09/15/2014 |
Abstract of work | The Sarcophaga bullata Genome Project seeks to assemble and annotate the genome of Sarcophaga bullata, an important model for cold tolerance and diapause. |
PI | Piotr Sliz |
---|---|
Organization | Harvard Medical School |
Department | Biological Chemistry and Molecular Pharmacology |
Field of Science | Biochemistry |
Sponsor | CG OSG Connect |
Date Registered | 04/18/2014 |
Abstract of work | SBGrid work using OSG Connect |
PI | Joe Boyd |
---|---|
Organization | Fermilab |
Department | N/A |
Field of Science | High Energy Physics |
Sponsor | VO SBND |
Date Registered | 03/15/2018 |
Abstract of work | Project entry corresponding to the SBND VO. |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | Multi-Science Community |
Sponsor | CG OSG Connect |
Date Registered | 06/18/2014 |
Abstract of work | Development of collection, aggregation, filtering and analysis of probes and metrics as related to distributed computation on the Open Science Grid. |
PI | Amit Goel |
---|---|
Organization | University of Central Florida |
Department | Advanced Research Computing Center |
Field of Science | Multi-Science Community |
Sponsor | CG OSG Connect |
Date Registered | 09/24/2015 |
Abstract of work | The aim of this project is to create examples, demos and training materials to get UCF Faculty and Researchers get started for using OSG for HTC applications in the field of Scientific Simulations, Computation and Visualizations. Primarily, we expect to use NAMD, VMD, Matlab and R application software. |
PI | Harish S. Bhat |
---|---|
Organization | University of California, Merced |
Department | Applied Mathematics |
Field of Science | Mathematical Sciences |
Sponsor | CG OSG Connect |
Date Registered | 05/12/2015 |
Abstract of work | The goal of the project is to develop fast, accurate algorithms for simulation and inference of stochastic differential equations (SDE). Many SDE models of interest in science feature drift and diffusion coefficients with superlinear growth, which causes convergence and stability problems for many time integrators. We seek improved methods that can overcome these problems, with a focus on correctly computing moments and densities of the solution. |
PI | David Christian |
---|---|
Organization | SeaQuest |
Department | N/A |
Field of Science | Nuclear Physics |
Sponsor | VO Fermilab |
Date Registered | 02/19/2018 |
Abstract of work | Project entry corresponding to the SeaQuest VO. This is purely for job accounting purposes. |
PI | Eddie Tysoe |
---|---|
Organization | University of Wisconsin Milwaukee |
Department | Chemistry |
Field of Science | Chemistry |
Sponsor | CG OSG Connect |
Date Registered | 03/23/2017 |
Abstract of work | The influence of directing agents in the self-assembly of molecular wires to produce two-dimensional electronic nanoarchitectures is studied here using a Monte Carlo approach to simulate the effect of arbitrarily locating nodal points on a surface, from which the growth of self-assembled molecular wires can be nucleated. |
PI | Peter Freddolino |
---|---|
Organization | University of Michigan |
Department | Biological Chemistry |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 02/05/2016 |
Abstract of work | We combine innovative high-throughput experiments with data mining approaches to identify functional regulatory elements in biological sequence, building the foundation for further experiments to map complete regulatory networks. |
PI | Paul Siders |
---|---|
Organization | University of Minnesota Duluth |
Department | Chemistry and Biochemistry |
Field of Science | Chemistry |
Sponsor | CG OSG Connect |
Date Registered | 10/03/2016 |
Abstract of work | Molecular-scale interaction between mobile and stationary phases as they relate to supercritical fluid chromatography (SFC) is modeled with hybrid Monte Carlo methods. Carbon dioxide is the main component of the mobile phase in SFC, which typically operates above the critical point. Simulations use seven mole percent methanol in the mobile phase. The objective of the proposed work is understanding the interaction between mobile-phase molecules and the alkylsilane-coated silica stationary phase. The computational method is Monte Carlo simulation. Hybrid molecular dynamics moves explore conformations of eighteen-carbon alkylsilane chains bonded to silica substrate. |
PI | Donny Shrum |
---|---|
Organization | Florida State University |
Department | Research Computing Center |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 01/16/2018 |
Abstract of work | I'm working with researchers at FSU to show them how to use docker, singularity and OSG and I'd like to be able to submit an example job during some tutorials. I'll keep the runtime to just a few seconds so as to not use up resources. |
PI | Ariella Gladstein |
---|---|
Organization | University of Arizona |
Department | Ecology and Evolutionary Biology |
Field of Science | Evolutionary Sciences |
Sponsor | CG OSG Connect |
Date Registered | 10/03/2017 |
Abstract of work | This project is for anyone using SimPrily to perform demographic simulations. |
PI | Wei Wang |
---|---|
Organization | University of Central Florida |
Department | Psychology |
Field of Science | Multi-Science Community |
Sponsor | CG OSG Connect |
Date Registered | 03/07/2016 |
Abstract of work | Simulate social networks to analyze statistical properties. |
PI | Wei Wang |
---|---|
Organization | University of Central Florida |
Department | Psychology |
Field of Science | Educational Psychology |
Sponsor | CG OSG Connect |
Date Registered | 10/23/2017 |
Abstract of work | This is project is to run conditions to determine the social network factors (e.g., structure, size,density) that affect the statistical power for detecting the interaction term of contagion parameter. |
PI | Joshua R Klein |
---|---|
Organization | University of Pennsylvania |
Department | Physics and Astronomy |
Field of Science | High Energy Physics |
Sponsor | VO OSG |
Date Registered | 09/03/2013 |
Abstract of work | SNO+ is a multi-purpose liquid scintillator detector with a primary goal of studying neutrino-less double beta decay in Tellurium-130, and is also capable of measurements involving solar neutrinos, reactor antineutrinos and geoneutrinos, supernovae, certain nucleon decay modes. Data collected by the detector are moved to (UK and Canadian) grid storage, where automated processing occurs. The large number of simulated data sets required for statistical analyses are also produced on grid resources. The total combined size of the data and simulations is expected to be on the order of 100 TB, which makes transfer, storage, and processing (i.e. running custom ROOT code) intractable on local resources available at collaborating US institutions. Hence, access to grid storage and processing is imperative for the analysis of the SNO+ data by US Collaborators. |
PI | Meenakshi Narain |
---|---|
Organization | Brown University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | VO OSG |
Date Registered | 08/16/2013 |
Abstract of work | Simulate hundreds of millions of high-energy proton proton collisions, which mimic the collisions expected at future hadron colliders. This simulated data is used to assess the physics potential of future colliders, allowing US decision makers and funding agencies to prioritize future physics projects. |
PI | shaikh saad |
---|---|
Organization | Oklahoma State University |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG OSG Connect |
Date Registered | 08/24/2016 |
Abstract of work | searching for different realistic SO(10) GUT models that are able to reproduce the experimentally observed fermion masses and mixings |
PI | Tyson Swetnam |
---|---|
Organization | University of Arizona |
Department | Geosciences |
Field of Science | Geographic Information Science |
Sponsor | VO OSG |
Date Registered | 03/10/2017 |
Abstract of work | The goal of this project is to implement Sol (a set of programs to compute solar insolation on complex landscapes and the energy available to drive weathering). |
PI | David Mitchell |
---|---|
Organization | New Mexico State University |
Department | Electrical Engineering |
Field of Science | Engineering |
Sponsor | CG OSG Connect |
Date Registered | 11/12/2015 |
Abstract of work | Lossy compression is one of the classic problems in communication systems. The goal is to compress a given digital sequence so that it can be reconstructed up to a specific distortion (Shannon bound). |
PI | Dong Xu |
---|---|
Organization | University of Missouri |
Department | Christopher S. Bond Life Sciences Center |
Field of Science | Plant Biology |
Sponsor | VO OSG |
Date Registered | 05/06/2014 |
Abstract of work | The Soybean Knowledge Base (SoyKB), a comprehensive all-inclusive web resource for soybean. SoyKB is designed to handle the storage and integration of the gene, genomics, EST, microarray, transcriptomics, proteomics, metabolomics, pathway and phenotype data. |
PI | Brook Milligan |
---|---|
Organization | New Mexico State University |
Department | Biology |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 06/27/2017 |
Abstract of work | Developing software applications for probabilistic graph models, predominantly for spatially explicit modeling. |
PI | Alabi Adebusola |
---|---|
Organization | UC Santa Cruz |
Department | Department of Astronomy and Astrophysics |
Field of Science | Astrophysics |
Sponsor | CG OSG Connect |
Date Registered | 07/05/2017 |
Abstract of work | Robust statistical inference of the kinematics from astrophysical spectra using Monte Carlo methods |
PI | Martin Purschke |
---|---|
Organization | Brookhaven National Laboratory |
Department | Physics Department |
Field of Science | Nuclear Physics |
Sponsor | VO OSG |
Date Registered | 08/20/2013 |
Abstract of work | Collaboration devoted to simulation and design optimization of the prospected Super PHENIX detector (the successor of the existing PHENIX detector) at Relativistic Heavy Ion Collider (RHIC) at BNL. |
PI | Samy Meroueh |
---|---|
Organization | Indiana University |
Department | Indiana Univseristy School of Medicine |
Field of Science | Medical Sciences |
Sponsor | VO CSIU |
Date Registered | 08/19/2013 |
Abstract of work | SPLINTER (Structural Protein-Ligand Interactome), an interactome that predicts the interaction of thousands of small organic molecules with thousands of proteins through structure-based molecular docking and scoring. A list of the top-ranking small-molecule ligands is provided for each protein target in SPLINTER along with purchasing information for experimental characterization. The site can also be used to rank proteins for individual active compounds to provide a list of potential targets for experimental validation in cells or in vivo. |
PI | John Carlstrom |
---|---|
Organization | University of Chicago |
Department | Kavil Institute for Cosmological Physics |
Field of Science | Astrophysics |
Sponsor | CG OSG Connect |
Date Registered | 09/24/2013 |
Abstract of work | The South Pole Telescope (or SPT) is a new telescope deployed at the South Pole that is designed to study the Cosmic Microwave background. Constructed between November 2006 and February 2007, the SPT is the largest telescope ever deployed at the South Pole. This telescope provides astronomers a powerful new tool to explore dark energy, the mysterious phenomena that may be causing the universe to accelerate. |
PI | Joerg Kliewer |
---|---|
Organization | New Jersey Institute of Technology |
Department | Electronic Engineering |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 01/30/2017 |
Abstract of work | Studying coding schemes for lossy source compression under privacy constraints |
PI | Julio Facelli |
---|---|
Organization | University of Utah |
Department | Biomedical Informatics |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 06/22/2017 |
Abstract of work | This project will use the OSG to demonstrate the feasibility of using a new steady state genetic algorithm (SSGA), recently introduced by the MGAC collaboration, to predict the crystal structures of molecules of pharmaceutical interest. The OSG resources are ideal for this project because the SSGA requires a large number of independent energy calculations of candidate structures. These calculations for simple molecules will use the DFT approach, using software already available in the OSG. |
PI | Ruth Marinshaw |
---|---|
Organization | Stanford University |
Department | RCC |
Field of Science | Community Grid |
Sponsor | CG OSG Connect |
Date Registered | 05/02/2014 |
Abstract of work | This project is for simulation work in the Stanford research community. |
PI | Yichen Cheng |
---|---|
Organization | Georgia State University |
Department | Institute for Insight |
Field of Science | Statistics |
Sponsor | CG OSG Connect |
Date Registered | 10/04/2017 |
Abstract of work | Find low dimensional representation of the high dimensional data |
PI | Duncan Brown |
---|---|
Organization | Syracuse University |
Department | Physics |
Field of Science | Astrophysics |
Sponsor | CG OSG Connect |
Date Registered | 01/26/2018 |
Abstract of work | Gravitational-wave astronomy and astrophysics. |
PI | Robert William Gardner Jr |
---|---|
Organization | IUPUI |
Department | OSG |
Field of Science | Community Grid |
Sponsor | CG OSG Connect |
Date Registered | 02/23/2015 |
Abstract of work | Joint Software Carpentry/OSG Workshop at IUPUI, March 3rd-6th 2015. |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 12/09/2014 |
Abstract of work | Software Carpentry/OSG Workshop at University of Chicago. Date Dec 15-17 2014. |
PI | Murat Acar |
---|---|
Organization | Yale University |
Department | Molecular Cellular and Developmental Biology |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 03/19/2018 |
Abstract of work | Running simulations using parameters sampled from large ranges |
PI | Michael Wilde |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 09/25/2013 |
Abstract of work | Software development and systems testing for the parallel scripting language. |
PI | Matthias Fripp |
---|---|
Organization | University of Hawaii, Manoa |
Department | Electrical Engineering |
Field of Science | Engineering |
Sponsor | CG OSG Connect |
Date Registered | 12/01/2015 |
Abstract of work | We are using the SWITCH power system planning model to design power systems for Hawaii that have minimal expected cost across a wide range of future fossil fuel prices. |
PI | John McGreevy |
---|---|
Organization | University of California San Diego |
Department | Physics |
Field of Science | Physics |
Sponsor | CG OSG Connect |
Date Registered | 04/17/2017 |
Abstract of work | DMRG simulation of many body fermion system |
PI | Stephen Ficklin |
---|---|
Organization | Washington State University |
Department | Horticulture |
Field of Science | Biological and Critical Systems |
Sponsor | CG OSG Connect |
Date Registered | 09/01/2016 |
Abstract of work | A project for teaching analysis of large data sets for construction of models (i.e. graphs) of biological systems. |
PI | Bhaskar Dutta |
---|---|
Organization | Texas A&M University |
Department | Department of Physics & Astronomy |
Field of Science | High Energy Physics |
Sponsor | CG OSG Connect |
Date Registered | 10/13/2014 |
Abstract of work | The Large Hadron Collider (LHC) experiments have successfully discovered the last missing piece of the standard model (SM)—the elusive Higgs boson. However, no sign of any physics beyond the SM has been observed yet. Although the standard model has been extremely effective, many unsolved questions still remain. The focus of our group is to study models of physics beyond the SM, which tries solve the aforementioned unsolved questions, and explore their possible signatures, at LHC experiments predominately. These models include Supersymmetric models, Grand Unified Theories, Left-Right Symmetric models and various Dark Matter models. LHC is going through an upgrade now and it will start functioning again next year with increased energy. We are pursuing a number of projects trying to predict the possible signature of new physics, pertaining to various models described above, in upcoming LHC experiments. Owing to these we need sufficient comuting power and intend to run collider simulators including MadGraph, Pythia, PGS, Delphes etc. |
PI | Chad Shaw |
---|---|
Organization | Baylor College of Medicine |
Department | Molecular and Human Genetics |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 02/14/2017 |
Abstract of work | This is a project to characterize partial correlation relationships within and between data types in the data available from The Cancer Genome Atlas (TCGA). |
PI | David Meyer |
---|---|
Organization | University of California San Diego |
Department | Mathematics |
Field of Science | Mathematical Sciences |
Sponsor | CG OSG Connect |
Date Registered | 05/24/2016 |
Abstract of work | Topological data analyses on various datasets |
PI | Amulya Yadav |
---|---|
Organization | University of Southern California |
Department | Computer Science |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG ISI |
Date Registered | 06/16/2015 |
Abstract of work | Solving large scale Partially Observable Markov Decision Processes (POMDPs) in order to discover efficient health intervention mechanisms which will assist in prevention of HIV spread amongst homeless youth in Los Angeles. |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | Multi-Science Community |
Sponsor | CG OSG Connect |
Date Registered | 10/08/2015 |
Abstract of work | Internet2 -TechEX15 Workshop on High Throughput Computing October 8th 2015 |
PI | Gordon Thomson |
---|---|
Organization | University of Utah |
Department | Physics |
Field of Science | Astrophysics |
Sponsor | CG OSG Connect |
Date Registered | 11/15/2017 |
Abstract of work | Telescope Array (TA) is the largest cosmic ray detector in the Northern hemisphere, which is located in Millard county, Utah. TA studies cosmic ray energy spectrum, mass composition, and arrival directions in the energy range from 4 PeV to 100 EeV and above. The address of the projects' website is http://www.telescopearray.org. |
PI | James Evans |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | Multi-Science Community |
Sponsor | CG OSG Connect |
Date Registered | 09/14/2015 |
Abstract of work | Data analytics on available text with python programs |
PI | David Rogers |
---|---|
Organization | University of South Florida |
Department | Chemistry |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/22/2013 |
Abstract of work | The proposed project aims to decrease the management overhead and code complexity of trajectory analysis from particle simulation data. Particle simulations produce trajectories, which are encoded by a stream of high-dimensional vectors (frames). Analysis on this data usually takes a map-reduce form consisting of mapping each frame to successively smaller vectors of descriptors.From this starting point, two typical data analysis cases will be considered. The first is statistical, through construction of order statistics, histograms, cumulants, or weighted averages. We will develop code generation methods to handle general nonlinear analysis functions. The second analysis goes one step further by fitting the analyzed data to an assumed functional form using Bayesian inference.Due to the map-reduce structure of these computations, these analysis methods can be parallelized while retaining a high-level programming model. This task requires automated consideration of data movement and task separation to match available computational resources. The result will be published under an open source license, and be immediately useful to computational chemistry and biology applications analyzing large molecular dynamics simulations.This work will make use of the open science grid and Pegasus software as well as the TACC Longhorn data analysis cluster for systems and application comparison. Project code storage on XWFS and scratch access on TACC will also be needed. FutureGrid may be explored for compatibility with the Unicore workflow specification and Pegasus if its production status is extended past September. |
PI | Francis Halzen |
---|---|
Organization | University of Wisconsin-Madison |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG OSG-XSEDE |
Date Registered | 05/07/2015 |
Abstract of work | The IceCube Neutrino Observatory is responsible for providing the IceCube collaboration with Monte Carlo data including cosmic-ray shower simulations and simulation of the IceCube detector response. These simulations are used for studying the systematics of our detector and performance of future geometries. In addition, a large volume of background cosmic ray simulation is needed in order to optimize data analyses. A key component of simulating the IceCube detector is the correct modeling of the optical properties of the Antarctic ice which requires a lot of computation and has been adapted to run on GPUs. The IceProd framework is a software package developed for IceCube with the goal of managing productions across distributed systems and pooling together isolated computing resources that are scattered throughout the Collaboration. It consists of a central database hosted at University of Wisconsin-Madison and a set of daemons that are responsible for management of grid jobs as and data handling through the use of existing grid technology and network protocols. The IceCube Monte Carlo production is configured as a distributed workflow DAG that utilizes both CPU and GPU resources for various portions of the simulation chain. The intent is to utilize the Keeneland cluster in Georgia Tech to run GPU tasks and OSG for general CPU tasks through XSEDE. Intermediate files can be stored on a GridFTP server and are typically kept until the individual DAG completes. For a large production run, a typical storage requirement might be on the order of 5 TB. The IceCube collaboration would like to request an initial allocation of 100,000 SU’s. This allocation will be used to produce and reconstruct Monte Carlo simulations for the IC86 in-ice detectors as well as the IT81 surface detector. |
PI | Gregory Snyder |
---|---|
Organization | Space Telescope Science Institute |
Department | Unknown |
Field of Science | Mathematical Sciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 04/23/2015 |
Abstract of work | We request a startup allocation to support development on two related projects. The main idea is to use three dimensional simulations to constrain the histories of observed galaxies. The majority of work (1) during the initial periods of this startup will be for Graduate Student S. Alireza Mortazavi to shift an existing Condor-based pipeline at the Space Telescope Science Institute (STScI) to the Open Science Grid in order to test and plan for an ambitious expansion of his research program to constrain the dynamical histories of galaxies (Mortazavi et al. 2015). PI Snyder will also begin to develop pipelines to exploit large-scale cosmological hydrodynamical simulations (2), which predict the evolution of entire populations of galaxies in representative model universes, requiring data-intensive computing. 1. Modeling the Initial Conditions of Interacting Galaxy Pairs Using Identikit We use the Identikit software (Barnes & Hibbard 2009, Barnes 2011; http://www.ifa.hawaii.edu/~barnes/research/identikit/ ) to model the dynamics of interacting galaxy pairs. By measuring the initial conditions of galaxy mergers, we can constrain both cosmology and galaxy astrophysics. A galactic encounter has several free parameters and it is time consuming to find the best match between model and data. However, Identikit combines multiple techniques to quickly explore parameter space to find the simulation most similar to the observed shape and constituent velocities. We have developed an automated pipeline based on the latest version of Identikit to scan parameter space and find robust matches and associated uncertainties (Mortazavi et al. 2015), implemented in an STScI-based Condor environment. We will continue to test our method against simulations of galaxy mergers to determine the systematic errors in our measurements. In addition, we will apply it to real data: We have observed a sample of ~30 interacting galaxy pairs using different telescopes. We have reached the limits of the HTCondor cluster at STScI, and therefore we seek to test the options available through XSEDE. We need around 50,000 SUs to compute matches and uncertainties of the measurements for each merging pair (observed or simulated), and so we are requesting a startup allocation of 150,000 SUs to perform tests while planning for a larger research allocation. This research will have direct applications for interpreting data from the Sloan Digital Sky Survey-IV survey "Mapping Nearby Galaxies at APO" (MaNGA). 2. Mock data applications from large hydrodynamical simulations PI Snyder will develop methods for converting large cosmological simulations of galaxy formation (e.g., the Illustris Project www.illustris-project.org) into direct predictions for astronomical observatories. With XSEDE resources, I will seek to expand our Mock Galaxy Observatory efforts in new and ambitious directions, such as creating synthetic survey fields and advanced spectroscopic data products. For instance, we will explore the possibility of using large cosmological simulations as benchmarks for the Identikit modeling described in project 1. For testing, we are requesting 50,000 SUs on Gordon, and Data Oasis storage of 5000GB, enough to store two Illustris Simulation (or similar) outputs plus post-processed data products. In future allocation requests, we may seek to make these model archives available to the community through an XSEDE Gateway. |
PI | Juliette Becker |
---|---|
Organization | University of Michigan |
Department | Astronomy |
Field of Science | Astrophysics |
Sponsor | CG OSG-XSEDE |
Date Registered | 06/26/2015 |
Abstract of work | The Kepler Mission has detected dozens of compact planetary systems with more than four transiting planets. This sample provides a collection of close-packed planetary systems with relatively little spread in the inclination angles of the inferred orbits. A large fraction of the observational sample contains limited multiplicity, begging the question whether there is a true diversity of multi-transiting systems, or if some systems merely possess high mutual inclinations, allowing them to appear as single-transiting systems in a transit-based survey. Planet formation is an active yet poorly understood field: insight to the histories and dynamics of multi-planet systems would be helpful towards understanding planet formation as a whole. In previous work, we have determined the regimes of parameter space for which orbital inclinations can be effectively excited by planet-planet interactions among the currently observed bodies. We found that the orbital inclination angles are not spread out appreciably through self-excitation. In contrast, we found that the two Kepler multi-planet systems with additional non-transiting planets are susceptible to oscillations of their inclination angles, which means their currently observed configurations could be due to planet-planet interactions alone. The multi-planet compact Kepler systems are found to be remarkably stable to oscillations of their inclination angles. The oscillations of inclination found in our previous work inform the recently suggested dichotomy in the sample of solar systems observed by Kepler. However, it would also be useful to study the behaviors of these systems with perturbing companions. This would enable a better understanding of the observed systems, resulting in a more accurate exoplanet population census. To do this, we must perform computationally intensive calculations and simulations. |
PI | Jennifer Lotz |
---|---|
Organization | Space Telescope Science Institute |
Department | Astronomical Sciences |
Field of Science | Astrophysics |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/22/2015 |
Abstract of work | We are requesting 1,700,000 SUs on Open Science Grid to model the initial conditions of a sample of 15 major galaxy mergers in the local universe. These measurements will place unique constraints on the role of galaxy mergers in shaping galaxy evolution, and on cosmological assembly. Our sample consists of 15 interacting galaxy pairs with Hα kinematic maps, 2 of which have both Hα and HI 2D kinematic maps and 3 of which are drawn from the SDSSIV MaNGA survey. We will use the Identikit software package (Barnes & Hibbard 2009; Barnes 2011) and our automated pipeline to model the dynamics of interacting galaxy pairs and constrain their initial orbital parameters and merger stage. |
PI | Suzanne Hawley |
---|---|
Organization | University of Washington |
Department | Astronomy |
Field of Science | Physics |
Sponsor | CG OSG-XSEDE |
Date Registered | 01/27/2016 |
Abstract of work | We are using several large codes to search the photometric database from the Kepler satellite for stars that exhibit flares and starspots, to characterize the flare and starspot behavior and to extract information on starspot locations and properties using transiting planets as probes of stellar surface brightness variations. The XSEDE resources will enable this project to proceed much more quickly than with the resources at our home institutions. |
PI | James Davenport |
---|---|
Organization | Western Washington University |
Department | Physics |
Field of Science | Astrophysics |
Sponsor | CG OSG-XSEDE |
Date Registered | 08/17/2016 |
Abstract of work | Starspots are dark regions on a star's surface that trace areas of strong magnetic fields. On the Sun, spots are typically small and occur in bands near the stellar equator. Sunspot occurrence frequency also peaks every 11 years due to the "solar cycle". For younger stars there are indications that spots are larger, and can form near the stellar poles, while evidence for spot activity cycles on other stars is sparse. These differences indicate that the shape and strength of the internal magnetic dynamo evolves throughout a stars life. However, because of their great distance we cannot directly observe the surface of other stars to map the locations and sizes of spots. We have developed new software to model the signature of starspots in Kepler data from transiting exoplanet systems. These star-planet systems are unique in having an orbiting planet that passes directly in front of its parent star. When the planet transits the star, it will briefly pass over spots on the star's surface, giving a very small change in the apparent brightness of the system. To trace the evolution of spot size and location with stellar age we must extend our analysis to many star systems with different transiting planet orientations. A startup allocation from XSEDE will allow us to test our software's ability to map spots from different system orientations, and using many years worth of Kepler data. |
PI | Leslie Hebb |
---|---|
Organization | Hobart and William Smith Colleges |
Department | Physics |
Field of Science | Physics |
Sponsor | CG OSG-XSEDE |
Date Registered | 11/07/2016 |
Abstract of work | Our ultimate goal with this proposal is to understand how magnetic dynamos work on stars other than the Sun. To do the science we propose which is to measure the typical starspot lifetime as a function of rotation rate and stellar mass and derive the starspot number and the spatial starspot distribution for stars other than the Sun, we must apply our light curve model ing program to the full duration (4 years) of publicly available short cadence Kepler time series photometry of as many of our targets as possible. We must run the code many times per target in a Monte Carlo fashion in order to explore the full parameter s pace of potential solutions. We must also do trials with different numbers of starspots in order to determine the optimal number of spots necessary to fit the light curves. For this initial research allocation, we proposal to use the Open Science Grid to do a series of runs for 5 high priority targets: HAT-P-11, Kepler-17, Kepler-63, KOI-340, and KOI-1786, using our STSP code designed specifically for high throughput computing. The core code for the work has already been completed. Now, we need to run i t many times in many different configurations in order extract the scientific results. This mode of operating is well suited to training the young students and scientists that will do this work. |
PI | Stephanie Hamilton |
---|---|
Organization | University of Michigan |
Department | Physics |
Field of Science | Astrophysics |
Sponsor | CG OSG-XSEDE |
Date Registered | 03/14/2017 |
Abstract of work | The outer solar system has been a topic of intense scientific research for twenty-five years, but particularly within the past year. In January 2016, astronomers Mike Brown and Konstantin Batygin announced ``Planet Nine'' -- a hypothetical 10 Earth-mass object in the distant solar system responsible for the statistically significant orbital clustering of the longest-period trans-Neptunian objects (TNOs). Since this announcement, several more long-period TNOs have been discovered. Our specific research focus is studying the orbital dynamics of these objects, both absent of and in the presence of a Planet Nine, with the ultimate goal of determining the mostly likely orbit of a potential Planet Nine. Such a study requires numerical N-body simulations of hundreds of ``clones'' of each object, where a clone is produced by varying the orbital elements of an object within uncertainties. These simulations must encompass the entirety of the solar system's history after the formation of the planets, or approximately 4.5 billion years. Additionally, we must conduct these simulations for a suite of potential Planet Nines, further increasing the computational demand. We intend to ascertain which simulations, and therefore which configurations of Planet Nine, allow for the dynamical survival and force the orbital alignment of the longest period TNOs. The computational demand for these simulations far exceeds what is available to us on a laptop or desktop computer, and therefore we are requesting a Startup allocation on OSG to complete this work. |
PI | Phillip Anderson |
---|---|
Organization | University of Texas at Dallas |
Department | Physics |
Field of Science | Atmospheric Sciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/15/2013 |
Abstract of work | The aim of this project is to create a global map that describes the functional distributions which characterize the spectraof precipitating auroral particles. Such a map would not only aid in efforts to model the ionosphere and the geospatial environment, but would also aid in the understanding of the magnetospheric source regions of these particles. The construction of this map will utilize programs that perform automated, nonlinear least squares fits of Maxwellian and Lorentzian distributions to data from the Defense Meteorological Satellite Program (DMSP) suite of spacecraft. These programs have been developed in C under the Fedora Coredistribution and are statically linked against the HDF4 and GNU Scientific libraries. Initial testing on an AMD Athlon II X4 645quad core processor has shown that the serial execution of four separate instances of the Maxwellian automated fitting program produces fits at an average rate of 1500 spectra per hour per core, while the Lorentzian program, when executed in the same fashion, will produce fits at an average rate of 500 spectra per hour per core. The 20-year catalog of data which we will use to populate this map contains roughly 200 million spectra. With these average rates, it would take our 16-core cluster approximately 8300 hours to fit Maxwellian distributions and 25,000 hours to fit Lorentzian distributions to the entire catalog. Given this amount of processing time and the serial nature of our programs, we wish to explore the feasability of using your HTC resources to complete this project. |
PI | Phillip Anderson |
---|---|
Organization | University of Texas at Dallas |
Department | Physics |
Field of Science | Atmospheric Sciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/22/2013 |
Abstract of work | The global distribution of precipitating auroral particles is a crucial input to models of the magnetosphere and the coupling between the magnetosphere-ionosphere. In particular, the spectral distributions which can be used to characterize the shape of precipitating electron spectra are equally important inputs to models and can be used provide information about the magnetospheric source regions of the precipitating particles. We detail the need for and the development of maps of characterized particle spectra and present a case for a resource request to aid with the development of these maps. |
PI | Thomas |
---|---|
Organization | Purdue University |
Department | Computer & Information Technology |
Field of Science | Biological and Critical Systems |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/22/2013 |
Abstract of work | The George E. Brown Jr. Network for Earthquake Engineering Simulation (NEES) project is a National Science Foundation funded project operating a shared national network of civil engineering experimental facilities that seeks to develop effective ways of mitigating earthquake damage and loss of life using improved designs, materials, construction techniques, and monitoring methods. Safer buildings and civil infrastructure are needed to reduce damage and loss from earthquakes and tsunamis. Preparing for and protecting against these threats makes American communities more resilient to future disasters. To support research in the Civil Engineering community that seeks to address these problems, NEES operates 14 distributed research equipment sites across the United States. The objectives of NEES are to: develop a national and multi-user research infrastructure to enable research and innovation in earthquake and tsunami loss reduction; create an educated workforce in hazard mitigation; and conduct broader outreach and lifelong learning activities. Experimental capabilities at the 14 NEES sites include large-scale shake tables, a tsunami wave basin, large-scale testing facilities, centrifuges, field and mobile facilities, a large-scale displacement facility, and cyberinfrastructure capabilities. NEEScomm, led by Purdue University, connects the 14 NEES research equipment sites and the earthquake engineering community with a powerful information technology infrastructure and a commitment to education, outreach and training related to earthquake engineering. The center facilitates community collaboration and discovery by working to advance research based on experimentation and computational simulations of the performance of buildings, bridges, utility systems, coastal regions, and geomaterials during seismic events. In conjunction with supporting research, NEES seeks to disseminate results through education, outreach, and training to reduce the devastation and loss of human life from earthquakes and tsunamis. Through a cooperative agreement with the National Science Foundation, the NEEScomm center is charged with leading and managing the operations of this national resource, and enabling collaboration between the 14 NEES research equipment sites and the earthquake engineering community through groundbreaking cyberinfrastructure, education and outreach efforts. NEES provides access to a variety of analysis and simulation tools for the NEES community, which includes OpenSees, OpenFresco, UI-SimCor, RDV, and Data Turbine. A groundbreaking cyberinfrastructure, the NEEShub (http://www.nees.org), connects researchers, practitioners, and the greater civil engineering community with the 14 research labs. NEEShub features the NEES Project Warehouse, which archives data gathered in all NEES experiments, along with a rich set of tools for data management, data viewing, and computational simulation. Most projects include, in addition to physical experimentation, a substantial computational component for comparison with and validation of the physical tests. As part of the Information Technology services provided to the NEES community, NEEScomm is expected to provide production quality cyberinfrastructure that is reliable and relevant to the needs of the NEES community, and to provide facilitated access to and use of campus and/or national computing resources. This proposal seeks to continue and extend the support for computational experiments in the NEES research community. |
PI | Ruth Marinshaw |
---|---|
Organization | Stanford University |
Department | Research Computing |
Field of Science | Training |
Sponsor | CG OSG-XSEDE |
Date Registered | 05/07/2014 |
Abstract of work | I am applying for a renewal of campus champion allocations for Stanford. |
PI | Shantenu Jha |
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Organization | Rutgers, the State University of New Jersey |
Department | Computer Engineering |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG-XSEDE |
Date Registered | 07/17/2015 |
Abstract of work | This allocation request is as the Rutgers Campus Champion to help serve the Rutgers Academic Community better. |
PI | Vikram Gazula |
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Organization | University of Kentucky |
Department | Center for Computational Sciences |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG-XSEDE |
Date Registered | 04/11/2014 |
Abstract of work | Allocation needed for Campus Champion Activities |
PI | Mark Reed |
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Organization | University of North Carolina, Chapel Hill |
Department | ITS Research Computing |
Field of Science | Mathematical Sciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 06/13/2014 |
Abstract of work | Campus Champion renewal to support the University of North Carolina at Chapel Hill. |
PI | Paul Siders |
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Organization | University of Minnesota, Duluth |
Department | Chemistry and Biochemistry |
Field of Science | Chemistry |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/10/2013 |
Abstract of work | Compressed carbon dioxide is the main component of the mobile phase in supercritical fluid chromatography, which separates solutes according to their interactions with solid stationary phases. Molecular-scale properties of carbon dioxide in the mobile phase, confined near a stationary phase, and interacting with solutes can be calculated by Monte Carlo molecular simulation methods. Atomistic potentials for carbon dioxide, for solutes, and for the co-solvent methanol must be tested and refined to reliably simulate interactions at the pressure-temperature conditions of supercritical fluid chromatography. Simulation code now under development is well-suited to high-throughput computing in that it is serial, portable, and requires little RAM and disk storage. Because runs are long the code will be made check-pointable so simulations can efficiently use the Open Science Grid. The startup allocation requested will be to continue development of the serial simulation code, to modify it to allow restarting from a checkpoint file, then to test and improve atomistic potentials for solute and solvent molecules. It is against bulk fluid phase equilibrium data that potentials will be refined. Should service units remain after development work, computing will shift to characterizing the solvent within a few molecular diameters of stationary-phase and solute molecules. |
PI | Jeremy Moix |
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Organization | Massachusetts Institute of Technology |
Department | Chemistry |
Field of Science | Chemistry |
Sponsor | CG OSG-XSEDE |
Date Registered | 11/01/2013 |
Abstract of work | Energy transport in disordered systems coupled to a thermal environment is a topic that is exceedingly important for a diverse set of technological applications including organic photovoltaic solar cells, conducting polymers and a host of others. Unfortunately, at present the dynamics in these systems is not well understood. The primary difficulty is that one must accurately simulate the dynamics of relatively large open quantum systems over lengthy timescales and across a broad range of parameters. Here we request XSEDE resources to focus on two specific questions on the energy transport process that will provide both key fundamental insights, as well as useful design principles to guide the construction of more efficient materials. First, we extend the results of our previous allocation to examine the energy transport in two dimensional thin films with realistic dipolar interactions. These systems are expected to undergo a metal-insulator (Anderson) transition as a function of both the orientation of the molecular dipoles and the strength of disorder. Simulations will be performed to elucidate this phase diagram. Secondly, the nature of the transport in the weak system-bath coupling regime will be explored, wherein the dynamics are largely governed by coherent, quantum effects. The scaling properties of the transport in this regime will be determined, providing insights into the interplay of Anderson localization with the dynamics of open quantum systems. |
PI | John Stubbs |
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Organization | University of New England |
Department | Chemistry and Physics |
Field of Science | Chemistry |
Sponsor | CG OSG-XSEDE |
Date Registered | 07/14/2014 |
Abstract of work | Hybridization and denaturation transitions between DNA duplex and single stranded forms will be studied using Monte Carlo molecular simulation and a coarse-grained model. Short oligomers, between 10 and 25 bases in length, will be studied for one to two sequences, for cases where both strands are in solution as well as where one strand is bound to a surface as a model for a DNA microarray. The effects of temperature and of surface binding density will also be studied, and the results analyzed in terms of structural effects and hydrogen bonding patterns within the duplex. |
PI | Paul Siders |
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Organization | University of Minnesota, Duluth |
Department | Chemistry and Biochemistry |
Field of Science | Chemistry |
Sponsor | CG OSG-XSEDE |
Date Registered | 12/16/2014 |
Abstract of work | The work proposed is Monte Carlo modeling of the interaction between mobile and sta- tionary phases as they relate to supercritical fluid chromatography (SFC). Proposed research continues that done with the startup allocation, which involved writing, testing, and porting Monte Carlo code to model intermolecular interactions and fluid phase equilibria in com- pressed carbon dioxide. Carbon dioxide is the main component of the mobile phase in SFC, which typically operates at temperatures and and pressures above the critical point. The objective of the proposed work is an understanding at the molecular level of the interac- tion between mobile-phase molecules and the alkylsilane-coated silica stationary phase. The computational method is Monte Carlo simulation, mainly in the constant-pressure Gibbs ensemble. Hybrid molecular dynamics moves will be used for alklylsilane chains. Proposed calculations will survey four alkylsilane coatings, eight pressures, three temperatures, and three mobile-phase compositions. Compositions will be pure carbon dioxide and carbon dioxide modified with 5% or 10% methanol. XSEDE resources requested are service units on the Open Science Grid, which suits the small portable nature of the Monte Carlo code. Weeks-long runs will be achieved by automatic resubmission of jobs. |
PI | John Stubbs |
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Organization | University of New England |
Department | Chemistry and Physics |
Field of Science | Chemistry |
Sponsor | CG OSG-XSEDE |
Date Registered | 12/03/2014 |
Abstract of work | Monte Carlo molecular simulation together with a coarse-grained model is used to study the single-stranded to double-stranded transition in DNA both in solution and with one strand bound to a surface. Representing DNA microarrays, hybridization on a surface is studied and the effect of surface density, strand length and sequence homology on duplex stability is investigated. Results can better inform empirical surface hybridization models. |
PI | Christopher Fennell |
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Organization | Oklahoma State University |
Department | Chemistry |
Field of Science | Chemistry |
Sponsor | CG OSG-XSEDE |
Date Registered | 03/16/2016 |
Abstract of work | The overarching goal of the research to be performed using XSEDE resources is to characterize the thermodyanmic and dynamic driving forces for the behavior and properties of systems at the molecular level. This work will involve calculation of molecular free energies of transfer between different systems, molecular flow in nanoporous materials, determination and refinement of molecular interactions in different environments, and simulations of biomolecular systems. One key focus of this work will by on optimizing our use of co-processor hardware, the Intel Xeon Phi cards in particular, to facilitate our brand of scientific discovery. |
PI | Robert Toonen |
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Organization | University of Hawaii, Manoa |
Department | Unknown |
Field of Science | Biological Sciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 04/11/2014 |
Abstract of work | We propose to test community level population genetic patterns of coral reef fishes as they pertain to the Depth Refuge Hypothesis (DRH) of coral reefs by applying a statistical framework for multi-species analyses using hierarchical Approximate Bayesian Computation (hABC). The DRH specifies that deep reefs are protected from disturbances that effect shallow habitat and can provide a viable reproductive source for shallow reef areas following disturbance. It has been proposed that these foundation reefs may provide refuge not only from local disturbances such as storms or pollution, but can act as a refuge for geographically broad scale major disturbances such as the glaceoeustatic sea-level fluctuations that occur on the order of approximately 100k years at an amplitude of over 100m. During the Last Glacial Maximum (LGM) sea level was thought to have reduced shallow habitat by as much as 90% in the tropical Pacific possibly resulting in increased habitat fragmentation, local extinction, or bottlenecks. We will combine multi-taxa population genetic datasets into a single analysis to determine the proportion of the current community that historically expanded in a temporally clustered pulse, when the pulse occurred, and in what direction (i.e. from shallow water to shallow water across locations, deep water to adjacent shallow water, from shallow water to adjacent deep water, or deep water to deep water across locations.) across the Hawaiian archipelago. |
PI | Emanuel Gull |
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Organization | University of Michigan |
Department | Physics |
Field of Science | Materials Science |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/10/2013 |
Abstract of work | We request high throughput computing resources to perform diagrammatic Monte Carlo calculations of strongly correlated non-equilibrium electron systems. The calculations employ existing implementations of real-time quantum Monte Carlo algorithms for the solution of quantum impurity models, which have been tested and benchmarked; they also involve extensions to these algorithms which are currently under development. We will use these codes to address two types of physics problems: strongly correlated lattice systems treated within the dynamical mean field approximation, and exact properties of model systems for mesoscopic and molecular electronic junctions. |
PI | Adrian Del Maestro |
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Organization | University of Vermont |
Department | Physics |
Field of Science | Materials Science |
Sponsor | CG OSG-XSEDE |
Date Registered | 12/19/2014 |
Abstract of work | When bulk helium-4 is cooled below T = 2.18 K, it undergoes a thermodynamic phase transition to a superfluid, characterized by zero viscosity and quantization of flow. The superfluid state of matter is a macroscopic manifestation of quantum mechanics, as it can be described by a single complex wave function with a phase that does not depend on position. The phase coherence can be probed in a container filled with helium-4, by reducing one or more of its dimensions until they are smaller than the coherence length; the spatial distance over which order propagates. As this dimensional reduction occurs, enhanced thermal and quantum fluctuations push the transition to the superfluid state to lower temperatures. However, this trend can be countered via the proximity effect, where a bulk 3D superfluid is coupled to a low (2D) dimensional superfluid via a weak link producing superfluid correlations in the film at temperatures above the Kosterlitz-Thouless temperature. Recent experiments probing the coupling between 3D and 2D superfluid helium-4 have uncovered an anomalously large proximity effect, leading to an enhanced superfluid density that cannot be explained using the correlation length alone.We intend to explore the microscopic origin of this enhanced proximity effect via large scale quantum Monte Carlo simulations of helium-4 in a topologically non-trivial geometry that incorporates the important aspects of the experiments. We will modify, test and deploy our research group's home-built high performance worm algorithm path integral quantum Monte Carlo code (http://code.delmaestro.org) at low temperatures with an eye toward improving efficiency through enhanced parallelization and hybridization. |
PI | Benjamin Ong |
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Organization | Michigan State University |
Department | Institute for Cyber Enabled Research |
Field of Science | Mathematical Sciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 04/11/2014 |
Abstract of work | This allocation will be used to help MSU users transition from local HPC resources to XEDE resrouces. |
PI | Shahriar Afkhami |
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Organization | New Jersey Institute of Technology |
Department | Mathematical Science |
Field of Science | Mathematical Sciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 02/18/2016 |
Abstract of work | This research project will focus on using high performance computing for accelerating the numerical methods for modeling the flows of viscoelastic liquids. The computational schemes developed for studying viscoelastic flows are based on an adaptive finite-volume discretization of the Navier-Stokes equations combined with various constitutive laws for viscoelastic liquids. The numerical method is based on a volume of fluid algorithm for tracking the interface, in case of the presence of a second phase. The numerical framework has parallel support using the MPI library, dynamic load-balancing, and parallel offline visualization. The parallel performance of the code will be tested and improved upon. Adaptivity combined with parallelization are essential components of the numerical framework, since transient computations of viscoelastic flows are often very intensive (due to small timestep and high mesh resolution required to resolve high stress regions) and therefore require a large computational resources. |
PI | Jon Pelletier |
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Organization | University of Arizona |
Department | Geosciences |
Field of Science | Geographic Information Science |
Sponsor | CG OSG-XSEDE |
Date Registered | 01/14/2016 |
Abstract of work | The goal of this project is to implement Sol (a set of programs to compute solar insolation on complex landscapes and the energy available to drive weathering). These programs current run on University of Arizona machines but we wish to test their portability to OpenTopography.org using SDSC resources. |
PI | Donald Krieger |
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Organization | University of Pittsburgh |
Department | Neurological Surgery |
Field of Science | Biological Sciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/10/2013 |
Abstract of work | The hope for magnetoencephalographic (MEG) measurements has been to produce functional brain mapping with high spatial (mm) and temporal (msec) resolution. Realizing this hope requires answers to these questions: (1) How many sources are active within the brain? (2) Where are they located. (3) What is their time course? MEG Virtual Recording (MVR) provides these while producing noninvasive measures of intracranial neuroelectric currents as if from 2,000,000+ directly implanted electrodes. It does so from single trial (unaveraged) data, has no free parameters, and provides very strong probabilistic measures to validate the existence of each identified source. We have demonstrated efficient implementation of MVR on the Open Sciences Grid. The measured computational load of 400 SU per second of MEG data makes supercomputing essential to practical implementation of MVR. We anticipate that MVR will enable identification of specific neurophysiological biomarkers of a variety of non-structural brain pathologies which have been refractory to date, e.g. concussion, post-traumatic stress disorder. |
PI | Joseph Cohen |
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Organization | University of Massachusetts, Boston |
Department | Computer Science |
Field of Science | Information, Robotics, and Intelligent Systems |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/10/2013 |
Abstract of work | Analysis of geospatial imagery has become a promising approach for characterizing Weapons of Mass Destruction (WMD) proliferation. The goal of this project is to design algorithms and computer executable that can extract man-made objects (e.g., building, road, gate, etc.) from high-resolution images (recording the boundary and location, and possible type). |
PI | Victor Hazlewood |
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Organization | National Institute for Computational Sciences |
Department | None |
Field of Science | Information, Robotics, and Intelligent Systems |
Sponsor | CG OSG-XSEDE |
Date Registered | 01/30/2017 |
Abstract of work | Staff allocation to support the mission of the XSEDE Community Infrastructure (XCI) team comprised of the RACD and XCRI groups to facilitate interaction, sharing, compatibility, campus integration and SP Coordination of all relevant software and related services across the national CI community building on and improving on the foundational efforts of XSEDE. |
PI | Jeffry D. Madura |
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Organization | Duquesne University |
Department | Chemistry & Biochemistry |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 01/07/2016 |
Abstract of work | This proposal is a request for supercomputer resources to carry out computations on five projects. The first project is to study the dynamics of a monoamine transporter in a novel single bilayer system. In this project we are investigating the resetting of the transporter through the movement of potassium ions. The second project is to calculate binding free energies for proposed antidepressant analogs that bind to serotonin. The third project is to investigate the aggregation properties of polyQ peptides. The fourth project is to study the electronic properties of diamond-like semiconductors using band structure methods. The fifth project is to apply quantum monte carlo methods to the study of water dimers and clusters. |
PI | Michael Hagan |
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Organization | Brandeis University |
Department | Physics |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/10/2013 |
Abstract of work | This proposal requests CPU time on XSEDE resources for research aimed at understanding assembly and pattern formation in biological and biomimetic systems. The first two subprojects will use coarse-grained simulations to explore two processes which are essential for replication of many viruses: the assembly of capsid proteins around RNA and the simultaneous assembly and budding of capsid proteins through lipid bilayers. The third subproject will study pattern formation and spontaneous flow in a far-from-equilibrium system containing microtubules and motor proteins studied by our experimental collaborators, the Dogic Lab at Brandeis. A common goal in each of the three subprojects is to reveal structural and dynamical information about key intermediates which are not accessible to experiments. The simulations of capsid assembly around RNA will be performed with the program HOOMD which enables great computational speedups on GPUs. The simulations of capsids assembling on lipid bilayers will use LAMMPS which affords excellent scaling for the large membranes being considered. The simulations of microtubules and motor proteins will use a self-written code optimized to characterize high aspect ratio, extensile bundles. Funding for Subprojects 1 & 2 is provided by NIH NIAID (R01AI080791) and Subproject 3 is funded by the NSF (NSF-MRSEC-0820492). |
PI | Shantenu Jha |
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Organization | Rutgers, the State University of New Jersey |
Department | None Stated |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/22/2013 |
Abstract of work | We propose to use multiple XSEDE resources to study several scientific problems. This work is built on theextensive efforts over the past three years we have carried out within a wide range of computational science,cyberinfrastructure and computer science projects, requiring us to use concurrent multiple resources onXSEDE. Specifically, in this proposal we request 10.04M on Stampede, 2.07M on Kraken, 0.37M on Tres-tles and 0.1M on Blacklight for four distinct projects: (i) Atomisitic simulation of Physiological Systems;Extensible and Scalable middleware and tools for XSEDE and Open Science Grid.This proposal is fundamentally multi-disciplinary and collaborative. Importantly resources being re-quested are part of and supported by multiple federally funded and even International funded projects (inconjunction with NSF). This work is primarily funded by NSF CAREER Award (OCI-1253644; PI Jha), aswell as by NSF Cyber-enabled Discovery and Innovation Award (CHE-1125332; co-PI Jha), NSF-ExTENCIergy Award (ASCR, DE-FG02-12ER26115, PI Jha). A significant grant (ExTASY) as part of the US-UKNSF-EPSRC call in Chemsitry has been awarded at the UK end and is awaiting processing at the US end. |
PI | Lillian Chong |
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Organization | University of Pittsburgh |
Department | Chemistry |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/10/2013 |
Abstract of work | The purpose of this proposal is to renew our XRAC Allocation TG-MCB100109. During the past year, this allocation has provided us with sufficient resources to further optimize our weighted ensemble path sampling software for the efficient simulation of rare events and to apply the software to the simulation of association kinetics for a model protein-peptide system (the MDM2-p53 peptide complex). We now request a larger allocation to enable the application of the weighted ensemble approach to explicit solvent simulations of binding events for a model protein-protein complex (barnase-barstar complex) with rigorous calculation of association rates. This allocation will also enable the QM/MM simulations of a diffusion-controlled chemical reaction in solution (the addition of azide ion to a series of triphenylmethyl-derived cations) with the aid of the weighted ensemble approach. These applications will be important milestones two grand challenges in computational chemistry: 1) the simulation of protein binding events, and 2) the simulation of chemical reactions in solution. It would not be possible to make meaningful progress on these simulations without the requested allocation on the XSEDE resources. |
PI | Benjamin Ong |
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Organization | Michigan State University |
Department | Institute for Cyber Enabled Research |
Field of Science | Mathematical Sciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/22/2013 |
Abstract of work | This allocation will be used to help MSU users transition from local HPC resources to XEDE resrouces |
PI | Ashok Mudgapalli |
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Organization | University of Nebraska Medical Center |
Department | Research IT Office |
Field of Science | Mathematical Sciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 12/29/2014 |
Abstract of work | Meta-genomics and Cancer research data |
PI | Jason Key |
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Organization | Harvard Medical School |
Department | BCMP / SBGrid |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 03/09/2016 |
Abstract of work | The molecules of life are large, complex machines that drive the operations of the cell. Modeling the atomic structure and underlying dynamics of these molecules is critical for understanding disease and developing therapeutics. Recent advances in experimental instrumentation and scientific software have have made high resolution biological structures more accessible than ever, but large data volumes and complex calculation often require extensive computation. Cryo-electron microscopy (Cryo-EM), for example, can now reveal structures from heterogeneous biological samples to atomic resolution - better than 3 angstroms. These structures require terabytes of experimental data and upwards of 20,000 hours of compute time for accurate determinations to be made. X-ray crystallography, the workhorse of structural biology, can now combine complex computational modeling algorithms like Rosetta with experimental data to arrive at a complete structure determination, which may require more than 1000 hours of compute time. Drug discovery efforts have embraced computational “virtual screening’ to filter the most likely targets from vast drug fragment libraries by combining computational chemistry and experimentally-determined molecular structures. In these screens, the only limit to the number of drug candidates screened is computational time. Finally, molecular dynamics simulations give insight into the motions biological molecules adopt as they perform their jobs, but also require high-performance computing resources for meaningful results. As a Campus Champion at Harvard Medical School and SBGrid, I support the research computing needs of a diverse structural biology community and XSEDE is an essential resource in driving this critical research. |
PI | David Rhee |
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Organization | Albert Einstein College of Medicine |
Department | Genetics |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 05/19/2014 |
Abstract of work | Description: RNA aptamers are small oligonucleotide molecules (~100 nucleotides) whose composition and resulting folded structure enable them to bind with high affinity and high selectivity to specific target ligands and therefore hold great promise as potential therapeutic drugs. The first aptamer to receive FDA approval was pegaptanib (Macugen), which is a treatment for wet age-related macular degeneration, a degenerative disease of the macula of the eye that leads to the loss of central vision. The pegaptanib aptamer acts by binding to and inhibiting the action of an isoform of vascular endothelial growth factor (VEGF), arresting degeneration. Functional aptamers are selected from a large, randomized initial library in a process known as SELEX (systematic evolution of ligands by exponential enrichment). This is an iterative process involving numerous rounds of binding, elution, and amplification against a specific target substrate. During each iteration - or round of selection - we enrich for the species with the highest binding affinity to the target. After multiple rounds, we ideally have an enriched aptamer library suitable for subsequent investigation. Modern techniques employ massively parallel sequencing, enabling the generation of large libraries (~10^{6} sequences) in a matter of hours for each round of selection. As RNA is single-stranded, the covariance model (CM) approach (Eddy, SR, Durbin, R (1994). RNA sequence analysis using covariance models. Nucleic Acids Res., 22, 11:2079-88) are ideal for representing motifs in their secondary structures, allowing us to discover patterns within functional aptamer populations following each round. CMs have been implemented in 'Infernal' (http://infernal.janelia.org) a program that infers RNA alignments based on RNA sequence and structure. Calibrating a single CM in Infernal however can take several hours and is a significant performance bottleneck for our work. However, as each CM calculation is itself independently determined and requires defined pr! ocessing and memory resources, their computation in parallel using the Open Science Grid offers a potential solution to this problem. Using part of a Campus Champion award to our institution, we have prototyped such a solution by making use of the Simple API for Grid Applications (SAGA) to interface with OSG and manage job submissions and file transfers. When run in parallel, our results showed a significant speed up, constrained by typical latencies and QoS associated with nominal OSG usage. This prior study demonstrated the feasibility of using SAGA and the OSG to support the parallelization of CM analysis of such large scale sequence based aptamer libraries, and forms the basis of this startup allocation request to further constrain workflow productivity and support the PhD research of Mr. Kevin Shieh. |
PI | Hong Qin |
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Organization | Spelman College |
Department | Biology |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 01/13/2015 |
Abstract of work | Why would a genotypically homogeneous population of cells live to different ages? We propose a mathematical model of cellular aging based on gene interaction network. This model network is made of only non-aging components, and interactions among genes are inherently stochastic. Death of a cell occurs in the model when an essential gene loses all of its interactions. The key characteristic of aging, the exponential increase of mortality rate over time, can arise from this model network with non-aging components. Hence, cellular aging is an emergent property of this model network. The model predicts that the rate of aging, defined by the Gompertz coefficient, is proportional to the number of active interactions per gene and that stochastic heterogeneity is an important factor in shaping the dynamics of the aging process. Hence, the Gompertz parameter is a proxy of network robustness. Preliminary studies on how aging is influenced by power-law configuration, synthetic lethal interaction, and allelic interactions will be presented. A general framework to study network aging as a quantitative trait will be studied, and the implication on missing heritability will be investigated. Empirical results to support these theoretic studies will also be presented. Preprint for the basic model is available at http://arxiv.org/abs/1305.5784 |
PI | Alan Chen |
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Organization | SUNY at Albany |
Department | Chemistry |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 03/03/2015 |
Abstract of work | A longstanding goal of molecular simulations is to accurately predict the three-dimensional fold of a biopolymer given only knowledge of its primary sequence. Although recent work has demonstrated the successful folding of proteins ranging from 10-80 amino acids from the unfolded state, no comparable results exist for the folding of structured RNAs. In recent work, we have shown that this is a result of underlying inaccuracies in the energy model itself, due to underlying assumptions that work well for describing amino acids but are inapplicable for describing nucleic acids in solution. We have systematically corrected these biases in order to more accurately capture the inherent flexibility of single-stranded RNA loops, accurate base stacking energetics, and purine anti-syn interconversions. In a departure from traditional quantum chemistry-centric parameterization schemes, we calibrate the molecular mechanics potentials directly against the relevant thermodynamic and kinetic measurements of aqueous nucleosides and nucleotides. This application is to continue the kinetic, thermodynamic characterization of improved RNA force-field to enable de-novo RNA folding. |
PI | Graziano Vernizzi |
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Organization | Siena College |
Department | Physics and Astronomy |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 05/24/2015 |
Abstract of work | The genome of many viruses is represented by a long single-stranded ribonucleic acid (RNA) molecule that appears to fold into a highly compact organized structure inside the viral shell. Such structure contains a variety of topological motifs, such as hairpins, bulges, multi-loops, and notably RNA pseudoknots. RNA pseudoknots play an important role also in natural RNAs for structural, regulatory and catalytic functions in various biological processes. In particular, it has been recently recognized an interesting interplay between the shape, structure and assembly of icosahedral viral capsids, and the compact RNA packaging topology. The topology of RNA pseudoknots can be effectively studied by using Random Matrix Theory (RMT), by exploiting a correspondence between a graphical representation of RNA structures with pseudoknots and Feynman diagrams of a particular field theory of large random matrices. The theoretical framework of RMT provides a natural analytic tool for the prediction and classification of pseudoknots, since all Feynman diagrams can be organized in a mathematical series, called topological expansion. The PI is interested in studying numerically some recent matrix models based on RMT to describe the structure of viral RNA encapsidated in a viral icosahedral shell. The PI has long experience in the application of RMT to the study of RNA pseudoknots with RMT, as well as on the simulation of the geometry and shapes of icosahedral shells. The simulations the PI intends to perform on XSEDE are Monte Carlo runs of large stochastic matrices, since the matrix model is naturally formulated as zero-dimensional SU(N) field theory of Hermitian matrices. The number of matrices L is equal to number of nucleotides of the RNA molecules, which in viral RNAs can be of the order of L~10^3. Past preliminary studies showed that the size N of the matrices should be sufficiently large to appreciate topological corrections of the order 1/N^2 and 1/N^4 (at least), which implies the simulation of Hermitian random matrices of order N~24 or N~32. Since the number of degrees of freedom for each matrix is N^2~1024, the configuration space has L*N^2~ 10^6 degrees of freedom. While matrix multiplication can benefit of parallel computing capabilities, the need of performing Monte Carlo simulations orients the PI to request High Throughput Computing resources for this initial XSEDE Startup application. Such initial experience will provide the PI a baseline to evaluate the possibility to steer future versions of the code towards HPC capabilities, including GPU or CPU-GPU clusters. Current local computational capabilities are sufficient for developing the codes and running toy-model simulations (N~4), but do not satisfy the PI’s needs for research purposes of large realistic systems. Therefore, XSEDE startup resources are requested to test larger systems, optimize the code and explore code’s scalability, as well as familiarize with the XSEDE platform. (1 row) |
PI | Emiliano Brini |
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Organization | SUNY at Stony Brook |
Department | Laufer Center |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/26/2015 |
Abstract of work | Solvation strongly affects the structures and properties of molecules. Molecular simulations for many problems in chemistry, physics, and biology require an accurate depiction of solvation, and the most ubiquitous and important solvent is water. Yet, water is difficult to model in molecular simulations - fast but sometimes erroneous modeling can be done with continuum solvent models, or relatively accurate but expensive modeling can be done explicitly. Users must generally compromise accuracy and efficiency for the problem of interest. Though widespread efforts are directed at testing water models, much of this work is duplicative and incomplete. Here we propose extensive computer simulations of biomolecular solvation using XSEDE. These simulations will provide a systematic database of solvation free energies for a large and diverse set of biomolecules and conformations. This database will extend our understanding of molecular solvation and will provide a communal resource for the development of continuum solvent models, a focus of many groups throughout the field. |
PI | Yang Zhang |
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Organization | University of Michigan |
Department | Department of Computational Medicine and Bioinformatics |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 05/18/2016 |
Abstract of work | Knowledge of 3D protein structures is paramount towards our understanding of biochemistry. Currently, there are many more known protein sequences than 3D protein structures and experimentally determining their structure can be both expensive and time consuming. Therefore, extensive efforts have been made to model these structures using computational methods. Our group has developed the I-TASSER method, which constructs protein structure models by iteratively assembling structure fragments obtained by multiple threading algorithms. The method was stringently tested in the community-wide CASP experiments and has been widely used by the community, including more than 65,000 registered scientists from 122 countries. Despite its success, a major obstacle in the optimization of I-TASSER involves a dearth of computational resources available for use. We have access to a computing cluster composed of 1,100 cores. However, I-TASSER has seen a surge in users on our web server, and as a result, there have been over 2,000 jobs waiting or running at any one time, far exceeding our current capacity. Therefore, an increase in computational resources for our research interests would greatly benefit the further optimization of the I-TASSER method, as well as the biological and medical community as a whole. Over the course of this allocation, we expect to run approximately 400 I-TASSER jobs; each of these jobs would take 500 CPU hours, thus we would require roughly 200,000 CPU hours total. This will be of critical importance for the improvement of the I-TASSER methods and enhance its capacity to serve for the general biological community. |
PI | Edward O'Brien |
---|---|
Organization | Pennsylvania State University |
Department | Chemistry |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 12/06/2016 |
Abstract of work | Experiments have shown that co-translational phe nomena can strongly influence protein function. A mechanistic understanding of co-translational phenomena such as nascent chain tension and protein misfolding can be gained with molecu lar dynamics simulations using multi-scale models of ribosome-nascent chain complexes (RNCs). Using atomistic and coarse-grained models of RNCs, we will measure the magnitude of the mec hanical force generated by co-translational folding, determine the effects of folding domain size and stability on this force, and investigate how codon translation rates can alter the probability of folding and misfolding. |
PI | Samuel Thompson |
---|---|
Organization | University of California, San Francisco |
Department | Bioengineering and Therapeutics |
Field of Science | Molecular and Structural Biosciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 01/30/2017 |
Abstract of work | Proteins custom-designed for specific molecular function have great promise to advance many areas of science and industry. High throughput methods – in particular, effective computational modeling of structure and function – are necessary to identify proteins with novel functions out of the vast number of candidate protein sequences. Nevertheless, state-of-the-art methods have only limited accuracy in predicting the functional impact of even a few mutations. To improve models for functional proteins, we are developing methods within the Rosetta computational protein design software suite that represent subtle structural fluctuations using flexible-backbone ensembles and integrate multiple functional constraints on proteins (i.e. catalytic conformations or binding partners). Promising initial results demonstrated improvement over standard fixed-backbone approaches in initial tests against large curated mutational datasets for experimentally determined binding affinities and high-throughput screening of protein-protein interactions. Our approach of using discrete ensembles to model flexible and dynamic systems is well suited to the distributed nature of high performance computing clusters. Our goal of predicting the functional effect of defined sequences is likewise well suited. In particular, the Open Science Grid will be very useful for our high-processing, low-memory requirements. The purpose of this Startup request is two-fold: benchmarking and optimizing computational methodologies to model functional proteins. First, we will streamline our methodology for XSEDE in preparation for a Research allocation application. Second, additional computing resources from XSEDE will greatly expand our ability develop methodology beyond the limitations of benchmarking on the computational resources at our home institution. |
PI | Yvonne Chan |
---|---|
Organization | University of Hawaii, Manoa |
Department | Hawaii Institute of Marine Biology |
Field of Science | Ocean Sciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/10/2013 |
Abstract of work | Methods that integrate population sampling from multiple taxa into a single analysis are a much needed addition to the comparative phylogeographic toolkit. Here we present a statistical framework for multi-species analysis based on hierarchical approximate Bayesian computation (hABC) for inferring community dynamics and concerted demographic response. Detecting community response to climate change is an important issue with regards to how species have and will react to past and future events. Furthermore, whether species responded individualistically or in concert is at the center of related questions about the abiotic and biotic determinants of community assembly. This method combines multi-taxon genetic datasets into a single analysis to determine the proportion of a contemporary community that historically expanded in a temporally clustered pulse as well as when the pulse occurred. We will apply this method to 59 species in the Hawaiian Archipelago in order to examine community response of coral reef taxa to sea-level change in Hawaii. The method can accommodate dataset heterogeneity such as variability in effective population size, mutation rates, and sample sizes across species and utilizes borrowing strength from the simultaneous analysis of multiple species. This hABC framework used in a multi-taxa demographic context can increase our understanding of the impact of historical climate change by determining what proportion of the community responded in concert or independently, and can be used with a wide variety of comparative phylogeographic datasets as biota-wide DNA barcoding data sets accumulate. |
PI | Yvonne Chan |
---|---|
Organization | University of Hawaii, Manoa |
Department | Hawaii Institute of Marine Biology |
Field of Science | Ocean Sciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/27/2014 |
Abstract of work | Methods that integrate population sampling from multiple taxa into a single analysis are a much needed addition to the comparative phylogeographic toolkit. Here we present a statistical framework for multi-species analysis based on hierarchical approximate Bayesian computation (hABC) for inferring community dynamics and concerted demographic response. Detecting community response to climate change is an important issue with regards to how species have and will react to past and future events. Furthermore, whether species responded individualistically or in concert is at the center of related questions about the abiotic and biotic determinants of community assembly. This method combines multi-taxon genetic datasets into a single analysis to determine the proportion of a contemporary community that historically expanded in a temporally clustered pulse as well as when the pulse occurred. We will apply this method to 59 species in the Hawaiian Archipelago in order to examine community response of coral reef taxa to sea-level change in Hawaii. The method can accommodate dataset heterogeneity such as variability in effective population size, mutation rates, and sample sizes across species and utilizes borrowing strength from the simultaneous analysis of multiple species. This hABC framework used in a multi-taxa demographic context can increase our understanding of the impact of historical climate change by determining what proportion of the community responded in concert or independently, and can be used with a wide variety of comparative phylogeographic datasets as biota-wide DNA barcoding data sets accumulate. |
PI | Pran Nath |
---|---|
Organization | Northeastern University |
Department | Physics |
Field of Science | Physics and astronomy |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/22/2013 |
Abstract of work | We propose to investigate signatures for the discovery of new physics at the LHC which would run at a center of mass energy of either 7 TeV, 8 TeV, 10 TeV or 14 TeV. Our goal is to first study the Standard Model background at these energies, and then develop analyses that strongly highlight and discriminate theories of new physics. We will use our actively developed software, FastSUSY, to carry out Bayesian analyses that estimate the parameters of the various models of new physics, in light of the most recent data. We also propose to study topological invariants of manifolds that are important in String Theory, searching for correlations to algebraic structures relevant to model building, and compute the properties of the vacua associated with these geometries. Additionally, we wish to extend our analyses to models of supergravity that including CP-violating phases. Our total request is for 7 million SUs and 5 TB of disk space for the proposed projects. |
PI | Qaisar Shafi |
---|---|
Organization | University of Delaware |
Department | Physics and astronomy |
Field of Science | Physics and astronomy |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/10/2013 |
Abstract of work | The discovery of a Higgs-like particle, announced in June 2012 by CERN, was a defining moment in the field of high energy physics. The excitement of this finding was felt world-wide and is a breakthrough in our understanding of the Universe at a fundamental level. Saying therefore that we now live in a post-Higgs era in high energy physics is no exaggeration. This breakthrough by the Large Hadron Collider (LHC) is just a first step towards testing much extensive theories such as supersymmetry and grand unification. Computing tools played an important role in the discovery of the Higgs and the need for these tools to explore ideas beyond the Standard Model is ever increasing. Resources like XSEDE therefore provide an opportunity to use cutting edge computing tools in order to explore novel ideas in high energy physics. Our startup allocation of 150,000 SU's resulted in four peer reviewed publications. With the second allocation of 3 million SUs our group managed to complete 10 articles out of which 7 have been published in peer reviewed journals and three are in process. The data for two other projects have been collected. These projects resulted from the consumption of only 32% of the total SUs that were allocated. Our consumption of the SUs was much less than anticipated since we have improved the computing techniques we use in our projects. We are therefore requesting an extension of our current SUs since a surplus of SUs is always useful for us to pursue projects even if the SU requirement is high. |
PI | Francis Halzen |
---|---|
Organization | University of Wisconsin-Madison |
Department | Physics |
Field of Science | Physics and astronomy |
Sponsor | CG OSG-XSEDE |
Date Registered | 01/14/2016 |
Abstract of work | IceCube is a neutrino detector built at the South Pole by instrumenting about a cubic kilometer of ice with 5160 light sensors. IceCube is taking data since 2006, and it is envisioned to continuing doing so for the next 20 years. One of the primary goals for IceCube is to elucidate the mechanisms for production of high-energy cosmic rays by detecting high-energy neutrinos from astrophysical sources. The excellent performance of IceCube plus the advances in understanding fundamental detector characteristics such as the ice properties have allowed to expand its scientific reach towards measurements and searches that require much higher precision and control of systematic error sources. Examples of these are the measurement of neutrino oscillations in a previously unexplored energy range from 10 to 60 GeV. The simulations proposed in this request will enable carrying out neutrino physics precision analysis which require of a very good understanding of possible sources of systematic errors. Examples of these are Tau neutrino appearance and Muon neutrino disappearance precision measurements as well as searches for low energy sterile neutrinos. |
PI | Terrance Figy |
---|---|
Organization | Wichita State University |
Department | Mathematica, Statistics, and Physics |
Field of Science | Physics |
Sponsor | CG OSG-XSEDE |
Date Registered | 01/29/2016 |
Abstract of work | XSEDE resources will be used to generate several trillion simulated collision events for the CERN Large Hadron Collider Experiment. The simulated events will be generated by the Monte Carlo simulation program called Herwig 7 (herwig.hepforge.org) interfaced with the module HJets++ (hjets.hepforge.org). The primary focus will the simulation of the scattering of two protons into a Higgs boson is association with jets (H+3 Jets). Jets are are clusters of energetic hadrons. Hadrons are composite particles that are comprised of fundamental particles called quarks and gluons. Results for the next-to-next leading order QCD corrections of H+3 Jets have been published in Physical Review Letters (http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.111.211802). However, further simulations are required to evaluate the theoretical uncertainties for the integrated scattering cross-section and kinematics distributions for H+3 Jets. In order to evaluate the scattering cross-section with a Monte Carlo integration error of 1 per mille, it is necessary to simulate at least a trillion weighted events. The parallel computing computing environment that XSEDE provides will provide the necessary events to achieve lower integration errors. |
PI | Nepomuk Otte |
---|---|
Organization | Georgia Institute of Technology |
Department | School of Physics & Center for Relativistic Astrophysics |
Field of Science | Mathematical Sciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 08/16/2016 |
Abstract of work | We request computing time on Stampede to perform air shower simulations for the VERITAS air Cherenkov gamma-ray telescope. The new set replaces an existing 5 year old set of shower simulations. Air shower simulations are essential to understand the instrument response of VERITAS and needed in the analysis of VERITAS data. The proposed new set of simulations will allow the VERITAS Collaboration to extend the usable energy range of the VERITAS instrument beyond 10 TeV and significantly reduce systematic uncertainties at all energies. |
PI | Sheila Kannappan |
---|---|
Organization | University of North Carolina, Chapel Hill |
Department | Physics & Astronomy |
Field of Science | Physics and astronomy |
Sponsor | CG OSG-XSEDE |
Date Registered | 07/08/2014 |
Abstract of work | Description: This proposal requests 20,000 SUs on XSEDE for 20 undergraduate students and mentors participating in the Computational Astronomy & Physics REU Program at the University of North Carolina-Chapel Hill in summer 2014. The time is needed for a computational methods tutorial on the Open Science Grid followed by optional use of the OSG for the students summer research projects, with possible continuing use through January 2014 to enable polishing the projects for presentation at conferences. The projects cover a range of topics in computational astronomy and physics. Details can be found in the supporting material attached. |
PI | Shaowen Wang |
---|---|
Organization | University of Illinois at Urbana-Champaign |
Department | Geography and Geographic Information Science |
Field of Science | Geographic Information Science |
Sponsor | CG OSG-XSEDE |
Date Registered | 02/27/2015 |
Abstract of work | Geographic Information Science (GIScience), crosscutting many fields (e.g., geography, social sciences, computer science, geodesy, and information sciences), plays essential roles for transforming geographic data into geospatial information and knowledge, breaking through scientific problems, and improving decision-making practices of broad and significant societal impact. However, fulfilling such roles is increasingly dependent on the ability to handle very large spatial datasets and complex analysis and modeling methods based on synthesizing computational and spatial thinking enabled by cyberinfrastructure (CI), which conventional GIS software approaches do not provide. CI-based integration of geographic information systems (GIS) and spatial analysis and modeling, as a holistic solution, is leading to unprecedented capabilities for transforming geospatial sciences.The purpose of this project is to extend and sustain GISolve, a TeraGrid Science Gateway toolkit for GIScience, for establishing a high performance, distributed, and collaborative CyberGIS framework that couples CI, GIS, and geospatial analysis and modeling capabilities. Through the continuous TeraGrid resource allocation support from previous three years, a set of spatial middleware components has been built into the GISolve Toolkit to glue generic cyberinfrastructure capabilities and geospatial analysis methods. This toolkit has been used to build the TeraGrid GIScience Gateway as a collaborative geospatial problem-solving environment for multi-disciplinary researchers to perform large-scale geospatial analysis and modeling, and help non-technical users directly benefit from accessing TeraGrid capabilities. With the support of TeraGrid high-end computing resources, we have developed a set of high-performance parallel and distributed geospatial computational methods for our research projects. Scalability and efficient use of high-end computing resources are the foci in developing these methods. For example, the parallel agent-based modeling and parallel land use optimization code are scalable to thousands of processors on Abe and Ranger with impressive computational performance. The methods so developed have been applied in solving large- and multi-scale geospatial science problems that could not be solved before, such as the study of geospatial pattern of the impact of global climate change on crop yields. With GISolve being widely used in the GIScience community, new methods continue to be identified, proposed, and integrated in the GISolve Toolkit. To support community-contributed applications, we have developed a streamlined application integration process to facilitate cyberinfrastructure-enabled computation and efficient integration into the science gateway for sharing. This project has been growing dramatically with consistent and extended research collaboration and education efforts such as the collaboration with the U.S. Geological Survey (USGS) in the National Map project and outreach activities with the University Consortium for Geographic Information Science (UCGIS). |
PI | Stephen McNally |
---|---|
Organization | University of Tennessee, Knoxville |
Department | NICS |
Field of Science | Other |
Sponsor | CG OSG-XSEDE |
Date Registered | 08/18/2014 |
Abstract of work | renewing project |
PI | Nancy Wilkins-Diehr |
---|---|
Organization | University of California-San Diego |
Department | San Diego Supercomputer Center |
Field of Science | Training |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/22/2013 |
Abstract of work | Staff Account for Training |
PI | Andrew Ruether |
---|---|
Organization | Swarthmore College |
Department | ITS |
Field of Science | Training |
Sponsor | CG OSG-XSEDE |
Date Registered | 10/22/2013 |
Abstract of work | Swarthmore College Campus Champion Renewal |
PI | Hadrian Djohari |
---|---|
Organization | Case Western Reserve University |
Department | ITS |
Field of Science | Chemistry |
Sponsor | CG OSG-XSEDE |
Date Registered | 07/27/2014 |
Abstract of work | Description: Campus Champions for Case Western Reserve University, helping faculty to start onboarding XSEDE resources. Some research work on Macromolecular Science and Materials Science. |
PI | Rob Lane |
---|---|
Organization | Columbia University in the City of New York |
Department | Columbia University Information Techonology |
Field of Science | Other |
Sponsor | CG OSG-XSEDE |
Date Registered | 02/02/2017 |
Abstract of work | This allocation will be used to help researchers at Columbia University understand how to use XSEDE resources. |
PI | Pol Llovet |
---|---|
Organization | Montana State University |
Department | Research Computing Group |
Field of Science | Evolutionary Sciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 04/11/2014 |
Abstract of work | This is the allocation for my Montana State University Campus Champion account. |
PI | Hanning Chen |
---|---|
Organization | George Washington University |
Department | Chemistry |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG-XSEDE |
Date Registered | 04/11/2014 |
Abstract of work | campus Champion at GWU |
PI | David Monismith |
---|---|
Organization | Northwest Missouri State University |
Department | Mathematics, Computer Science, and Information Systems |
Field of Science | Training |
Sponsor | CG OSG-XSEDE |
Date Registered | 09/30/2014 |
Abstract of work | This is a renewal request for the Campus Champion allocation for Northwest Missouri State University. |
PI | John Chrispell |
---|---|
Organization | Indiana University of Pennsylvania |
Department | Mathematics |
Field of Science | Other |
Sponsor | CG OSG-XSEDE |
Date Registered | 05/13/2015 |
Abstract of work | This allocation will be used to support the use of high performance computing at Indiana University of Pennsylvania. This allocation is a gateway for faculty and students at IUP to gain experience and start using XSEDE resources to further their education and research objectives. This is the Campus Champion allocation request for IUP. |
PI | Neranjan Edirisinghe Pathirannehelage |
---|---|
Organization | Georgia State University |
Department | Information Technology |
Field of Science | Mathematical Sciences |
Sponsor | CG OSG-XSEDE |
Date Registered | 09/11/2015 |
Abstract of work | I like to request renewal for my CC allocation. This allocation will help me to provide temporary resources for new users who wish to test XSEDE resources. |
PI | Scott Hampton |
---|---|
Organization | University of Notre Dame |
Department | Center for Research Computing |
Field of Science | Other |
Sponsor | CG OSG-XSEDE |
Date Registered | 04/06/2016 |
Abstract of work | The immediate purpose of this request is to have small allocations available for showcasing and quick access to a variety of XSEDE resources. Long term goals are to encourage and assist campus users in applying for their own allocations. |
PI | Igor Yakushin |
---|---|
Organization | Pennsylvania State University |
Department | Institute for CyberScience |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG-XSEDE |
Date Registered | 03/31/2016 |
Abstract of work | Campus Champion allocation |
PI | Stephen Wolbers |
---|---|
Organization | Oregon State University |
Department | Information Services |
Field of Science | Other |
Sponsor | CG OSG-XSEDE |
Date Registered | 12/03/2015 |
Abstract of work | A request for initial campus champion resources for Oregon State University researchers. |
PI | Jason H. Moore |
---|---|
Organization | University of Pennsylvania |
Department | Institute for Biomedical Informatics |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 01/29/2016 |
Abstract of work | Project Description: TPOT is an open source Python tool that automatically creates and optimizes Machine Learning pipelines using genetic programming. GitHub repo: http://github.com/rhiever/tpot |
PI | Kathryne J Daniel |
---|---|
Organization | Bryn Mawr College |
Department | Physics |
Field of Science | Astrophysics |
Sponsor | CG OSG Connect |
Date Registered | 06/20/2016 |
Abstract of work | Computing a bunch of orbits in a disk galaxy in the presence of a spiral arm. The aim is to identify trapped orbits and determine the physical parameters that determine the rate of scattering out of trapped orbits. |
PI | Asia Aljahdali |
---|---|
Organization | Florida State University |
Department | Computer Science |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 03/15/2017 |
Abstract of work | Testing Random number Generators via parallel Testu01 package. |
PI | Shripad Tuljapurkar |
---|---|
Organization | Stanford University |
Department | Biology |
Field of Science | Biological Sciences |
Sponsor | CG OSG Connect |
Date Registered | 10/09/2017 |
Abstract of work | Analyze U-5 mortality convergence and compression in developed and developing countries. Analyze lifespan inequality in U-5 mortality and how it correlates with other sources of inequality across and within countries. |
PI | Nirav Merchant |
---|---|
Organization | University of Arizona |
Department | Arizona Research Laboratories |
Field of Science | Multi-Science Community |
Sponsor | CG OSG Connect |
Date Registered | 11/22/2016 |
Abstract of work | Enabling scalable data analytics for University of Arizona researchers |
PI | Robert William Gardner Jr |
---|---|
Organization | University of Chicago |
Department | Computation Institute |
Field of Science | Multi-Science Community |
Sponsor | CG OSG Connect |
Date Registered | 09/15/2014 |
Abstract of work | General use Project for the University of Chicago |
PI | Birali Runesha |
---|---|
Organization | University of Chicago |
Department | Research Computing Center |
Field of Science | Training |
Sponsor | CG OSG Connect |
Date Registered | 09/25/2013 |
Abstract of work | University of Chicago Research Computing Center (http://rcc.uchicago.edu) supporting the computational requirements of multiple science domains. |
PI | Frank Wuerthwein |
---|---|
Organization | UCSD |
Department | Physics |
Field of Science | Engineering |
Sponsor | CG UCSD |
Date Registered | 05/15/2014 |
Abstract of work | Earthquake Engineering from UCSD supported users |
PI | Frank Wuerthwein |
---|---|
Organization | UCSD |
Department | Physics |
Field of Science | Astrophysics |
Sponsor | CG UCSD |
Date Registered | 05/15/2014 |
Abstract of work | Experimental Astrophysics from UCSD supported users |
PI | Frank Wuerthwein |
---|---|
Organization | UCSD |
Department | Physics |
Field of Science | Astrophysics |
Sponsor | CG UCSD |
Date Registered | 05/15/2014 |
Abstract of work | Theoretical Astrophysics from UCSD supported users |
PI | Frank Wuerthwein |
---|---|
Organization | UCSD |
Department | Physics |
Field of Science | Biophysics |
Sponsor | CG UCSD |
Date Registered | 05/16/2014 |
Abstract of work | Biological Physics from UCSD supported users |
PI | Frank Wuerthwein |
---|---|
Organization | UCSD |
Department | Physics |
Field of Science | High Energy Physics |
Sponsor | CG UCSD |
Date Registered | 05/15/2014 |
Abstract of work | Non-CMS Particle Physics from UCSD supported users |
PI | Sean Cleveland |
---|---|
Organization | University of Hawaii |
Department | Cyberinfrastructure |
Field of Science | Computer and Information Science and Engineering |
Sponsor | CG OSG Connect |
Date Registered | 02/15/2018 |
Abstract of work | A project to help get users from UH onto open science grid. |
PI | Paul Wolberg |
---|---|
Organization | University of Michigan |
Department | Microbiology and Immunology |
Field of Science | Microbiology |
Sponsor | VO OSG |
Date Registered | 08/14/2013 |
Abstract of work | To use a systems biology approach to directly and significantly impact our understanding and treatment of tuberculosis. |
PI | David Stark |
---|---|
Organization | UNC Chapel Hill |
Department | Department of Physics and Astronomy |
Field of Science | Physics and astronomy |
Sponsor | VO OSG |
Date Registered | 10/08/2013 |
Abstract of work | Astronomy image manipulation |
PI | Dequan Xiao |
---|---|
Organization | University of New Haven |
Department | Chemistry |
Field of Science | Chemistry |
Sponsor | CG OSG Connect |
Date Registered | 01/03/2017 |
Abstract of work | We are interested in developing new quantum chemistry methods and chemical structure optimization algorithms to design green heterogeneous catalysts. |
PI | Jean-Jack M. Riethoven |
---|---|
Organization | University of Nebraska-Lincoln |
Department | Center for Biotechnology |
Field of Science | Bioinformatics |
Sponsor | CG OSG Connect |
Date Registered | 03/02/2017 |
Abstract of work | The Bioinformatics Core Research Facility at UNL runs several large scale compute projects a year. Our main compute is focused on sequence analysis, de-novo assembly and gene prediction/annotation, secondary structure prediction, peptide-protein docking, and phenotype image analysis. We tend to run projects that deal with species critical for agriculture, both crops and livestock, but also with human-virus or food-gut microbiome interactions. |
PI | Adam Caprez |
---|---|
Organization | University of Nebraska - Lincoln |
Department | Bioinformatics |
Field of Science | Bioinformatics |
Sponsor | VO HCC |
Date Registered | 07/08/2014 |
Abstract of work | The Comparison of Protein Active Site Structures (CPASS) database and software is used as part of our FAST-NMR assay to assign the function of a hypothetical protein or a protein of unknown function. The CPASS database and software enable the comparison of experimentally identified ligand binding sites to infer biological function and aid in drug discovery. The CPASS database is comprised of unique ligand-defined active sites identified in the Protein Data Bank, and the CPASS program compares these ligand-defined active sites to determine sequence and structural similarity without maintaining sequence connectivity, along with ligand similarity, if desired. CPASS will compare any set of ligand-defined protein active sites irrespective of the identity of the bound ligand. |
PI | Rob Quick |
---|---|
Organization | Indiana University |
Department | Research Technologies |
Field of Science | Computational Condensed Matter Physics |
Sponsor | CG OSG Connect |
Date Registered | 12/13/2017 |
Abstract of work | Researchers from UNAL will be using OSG and running example jobs on Monte Carlo simulations, they will be submitting jobs related to bit patterned media, following this work http://www.sciencedirect.com/science/article/pii/S1386947715303222, and will also be submitting jobs related to research in critical phenomena, similar to what was done here: http://www.sciencedirect.com/science/article/pii/S0304885316324933?via%3Dihub and here http://www.sciencedirect.com/science/article/pii/S0304885316320169?via%3Dihub |
PI | Steven Massey |
---|---|
Organization | Universidad de Puerto Rico, Rio Piedras Campus (UPRRP) |
Department | Physics / Biology |
Field of Science | Bioinformatics |
Sponsor | VO OSG |
Date Registered | 10/18/2013 |
Abstract of work | In this collaborative project between bioinformatics and physics we use molecular evolution simulations to evolve a population of proteins. We look for the emergence of mutational robustness of proteins in the population. This quantity measures how resistant they are to the deleterious effects of mutations. Previous results from Dr. Massey's group suggest that mutational robustness increases and eventually converges over time. This appears to be an emergent property of proteins. It has profound evolutionary implications. The protein structures are obtained from the Protein Data Bank. Non-robust sequences are threaded onto the structure and are subjected to random mutations. The resulting sequences are selected for their free energy of folding. Once the sequences are generated the mutational robustness is calculated in parallel (through Condor). |
PI | Tim Cartwright |
---|---|
Organization | OSG |
Department | OSG |
Field of Science | Multi-Science Community |
Sponsor | CG OSG Connect |
Date Registered | 06/11/2014 |
Abstract of work | Training project for OSG User School 2014. |
PI | Tim Cartwright |
---|---|
Organization | University of Wisconsin - Madison |
Department | Computer Science |
Field of Science | Education |
Sponsor | CG OSG Connect |
Date Registered | 07/28/2015 |
Abstract of work | User School 2015 at University of Wisconsin - Madison |
PI | Tim Cartwright |
---|---|
Organization | University of Wisconsin Madison |
Department | Computer Science |
Field of Science | Education |
Sponsor | CG OSG Connect |
Date Registered | 07/20/2016 |
Abstract of work | Training project for OSG User School 2016 |
PI | Tim Cartwright |
---|---|
Organization | University of Wisconsin Madison |
Department | Computer Science |
Field of Science | Multi-Science Community |
Sponsor | CG OSG Connect |
Date Registered | 07/05/2017 |
Abstract of work | Training project for OSG User School 2017 |
PI | Julian Velev |
---|---|
Organization | University of Puerto Rico |
Department | Physics |
Field of Science | Computational Condensed Matter Physics |
Sponsor | CG OSG Connect |
Date Registered | 07/15/2014 |
Abstract of work | Electronic structure of solids. Electron and spin transport in nanoscale devices. |
PI | Nepomuk Otte |
---|---|
Organization | Georgia Institute of Technology |
Department | School of Physics & Center for Relativistic Astrophysics |
Field of Science | Astrophysics |
Sponsor | CG OSG Connect |
Date Registered | 08/24/2016 |
Abstract of work | VERITAS is an array of four imaging atmospheric Cherenkov telescopes to detect gamma-rays with energies above 100 GeV from astrophysical sources. This project produces Monte Carlo simulations of air showers and the detector response for VERITAS and other imaging Cherenkov telescope project |
PI | Dr. Andrew Leakey |
---|---|
Organization | University of Illinois Urbana-Champaign |
Department | Plant Biology |
Field of Science | Plant Biology |
Sponsor | CG OSG Connect |
Date Registered | 09/05/2017 |
Abstract of work | Phenotyping leaf epidermis by optical tomography and computer vision to evaluate stomatal patterning across natural diversity and transgenic lines of Sorghum and Setaria |
PI | Ghana Challa |
---|---|
Organization | South Dakota State University |
Department | Biology |
Field of Science | Bioinformatics |
Sponsor | CG CMS Connect |
Date Registered | 04/17/2017 |
Abstract of work | Analysis of wheat genome and transcriptome datasets |
PI | Alfio Rizzo |
---|---|
Organization | Columbia University |
Department | Astrophysics |
Field of Science | Astrophysics |
Sponsor | VO OSG |
Date Registered | 09/18/2013 |
Abstract of work | The XENON Dark Matter Experiment located at the Gran Sasso Laboratories (INFN, Italy), is currently the leader world project searching for the so called Dark Matter, something which is completely different from ordinary matter. This Dark Matter is not (as the name hints) visible, but it should pervade the entire Universe. Its presence has been confirmed by different experimental evidences, however its intrinsic nature is one of the big puzzle of Modern Physics. The XENON Experiment could reveal the nature of the DM looking at the possible interactions of the DM with ordinary matter, for instance with the Xenon, a noble gas been liquified at very low temperature. The study of the background signal, from the environment and from the materials that make up the new detector containing the Xenon (which is currently under construction and called XENON1T), is essential to understand the detector's behavior and its implications on its performances. For this purpose an extensive Montecarlo simulation and study is needed, and this require quite a lot of CPU time. The MC simulation of the XENON experiment is based on the open source codes called GEANT4 and ROOT. |
PI | Luca Grandi |
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Organization | University of Chicago |
Department | Physics |
Field of Science | Astrophysics |
Sponsor | CG OSG Connect |
Date Registered | 09/02/2015 |
Abstract of work | The XENON Dark Matter Experiment located at the Gran Sasso Laboratories (INFN, Italy), is currently the leader world project searching for the so called Dark Matter, something which is completely different from ordinary matter. This Dark Matter is not (as the name hints) visible, but it should pervade the entire Universe. Its presence has been confirmed by different experimental evidences, however its intrinsic nature is one of the big puzzle of Modern Physics. The XENON Experiment could reveal the nature of the DM looking at the possible interactions of the DM with ordinary matter, for instance with the Xenon, a noble gas been liquified at very low temperature. The study of the background signal, from the environment and from the materials that make up the new detector containing the Xenon (which is currently under construction and called XENON1T), is essential to understand the detector's behavior and its implications on its performances. For this purpose an extensive Montecarlo simulation and study is needed, and this require quite a lot of CPU time. The MC simulation of the XENON experiment is based on the open source codes called GEANT4 and ROOT. |
PI | Adam Para |
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Organization | Fermilab |
Department | Scientific Computing Simulation |
Field of Science | High Energy Physics |
Sponsor | VO Fermilab |
Date Registered | 12/29/2014 |
Abstract of work | Investigate the physics potential of high pressure Xenon TPC for detection of rare processes and develop reconstruction techniques for extremely high granularity detectors. |
PI | Snir Gazit |
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Organization | University of California Berkeley |
Department | Physics |
Field of Science | Physics |
Sponsor | CG OSG Connect |
Date Registered | 12/15/2015 |
Abstract of work | We study Z2 lattice gauge theory coupled to fermonic matter fields. The problem can be studied using sign problem free quantum Monte Carlo allowing a numerically unbiased computation. |
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