Projects

AdHocComm
PITrevor Santarra
OrganizationUniversity of California Santa Cruz
DepartmentComputer Science
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG Connect
Date Registered01/26/2017
Abstract of workWe are evaluating heuristic approaches from active learning for communicating partial policy information in ad hoc teamwork scenarios.
AfricanSchool
PIRob Quick
OrganizationIndiana University
DepartmentUITS
Field of ScienceEducation
SponsorCG OSG Connect
Date Registered06/10/2016
Abstract of workA project for teaching the grid computing component of the African School of Physics.
AlGDock
PIDavid Minh
OrganizationIllinois Institute of Technology
DepartmentChemistry
Field of ScienceChemistry
SponsorCG OSG Connect
Date Registered05/06/2014
Abstract of workBinding 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.
all
PIJohn Carlstrom
OrganizationUniversity of Chicago
DepartmentPhysics
Field of ScienceAstrophysics
SponsorCG SPT Connect
Date Registered10/24/2016
Abstract of workThe 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.
AMFORA
PIIan Foster
OrganizationUniversity of Chicago
DepartmentComputer Science
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG Connect
Date Registered11/27/2013
Abstract of workAmfora 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.
AmorphousOrder
PIPatrick Charbonneau
OrganizationDuke University
DepartmentChemistry
Field of ScienceChemistry
SponsorCG OSG Connect
Date Registered01/11/2016
Abstract of workGlass-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.
AMS
PIBaosong Shan
OrganizationMIT
DepartmentLNS
Field of ScienceParticle Physics
SponsorVO OSG
Date Registered02/16/2016
Abstract of workMonte Carlo simulation for the AMS experiment
AnimalSocialNetworks
PIErol Akcay
OrganizationUniversity of Pennsylvania
DepartmentBiology
Field of ScienceBiological Sciences
SponsorCG OSG Connect
Date Registered11/30/2015
Abstract of workProject 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
aprime
PIJan Balewski
OrganizationMIT
DepartmentLNS
Field of ScienceNuclear Physics
SponsorCG OSG Connect
Date Registered04/08/2014
Abstract of workDarkLight 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.
ASPU
PIilyoup kwak
OrganizationUniversity of Minnesota
DepartmentDivision of Biostatistics
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered05/01/2015
Abstract of workdeveloping genetic association tests using GWAS data
atlas-org-albany
PIRobert William Gardner Jr
OrganizationState University of New York — Albany
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for SUNY Albany
atlas-org-anl
PIRobert William Gardner Jr
OrganizationArgonne National Laboratory
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Argonne National Laboratory
atlas-org-arizona
PIRobert William Gardner Jr
OrganizationUniversity of Arizona
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for University of Arizona
atlas-org-bnl
PIRobert William Gardner Jr
OrganizationBrookhaven National Laboratory
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Brookhaven National Laboratory
atlas-org-brandeis
PIRobert William Gardner Jr
OrganizationBrandeis University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Brandeis University
atlas-org-bu
PIRobert William Gardner Jr
OrganizationBoston University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Boston University
atlas-org-columbia
PIRobert William Gardner Jr
OrganizationColumbia University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Columbia University
atlas-org-duke
PIDoug Benjamin
OrganizationDuke University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered06/05/2014
Abstract of workDuke University's Tier 2 ATLAS group in ATLAS Connect.
atlas-org-fresnostate
PIHarinder Singh Bawa
OrganizationFresno State University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered06/05/2014
Abstract of workFresno State University's Tier 3 ATLAS group in ATLAS Connect.
atlas-org-hamptonu
PIRobert William Gardner Jr
OrganizationHampton University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Hampton University
atlas-org-harvard
PIRobert William Gardner Jr
OrganizationHarvard University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Harvard University
atlas-org-iastate
PIRobert William Gardner Jr
OrganizationIowa State University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Iowa State University
atlas-org-illinois
PIMark Neubauer
OrganizationUniversity of Illinois
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered06/05/2014
Abstract of workUniversity of Illinois Urbana/Champaign Tier 3 ATLAS group.
atlas-org-indiana
PIFrederick Luehring
OrganizationIndiana University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered06/05/2014
Abstract of workIndiana University Tier 3 ATLAS group.
atlas-org-Jet-EtMiss
PIRobert William Gardner Jr
OrganizationUS ATLAS
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Jet EtMiss
atlas-org-latech
PIRobert William Gardner Jr
OrganizationLouisiana Tech University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Louisiana Tech University
atlas-org-lbnl
PIRobert William Gardner Jr
OrganizationLawrence Berkeley National Laboratory
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Lawrence Berkeley National Laboratory
atlas-org-louisville
PIRobert William Gardner Jr
OrganizationUniversity of Louisville
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workUniversity of Louisville
atlas-org-mit
PIRobert William Gardner Jr
OrganizationMIT
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for MIT
atlas-org-msu
PIRobert William Gardner Jr
OrganizationMichigan State University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Michigan State University
atlas-org-niu
PIRobert William Gardner Jr
OrganizationNorthern Illinois University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Northern Illinois University
atlas-org-nyu
PIRobert William Gardner Jr
OrganizationNew York University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for New York University
atlas-org-okstate
PIRobert William Gardner Jr
OrganizationOklahoma State University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Oklahoma State University
atlas-org-osu
PIRobert William Gardner Jr
OrganizationThe Ohio State University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for The Ohio State University
atlas-org-ou
PIRobert William Gardner Jr
OrganizationOklahoma University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Oklahoma University
atlas-org-pitt
PIRobert William Gardner Jr
OrganizationUniversity of Pittsburgh
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for University of Pittsburgh
atlas-org-sc
PIRobert William Gardner Jr
OrganizationUniversity of South Carolina
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for University of South Carolina
atlas-org-slac
PIRobert William Gardner Jr
OrganizationSLAC National Accelerator Laboratory
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for SLAC National Accelerator Laboratory
atlas-org-smu
PIRobert William Gardner Jr
OrganizationSouthern Methodist University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Southern Methodist University
atlas-org-stonybrook
PIRobert William Gardner Jr
OrganizationState University of New York — Stony Brook
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for State University of New York — Stony Brook
atlas-org-Tau
PIRobert William Gardner Jr
OrganizationUS ATLAS
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Tau
atlas-org-tufts
PIRobert William Gardner Jr
OrganizationTufts University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Tufts University
atlas-org-uchicago
PIRobert William Gardner Jr
OrganizationUniversity of Chicago
DepartmentHigh Energy Physics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered03/07/2014
Abstract of workTier3 computing for the UChicago ATLAS group via the ATLAS Connect service
atlas-org-uci
PIRobert William Gardner Jr
OrganizationUniversity of California — Irvine
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for University of California — Irvine
atlas-org-ucsc
PIRobert William Gardner Jr
OrganizationUniversity of California — Santa Cruz
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for University of California — Santa Cruz
atlas-org-uiowa
PIRobert William Gardner Jr
OrganizationUniversity of Iowa
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for University of Iowa
atlas-org-umass
PIRobert William Gardner Jr
OrganizationUniversity of Massachusetts
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for University of Massachusetts
atlas-org-unm
PIRobert William Gardner Jr
OrganizationUniversity of New Mexico
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for University of New Mexico
atlas-org-uoregon
PIRobert William Gardner Jr
OrganizationUniversity of Oregon
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for University of Oregon
atlas-org-upenn
PIRobert William Gardner Jr
OrganizationUniversity of Pennsylvania
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for University of Pennsylvania
atlas-org-uta
PIRobert William Gardner Jr
OrganizationUniversity of Texas - Arlington
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for University of Texas - Arlington
atlas-org-utdallas
PIRobert William Gardner Jr
OrganizationUniversity of Texas - Dallas
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect Team for University of Texas - Dallas
atlas-org-utexas
PIRobert William Gardner Jr
OrganizationUniversity of Texas-Austin
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for University of Texas-Austin
atlas-org-washington
PIRobert William Gardner Jr
OrganizationUniversity of Washington
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for University of Washington
atlas-org-wisc
PIRobert William Gardner Jr
OrganizationUniversity of Wisconsin
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for University of Wisconsin
atlas-org-yale
PIRobert William Gardner Jr
OrganizationYale University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Yale University
atlas-wg-B-Physics
PIRobert William Gardner Jr
OrganizationUS ATLAS
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for B Physics
atlas-wg-combined-muon
PIRobert William Gardner Jr
OrganizationUS ATLAS
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Combined Muon
atlas-wg-E-Gamma
PIRobert William Gardner Jr
OrganizationUS ATLAS
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for E Gamma
atlas-wg-Exotics
PIRobert William Gardner Jr
OrganizationATLAS
DepartmentATLAS
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered10/29/2015
Abstract of workWe study exotics.
atlas-wg-Flavour-Tagging
PIRobert William Gardner Jr
OrganizationUS ATLAS
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Flavour Tagging
atlas-wg-Heavy-Ions
PIRobert William Gardner Jr
OrganizationUS ATLAS
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Heavy Ions
atlas-wg-Higgs
PIRobert William Gardner Jr
OrganizationUS ATLAS
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Higgs
atlas-wg-Inner-Tracking
PIRobert William Gardner Jr
OrganizationUS ATLAS
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Inner Tracking
atlas-wg-Monte-Carlo
PIRobert William Gardner Jr
OrganizationUS ATLAS
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Monte Carlo
atlas-wg-Standard-Model
PIRobert William Gardner Jr
OrganizationUS ATLAS
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Standard Model
atlas-wg-SUSY
PIRobert William Gardner Jr
OrganizationUS ATLAS
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for SUSY
atlas-wg-Top
PIRobert William Gardner Jr
OrganizationUS ATLAS
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered11/10/2015
Abstract of workATLAS Connect team for Top
atlas-wg-USAtlas-TechSupport
PIRobert William Gardner Jr
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of ScienceHigh Energy Physics
SponsorCG ATLAS Connect
Date Registered03/08/2016
Abstract of workAtlas Connect training project
AtlasConnect
PIRobert William Gardner Jr
OrganizationUniversity of Chicago
DepartmentComputation and Enrico Fermi Institutes
Field of ScienceHigh Energy Physics
SponsorCG OSG Connect
Date Registered09/25/2013
Abstract of workTo 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.
BakerLab
PIDavid Baker
OrganizationUniversity of Washington
DepartmentMolecular Engineering and Sciences
Field of ScienceMolecular and Structural Biosciences
SponsorVO OSG
Date Registered02/26/2016
Abstract of workProtein folding
BGAgenomics
PISucheta Tripathy
OrganizationIndian Institute of Chemical Biology
DepartmentStructural Biology and Bioinformatics division
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered08/03/2015
Abstract of workThis is a cyanobacteria genomics program
BioAlgorithms
PINatasha Pavlovikj
OrganizationUniversity of Nebraska - Lincoln
DepartmentComputer Science
Field of ScienceBioinformatics
SponsorVO HCC
Date Registered04/27/2017
Abstract of workAlgorithmic development for Bioinformatics
BioGraph
PIAlex Feltus
OrganizationClemson University
DepartmentGenetics & Biochemistry
Field of ScienceBiological Sciences
SponsorCG OSG Connect
Date Registered07/06/2015
Abstract of workConstructing gene interaction graphs at high scale
BioMolMach
PIBenoit Roux
OrganizationUniversity of Chicago
DepartmentBiology
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG Connect
Date Registered07/07/2014
Abstract of workThe 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.
BioStat
PIJanice McCarthy
OrganizationDuke University
DepartmentMedical Center
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered09/25/2013
Abstract of workBioinformatics and biostatistics for genetic risk factors at the Duke Medical Center.
BNL-PHENIX
PIMatthew Snowball
OrganizationBrookhaven National Laboratory
DepartmentPhysics Department
Field of ScienceNuclear Physics
SponsorVO OSG
Date Registered11/25/2014
Abstract of workRunning HEP/NP Monte Carlo simulations for the collaboration of the PHENIX detector at Relativistic Heavy Ion Collider (RHIC) at BNL.
BNLPET
PIMartin Purschke
OrganizationBrookhaven National Laboratory
DepartmentPhysics Department
Field of ScienceMedical Sciences
SponsorVO OSG
Date Registered08/20/2013
Abstract of workPositron 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/ .
boostconf
PIDavid Wilkins Miller
OrganizationUniversity of Chicago
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG OSG Connect
Date Registered11/14/2014
Abstract of workProject for data sharing and analysis of boosted object physics and jet phenomenology for topics discussed in the BOOST Conference Series
CentaurSim
PINathan Kaib
OrganizationNorthwestern University
DepartmentPhysics and Astronomy
Field of ScienceAstrophysics
SponsorCG OSG Connect
Date Registered08/14/2014
Abstract of workCentaurs 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.
cgdna
PIJuan J de Pablo
OrganizationUniversity of Chicago
DepartmentInstitute of Molecular Engineering
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG Connect
Date Registered04/08/2015
Abstract of workMolecular-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.
cgl
PIJason H. Moore
OrganizationUniversity of pennsylvania
DepartmentBiostatistics and Epidemiology
Field of ScienceBiological Sciences
SponsorCG OSG Connect
Date Registered05/11/2015
Abstract of workWe use machine learning to look for complex epistatic interactions associated with disease risk. Website: http://www.epistasis.org
CGS
PIPanthea Sepehrband
OrganizationSanta Clara University
DepartmentMechanical Engineering
Field of ScienceMaterials Science
SponsorCG OSG Connect
Date Registered11/18/2015
Abstract of workProject 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.
CHomP
PIKonstantin Mischaikow
OrganizationRutgers, The State University of New Jersey
DepartmentMathematics
Field of ScienceMathematical Sciences
SponsorCG OSG Connect
Date Registered05/12/2015
Abstract of workOur 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.
Clemson
PIMarcin Ziolkowski
OrganizationClemson University
DepartmentComputational Science
Field of ScienceMulti-Science Community
SponsorCG OSG Connect
Date Registered03/11/2016
Abstract of workHTC training for the computational scientist at Clemson University.
ClusterJob
PIHatef Monajemi
OrganizationStanford University
DepartmentStatistics
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG Connect
Date Registered03/14/2017
Abstract of workClusterJob is a project for 'painless massive computational experiments'. Visit www.clusterjob.org
cms-org-baylor
PIKenichi Hatakeyama
OrganizationBaylor University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Baylor University
cms-org-brown
PIMeenakshi Narain
OrganizationBrown University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Brown University
cms-org-bu
PIJim Rohlf
OrganizationBoston University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Boston University
cms-org-buffalo
PIAvto Kharchilava
OrganizationSUNY Buffalo
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at State University of New York at Buffalo
cms-org-caltech
PIHarvey Newman
OrganizationCaltech
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Caltech
cms-org-cern
PIAchille Petrilli
OrganizationCERN
DepartmentPhysics
Field of ScienceParticle Physics
SponsorCG CMS Connect
Date Registered10/11/2016
Abstract of workCMS Connect group for CERN
cms-org-cmu
PIManfred Paulini
OrganizationCarnegie-Mellon University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Carnegie-Mellon University
cms-org-colorado
PIDouglas Johnson
OrganizationUniversity of Colorado Boulder
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered02/25/2015
Abstract of workCMS Connect project for University of Colorado
cms-org-cornell
PIJim Alexander
OrganizationCornell University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Cornell University
cms-org-fairfield
PIDave Winn
OrganizationFairfield
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Fairfield
cms-org-fit
PIMarc Baarmand
OrganizationFlorida Institute of Technology
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Florida Institute of Technology
cms-org-fiu
PIPete Markowitz
OrganizationFlorida International University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Florida International University
cms-org-fnal
PILothar Bauerdick
OrganizationFermi National Accelerator Laboratory
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered02/25/2015
Abstract of workCMS Connect group for FNAL
cms-org-fsu
PITodd Adams
OrganizationFlorida State University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Florida State University
cms-org-jhu
PIMorris Swartz
OrganizationJohns Hopkins University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Johns Hopkins University
cms-org-ksu
PIYurii Maravin
OrganizationKansas State University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Kansas State University
cms-org-ku
PIAlice Bean
OrganizationThe University of Kansas
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at The University of Kansas
cms-org-llnl
PIDoug Wright
OrganizationLawrence Livermore National Laboratory
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Lawrence Livermore National Laboratory
cms-org-mit
PIChristoph Paus
OrganizationMassachusetts Institute of Technology
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Massachusetts Institute of Technology
cms-org-nd
PIKevin Lannon
OrganizationUniversity of Notre Dame
DepartmentHigh Energy Physics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered01/05/2015
Abstract of workCMS Connect at Notre Dame
cms-org-neu
PIEmanuela Barbaris
OrganizationNortheastern University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Northeastern University
cms-org-northwestern
PIMayda Velasco
OrganizationNorthwestern University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Northwestern University
cms-org-ohiostate
PIStan Durkin
OrganizationOhio State University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS connect at Ohio State University
cms-org-olemiss
PILucien Cremaldi
OrganizationUniversity of Mississipi
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at University of Mississipi
cms-org-princeton
PIDan Marlow
OrganizationPrinceton University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Princeton University
cms-org-purdue
PINorbert Neumeister
OrganizationPurdue University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Purdue University
cms-org-purduecal
PINeeti Parashar
OrganizationPurdue University Calumet
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Purdue University Calumet
cms-org-rice
PIJay Roberts
OrganizationRice University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Rice University
cms-org-rochester
PIRegina Demina
OrganizationUniversity of Rochester
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at University of Rochester
cms-org-rockefeller
PIDino Goulianos
OrganizationRockefeller University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Rockefeller University
cms-org-rutgers
PIAmit Lath
OrganizationRutgers University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Rutgers University
cms-org-tamu
PIAlexei Safonov
OrganizationTexas A&M University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Texas A&M University
cms-org-ttu
PINural Akchurin
OrganizationTexas Tech University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Texas Tech University
cms-org-ua
PIConor Henderson
OrganizationUniversity of Alabama
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at University of Alabama
cms-org-ucdavis
PIJohn Conway
OrganizationUC Davis
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at University of California, Davis
cms-org-ucla
PIJay Hauser
OrganizationUCLA
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Universify of California, Los Angeles
cms-org-ucr
PIGail Hanson
OrganizationUCR
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at University of California, Riverside
cms-org-ucsb
PIJoe Incandela
OrganizationUCSB
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at University of California, Santa Barbara
cms-org-ucsd
PIFrank Wuerthwein
OrganizationUniversity of California, San Diego
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered02/25/2015
Abstract of workCMS Connect group for UCSD
cms-org-ufl
PIGena Mitselmakher
OrganizationUniversity of Florida
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at University of Florida
cms-org-uic
PINikos Varelas
OrganizationUniversity of Illinois at Chicago
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at University of Illinois at Chicago
cms-org-uiowa
PIYasar Onel
OrganizationUniversity of Iowa
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at University of Iowa
cms-org-umd
PIAndris Skuja
OrganizationUniversity of Maryland
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at University of Maryland
cms-org-umn
PIRoger Rusack
OrganizationUniversity of Minnesota
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at University of Minnesota
cms-org-unl
PIKenneth Bloom
OrganizationUniversity of Nebraska-Lincoln
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered02/25/2015
Abstract of workCMS Connect group for UNL
cms-org-upr
PIMalik Sudhir
OrganizationUniversity of Puerto Rico
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at University of Puerto Rico
cms-org-utk
PIStefan Spanier
OrganizationUniversity of Tennessee
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at University of Tennessee
cms-org-vanderbilt
PIWill Johns
OrganizationVanderbilt University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at Vanderbilt University
cms-org-virginia
PIBrad Cox
OrganizationUniversity of Virginia
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at University of Virginia
cms-org-wayne
PIPaul Karchin
OrganizationWayne State University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workWayne State University
cms-org-wisc
PIWesley Smith
OrganizationUniversity of Wisconsin
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG CMS Connect
Date Registered10/22/2015
Abstract of workCMS Connect at University of Wisconsin
CombinedPS
PIOzkan Celik
OrganizationColorado School of Mines
DepartmentMechanical Engineering
Field of ScienceBiological and Critical Systems
SponsorCG OSG Connect
Date Registered01/04/2017
Abstract of workDesign 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.
CometCloud
PIJavier Diaz-Montes
OrganizationRutgers
DepartmentElectrical and Computer Engineering
Field of ScienceComputer and Information Science and Engineering
SponsorVO OSG
Date Registered11/27/2013
Abstract of workCometCloud 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.
CompChem
PIChaoren Liu
OrganizationDuke University
DepartmentChemistry
Field of ScienceChemistry
SponsorCG OSG Connect
Date Registered09/25/2013
Abstract of workModeling and simulation of molecules.
compcomb
PIDerrick Stolee
OrganizationIowa State University
DepartmentMathematics
Field of ScienceMathematical Sciences
SponsorVO HCC
Date Registered06/27/2014
Abstract of workComputational Combinatorics uses significant computational resources to solve problems in combinatorics, graph theory, and discrete mathematics.
CompNeuro
PIPo-He Tseng
OrganizationDuke University
DepartmentNeurobiology
Field of ScienceNeuroscience
SponsorCG OSG Connect
Date Registered09/25/2013
Abstract of workTo 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.
ConnectTrain
PIRobert William Gardner Jr
OrganizationUniversity of Chicago
DepartmentComputation and Enrico Fermi Institutes
Field of ScienceTraining
SponsorCG OSG Connect
Date Registered09/25/2013
Abstract of workOSG Connect training activity.
ContinuousIntegration
PIRobert William Gardner Jr
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of ScienceTechnology
SponsorCG OSG Connect
Date Registered07/16/2014
Abstract of workProvides continuous build and test services for OSG Connect via Jenkins.
CotranslationalFolding
PIEdward O'Brien
OrganizationThe Pennsylvania State University
DepartmentChemistry
Field of ScienceBiophysics
SponsorVO OSG
Date Registered07/25/2014
Abstract of workThere 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.
CpDarkMatterSimulation
PIChristoph Paus
OrganizationMIT
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorVO OSG
Date Registered03/10/2016
Abstract of workGenerate a grid of Monte Carlo samples to be used in collider-based searches for dark matter
DataTrieste
PIRob Quick
OrganizationInternational Center for Theoretical Physics
DepartmentEducation
Field of ScienceMulti-Science Community
SponsorVO OSG
Date Registered08/04/2016
Abstract of workCODATA/RDA Summer School on Research Data Science
DBConcepts
PIRichard Jean So
OrganizationUniversity of Chicago
DepartmentInterdisciplinary
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG Connect
Date Registered02/05/2014
Abstract of workWe're conducting a network analysis of a 10% sample (1.6TB; 3.6m files) of the Google Books corpus.
DeepMail
PIMicheal Marasco
OrganizationNorthwestern University
DepartmentFarley Center for Entrepreneurship and Innovation
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG Connect
Date Registered04/27/2017
Abstract of workTo 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.
DeerDisease
PILene Jung Kjaer
OrganizationSouthern Illinois University
DepartmentDepartment of Zoology
Field of ScienceBiological Sciences
SponsorVO OSG
Date Registered12/04/2013
Abstract of workI 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.
DelhiWorkshop2015
PIRobert William Gardner Jr
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of SciencePhysics
SponsorCG OSG Connect
Date Registered03/10/2015
Abstract of workWorkshop at Delhi
DemandSC
PIFernando Luco
OrganizationTexas A&M University, University of Illinois at Urbana-Champaign
DepartmentEconomics
Field of ScienceEconomics
SponsorCG OSG Connect
Date Registered08/03/2015
Abstract of workWe 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
DetectorDesign
PIJohn Strologas
OrganizationUniversity of New Mexico
DepartmentPhysics and Astronomy
Field of ScienceMedical Sciences
SponsorVO OSG
Date Registered08/15/2013
Abstract of workInvestigate how different simulated SPECT system geometries can affect reconstructed images.
duke-4fermion
PIShailesh Chandrasekharan
OrganizationDuke University
DepartmentPhysics Department
Field of ScienceHigh Energy Physics
SponsorCG Duke
Date Registered01/13/2014
Abstract of workWe 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.
duke-bgswgs
PIHai Yan
OrganizationDuke University
DepartmentPathology
Field of ScienceBioinformatics
SponsorCG Duke
Date Registered12/15/2016
Abstract of workTo study the genomic and genetic aspects of brainstem gliomas
duke-boolnet
PIDaniel Gauthier
OrganizationDuke University
DepartmentPhysics
Field of SciencePhysics
SponsorCG Duke
Date Registered02/09/2016
Abstract of workExperimental Boolean networks built on FPGAs, with the purpose of studying the fundamental dynamical properties of complex
duke-campus
PITom Milledge
OrganizationDuke University
DepartmentScalable Computing Suport Center-OIT
Field of ScienceCommunity Grid
SponsorCG Duke
Date Registered01/30/2014
Abstract of workDefault project for new Duke users
duke-CMT
PIHarold U. Baranger
OrganizationDuke University
DepartmentPhysics
Field of ScienceComputational Condensed Matter Physics
SponsorCG Duke
Date Registered08/16/2016
Abstract of workWe 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.
duke-duke-campus
PITom Milledge
OrganizationDuke University
DepartmentIT
Field of ScienceCommunity Grid
SponsorCG Duke
Date Registered02/01/2017
Abstract of workduke campus project
duke-EfficientScore
PIKonosuke Iwamoto
OrganizationDuke University
DepartmentBiostatistics
Field of ScienceStatistics
SponsorCG Duke
Date Registered02/01/2017
Abstract of workWe will benchmark various algorithms to benchmark the efficient score.
Duke-QGP
PISteffen A. Bass
OrganizationDuke University
DepartmentPhysics
Field of ScienceNuclear Physics
SponsorVO OSG
Date Registered08/28/2013
Abstract of workEvent-by-event simulations of relativistic heavy-ion collisions. QGP characterization via model-to-data comparison.
duke-staff
PITom Milledge
OrganizationDuke University
DepartmentIT
Field of ScienceCommunity Grid
SponsorCG Duke
Date Registered02/01/2017
Abstract of workcampus project
duke-SWC-Duke15
PIMark R. DeLong
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of ScienceMulti-Science Community
SponsorCG Duke
Date Registered01/08/2016
Abstract of workTraining Workshop
duke-swcstaff
PIMark R. DeLong
OrganizationDuke University
DepartmentOffice of Information Technology
Field of ScienceMulti-Science Community
SponsorCG Duke
Date Registered09/29/2015
Abstract of workDuke Software Carpentry Workshop from Oct 27th to Oct 29th 2015 http://swc-osg-workshop.github.io/2015-10-27-duke/index.html
duke-WaterCrystal
PIPatrick Charbonneau
OrganizationDuke University
DepartmentChemistry
Field of ScienceBiochemistry
SponsorCG Duke
Date Registered07/16/2014
Abstract of workWater structure in protein crystals
dVdT
PIEwa Deelman
OrganizationUniversity of Southern California
DepartmentInformation Sciences Institute
Field of ScienceComputer and Information Science and Engineering
SponsorVO OSG
Date Registered06/06/2014
Abstract of workThe 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.
ECFA
PIMeenakshi Narain
OrganizationBrown University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorVO OSG
Date Registered08/16/2013
Abstract of workSimulate 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.
EDFCHT
PIJianghao Chu
OrganizationUC Riverside
DepartmentEconomics
Field of ScienceEconomics
SponsorCG OSG Connect
Date Registered08/26/2016
Abstract of workThe 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.
EHEC
PIChuck Kaspar
OrganizationUniversity of Wisconsin-Madison
DepartmentBacteriology
Field of ScienceMicrobiology
SponsorCG OSG Connect
Date Registered09/23/2015
Abstract of workProject 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.
EIC
PITobias Toll
OrganizationBrookhaven National Laboratory
DepartmentPhysics Department
Field of ScienceHigh Energy Physics
SponsorVO OSG
Date Registered08/20/2013
Abstract of workElectron 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
EmpModNatGas
PIAshley Vissing
OrganizationUniversity of Chicago
DepartmentEconomics
Field of ScienceEconomics
SponsorCG OSG Connect
Date Registered09/27/2016
Abstract of workI 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.
errorstudy
PIChristopher Richards
OrganizationUSDA Agricultural Research Service
DepartmentNational Center for Genetic Resources Preservation
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG Connect
Date Registered11/14/2014
Abstract of workMissing 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.
ERVmodels
PIFabricia Nascimento
OrganizationUniversity of Oxford
DepartmentDepartment of Zoology
Field of ScienceZoology
SponsorCG OSG Connect
Date Registered10/06/2015
Abstract of workProject 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.
evolmarinva
PIErik Sotka
OrganizationCollege of Charleston
DepartmentDepartment of Biology
Field of ScienceEvolutionary Sciences
SponsorCG OSG Connect
Date Registered03/20/2017
Abstract of workOur group uses genomic tools to understand the evolutionary process of marine invasions.
EvolSims
PIOana Carja
OrganizationUniversity of Pennsylvania
DepartmentBiology
Field of ScienceBiological Sciences
SponsorCG OSG Connect
Date Registered06/26/2015
Abstract of workEvolutionary simulation tracking gene frequencies under a variety of environmental conditions.
EvolvingAI
PIJeff Clune
OrganizationUniversity of Wyoming
DepartmentComputer Science
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG Connect
Date Registered08/11/2015
Abstract of workModern 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.
EvoProtDrug
PIMilo Lin
OrganizationUT Southwestern
DepartmentGreen Center for Systems Biology
Field of ScienceBiophysics
SponsorCG OSG Connect
Date Registered08/22/2016
Abstract of workLittle 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.
EvoTheory
PIChristina Burch
OrganizationUniversity of North Carolina at Chapel Hill
DepartmentBiology
Field of ScienceEvolutionary Sciences
SponsorCG OSG Connect
Date Registered09/25/2013
Abstract of workLinkage 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.
ExhaustiveSearch
PISam Volchenboum
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered03/28/2014
Abstract of workExhaustiveSearch (or ExSearch) is a machine learning application tuned to analyze class-labeled data using n-tuple feature vectors.
FFValidate
PIVijay Pande
OrganizationStanford University
DepartmentDepartment of Chemistry
Field of ScienceChemistry
SponsorCG OSG Connect
Date Registered06/25/2014
Abstract of workThis 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.
fluidsim
PIErkan Tuzel
OrganizationWorcester Polytechnic Institute
DepartmentPhysics
Field of SciencePhysics
SponsorCG OSG Connect
Date Registered03/09/2016
Abstract of workIn this project we study fluid/structure interactions using a novel particle-based fluid simulation technique.
freesurfer
PIDonald Krieger
OrganizationUniversity of Pittsburgh
DepartmentDepartment of Neurological Surgery
Field of ScienceNeuroscience
SponsorCG OSG Connect
Date Registered11/06/2015
Abstract of workBrain image analysis with free surfer software
FRISpoilageProject
PIChuck Kaspar
OrganizationUniversity of Wisconsin Madison
DepartmentMicrobiology
Field of ScienceMicrobiology
SponsorCG OSG Connect
Date Registered09/19/2016
Abstract of workWe 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)
FutureColliders
PISergei Chekanov
OrganizationArgonne National Lab
DepartmentHigh Energy Physics
Field of ScienceHigh Energy Physics
SponsorCG OSG Connect
Date Registered08/27/2015
Abstract of workStudies 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
gem5
PIDean Tullsen
OrganizationUniversity of California San Diego
DepartmentComputer Science and Engineering
Field of ScienceMulti-Science Community
SponsorCG OSG Connect
Date Registered02/23/2015
Abstract of workThe 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.
Genie
PIGabriel Nathan Perdue
OrganizationFermilab
DepartmentScientific Computing Simulation
Field of ScienceHigh Energy Physics
SponsorVO Fermilab
Date Registered12/16/2014
Abstract of workGenerates 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.
GenomicIntegration
PICasey Greene
OrganizationDartmouth College
DepartmentGenetics
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered05/13/2015
Abstract of workIntegration of publicly available large-scale genomic data.
GeoTunnel
PIElena Guardincerri
OrganizationLas Alamos National Lab
DepartmentPhysics
Field of ScienceNuclear Physics
SponsorCG OSG Connect
Date Registered06/16/2016
Abstract of workAnalyzing muon data to obtain information about the objects they traversed.
GlassySystems
PIDavid Reichman
OrganizationColumbia University
DepartmentChemistry
Field of ScienceChemistry
SponsorCG OSG Connect
Date Registered09/25/2013
Abstract of workStudies 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.
GLUEX
PIKurt Johann Strosahl
OrganizationJLAB
DepartmentPhysics
Field of ScienceNuclear Physics
SponsorVO JLab
Date Registered03/23/2017
Abstract of workGlueX project
GRASP
PIRichard Irving
OrganizationUniversity of Toledo
DepartmentPhysics
Field of SciencePhysics and astronomy
SponsorCG OSG Connect
Date Registered07/01/2014
Abstract of workAtomic structure calculations based on multiconfiguration Dirac–Hartree–Fock theory utilizing Grasp2k, a general-purpose relativistic atomic structure package.
gridsgenomes
PIDavid Rhee
OrganizationAlbert Einstein College of Medicine
DepartmentGenetics
Field of ScienceBiological Sciences
SponsorVO OSG
Date Registered11/25/2013
Abstract of workThe 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.
Groundhog
PIEric Halgren
OrganizationUniversity of California San Diego
DepartmentSchool of Medicine
Field of ScienceNeuroscience
SponsorCG OSG Connect
Date Registered01/06/2017
Abstract of workDefine 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.
GTConvertHTC
PIMehmet Belgin
OrganizationGeorgia Tech
DepartmentAdvanced Research Computing
Field of ScienceMulti-Science Community
SponsorCG OSG Connect
Date Registered07/20/2016
Abstract of workhelp GT researchers convert their existing projects into HTC workloads
hABCNWHI
PIYvonne Chan
OrganizationIolani School
DepartmentBiology
Field of ScienceBiological Sciences
SponsorCG OSG Connect
Date Registered11/27/2015
Abstract of workHierarchical 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.
HCCLocalSubmit
PIDavid Swanson
OrganizationUniversity of Nebraska
DepartmentHolland Computing Center
Field of ScienceCommunity Grid
SponsorVO HCC
Date Registered09/12/2016
Abstract of workJobs from our clusters that flock to the OSG
HealthInformatics
PIKarl Jablonowski
OrganizationUniversity of Washington
DepartmentBiomedical and Health Informatics
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered08/24/2016
Abstract of workMy 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.
HL-LHC-TP
PIMeenakshi Narain
OrganizationBrown University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorVO OSG
Date Registered03/12/2014
Abstract of workSimulate 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.
holosim
PIAllan Strand
OrganizationCollege of Charleston
DepartmentBiology
Field of ScienceEvolutionary Sciences
SponsorCG OSG Connect
Date Registered01/23/2017
Abstract of worksimulations of population genetics in 2d landscapes
HTCC
PIRob Quick
OrganizationIndiana University
DepartmentResearch Technologies
Field of ScienceCommunity Grid
SponsorVO OSG
Date Registered04/01/2014
Abstract of workThis project will be used for the OSG AHM HTC Challenge. It may also be the home of future challenges.
HypergraphDegreeSeq
PISarah Lynne Behrens
OrganizationUniversity of Nebraska - Lincoln
DepartmentMathematics
Field of ScienceMathematical Sciences
SponsorVO HCC
Date Registered02/26/2015
Abstract of workA 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.
IBN130001-Plus
PIDonald Krieger
OrganizationUniversity of Pittsburgh
DepartmentNeurosurgery
Field of ScienceNeuroscience
SponsorCG OSG-XSEDE
Date Registered01/25/2016
Abstract of workChild project of TG-IBN130001
IceCube
PIFrancis Halzen
OrganizationUniversity of Wisconsin
DepartmentPhysics
Field of ScienceAstrophysics
SponsorCG OSG Connect
Date Registered06/02/2014
Abstract of workIceCube 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.
idTrackerParallel
PIAndrew Ruether
OrganizationSwarthmore College
DepartmentITS
Field of ScienceEvolutionary Sciences
SponsorCG OSG Connect
Date Registered09/22/2016
Abstract of workRunning the idTracker software (http://www.idtracker.es/) in parallel on OSG.
IngaCFMID
PIThomas A. Kursar
OrganizationUniversity of Utah
DepartmentBiology
Field of ScienceBiological Sciences
SponsorCG OSG Connect
Date Registered03/01/2017
Abstract of workWe 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.
IRRI
PIMats Rynge
OrganizationUniversity of Southern Caliornia
DepartmentISI
Field of ScienceBioinformatics
SponsorCG ISI
Date Registered05/11/2016
Abstract of workCollaboration with the Rice3k IRRI project
IU-GALAXY
PIRob Quick
OrganizationIndiana University
DepartmentBioinformatics
Field of ScienceBioinformatics
SponsorVO CSIU
Date Registered08/20/2013
Abstract of workSubmitting blast queries via Galaxy portal on OSG resources.
IVSelection
PIHao Xu
OrganizationUniversity of California Riverside
DepartmentEconimics
Field of ScienceEconomics
SponsorCG OSG Connect
Date Registered10/06/2016
Abstract of workWe could like to preform instruments selection in the IV model by Machine Learning technique, and estimated the structure parameters by GMM method.
JediNetworks
PIBradley Voytek
OrganizationUniversity of California San Diego
DepartmentNeuroscience
Field of ScienceNeuroscience
SponsorCG OSG Connect
Date Registered04/04/2017
Abstract of workTraining recurrent neural nets on various tasks; discretizing the dynamics of the networks and observing changes in network stability, performance and topology.
KickstarterDataAnalysis
PIFeng Bill Shi
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of ScienceStatistics
SponsorCG OSG Connect
Date Registered05/07/2015
Abstract of workProject 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.
KnowledgeLab
PIJames Evans
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of ScienceOther
SponsorCG OSG Connect
Date Registered03/26/2014
Abstract of workKnowledge Lab / CI
KnowledgeSys
PIMichael J. Culbertson
OrganizationUniversity of Illinois, Urbana-Champaign
DepartmentPsychology
Field of ScienceEducational Psychology
SponsorCG OSG Connect
Date Registered09/25/2013
Abstract of workIn 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.
KORDrugdiscov
PIDavid Toth
OrganizationCentre College
DepartmentChemistry
Field of ScienceChemistry
SponsorCG OSG Connect
Date Registered04/18/2017
Abstract of workIt 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.
Leaderbipartite
PIJozsef Balogh
OrganizationUniversity of Illinois Urbana-Champaign
DepartmentMathematics
Field of ScienceMathematical Sciences
SponsorCG OSG Connect
Date Registered04/04/2017
Abstract of workLeader-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.
lftsim
PIJoel Giedt
OrganizationRensselaer Polytechnic Institute
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG OSG Connect
Date Registered10/04/2016
Abstract of workWe 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.
Lg-Attenuation
PIAndrea C Gallegos
OrganizationNew Mexico State University
DepartmentEarth Sciences
Field of ScienceEarth Sciences
SponsorCG OSG Connect
Date Registered03/02/2016
Abstract of workDetermine the attenuation of the regional shear wave Lg for NE China and the contiguous United States using broadband seismograms.
LIGO
PIPeter F. Couvares
OrganizationSyracuse University
DepartmentPhysics
Field of ScienceGravitational Physics
SponsorCG OSG Connect
Date Registered10/03/2014
Abstract of workGravitational Wave Astronomy
LiuLab
PIKevin Jensen Liu
OrganizationMichigan State University
DepartmentComputer Science and Engineering
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered07/07/2016
Abstract of workThe project goal is to create new computational methodologies for large-scale phylogenomic analyses involving complex evolutionary histories.
mab
PIVivek Farias
OrganizationMassachusetts Institute of Technology
DepartmentSloan School of Management
Field of ScienceInformation Theory
SponsorCG OSG Connect
Date Registered09/21/2015
Abstract of workDeveloping new policies for the (classical) Multi-Armed Bandit problem.
macsSwigmodels
PIAriella Gladstein
OrganizationUniversity of Arizona
DepartmentEcology and Evolutionary Biology
Field of ScienceEvolutionary Sciences
SponsorCG OSG Connect
Date Registered03/14/2017
Abstract of workEvery 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.
MaizeAminoAcids
PITimothy M Beissinger
OrganizationUniversity of Missouri
DepartmentDivison of Plant Sciences
Field of ScienceEvolutionary Sciences
SponsorCG OSG Connect
Date Registered03/20/2017
Abstract of workThe 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.
MCP
PIC. S. Raman
OrganizationUniversity of Maryland Baltimore
DepartmentPharmaceutical Sciences
Field of ScienceBiochemistry
SponsorCG OSG Connect
Date Registered07/16/2015
Abstract of workWe 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.
MCSpinLiquid
PIJohn McGreevy
OrganizationUniversity of California San Diego
DepartmentPhysics
Field of SciencePhysics
SponsorCG OSG Connect
Date Registered04/17/2017
Abstract of workPerform monte carlo simulation on spin liquid systems
MedInf
PIAlex Langerman
OrganizationThe University of Chicago
DepartmentOtolaryngology
Field of ScienceMedical Sciences
SponsorCG OSG Connect
Date Registered08/24/2016
Abstract of workAnalysis 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.
megaprobe
PIHumberto Ortiz-Zuazaga
OrganizationUniversity of Puerto Rico
DepartmentComputer Science
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG Connect
Date Registered10/13/2014
Abstract of workhigh performance sequence analysis
microphases
PIPatrick Charbonneau
OrganizationDuke University
DepartmentChemistry
Field of ScienceChemistry
SponsorCG OSG Connect
Date Registered11/04/2015
Abstract of workPeriodic 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.
MiniWorkshopUC15
PIRobert William Gardner Jr
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG Connect
Date Registered04/08/2015
Abstract of workOpen Science Grid Mini-Workshop at University of Chicago on April 9th 2015
MMHA
PIIkuo Takei
OrganizationUniversity of Wisconsin Madison
DepartmentEconomics
Field of ScienceEconomics
SponsorCG OSG Connect
Date Registered10/07/2016
Abstract of workThe 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.
molcryst
PIOlexandr Isayev
OrganizationUniversity of North Carolina at Chapel Hill
DepartmentChemistry
Field of ScienceChemistry
SponsorCG OSG Connect
Date Registered10/26/2016
Abstract of workQuantum chemical and machine learning insights into supra-molecular organization of molecular crystals.
MS-EinDRC
PIJacob Pessin
OrganizationAlbert Einstein College of Medicine
DepartmentEndocrinology
Field of ScienceMedical Sciences
SponsorCG OSG Connect
Date Registered12/23/2014
Abstract of workFor modeling and other computational projects of the Mt. Sinai-Einstein DRC and affiliates, primarily structurally related protein Modeling and Docking.
NapusGenome
PIJoel Bader
OrganizationJohns Hopkins University
DepartmentDepartment of Biomedical Engineering
Field of ScienceBiological Sciences
SponsorCG OSG Connect
Date Registered10/29/2014
Abstract of workAssembling the genome of a number of plant lines, and conducting RNASeq studies for the development of a transcriptome and differential expression analysis.
ncidft
PIAlberto Otero de la Roza
OrganizationNational Research Council of Canada
DepartmentNational Institute for Nanotechnology
Field of ScienceChemistry
SponsorCG OSG Connect
Date Registered09/09/2015
Abstract of workProject 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.
NCOppSchool
PIMichael Dinerstein
OrganizationThe University of Chicago
DepartmentEconomics
Field of ScienceEconomics
SponsorCG OSG Connect
Date Registered02/28/2017
Abstract of workStudying the effects of the North Carolina Opportunity Scholarship using a discrete choice model. The estimation recovers utility parameters for school choice using school enrollments.
ND-GALAXY
PISandra Gesing
OrganizationNotre Dame
DepartmentComputer Science and Engineering
Field of ScienceBioinformatics
SponsorVO CSIU
Date Registered09/18/2014
Abstract of workSubmitting blast queries via Notre Dame Galaxy portal on OSG resources.
NEESTools
PIFrank McKenna
OrganizationUC Berkeley
DepartmentCivil Engineering
Field of ScienceCivil Engineering
SponsorVO OSG
Date Registered05/20/2014
Abstract of workEarthquake 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.
NeoflAnnot
PIPetra Lenz
OrganizationUniversity of Hawaii at Manoa
DepartmentPacific Biosciences Research Center
Field of ScienceBiological Sciences
SponsorCG OSG Connect
Date Registered09/22/2015
Abstract of workGeneration of a transcriptome for the copepod Neocalanus flamingeri in the gulf of Alaska.
NESCent
PIFabricia Nascimento
OrganizationDuke University, The University of North Carolina at Chapel Hill, and North Carolina State University
DepartmentNESCent Center
Field of ScienceEvolutionary Sciences
SponsorCG OSG Connect
Date Registered09/25/2013
Abstract of workNESCent 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.
NeurOscillation
PIBradley Voytek
OrganizationUniversity of California San Diego
DepartmentCognitive Science
Field of ScienceNeuroscience
SponsorCG OSG Connect
Date Registered07/28/2016
Abstract of workOur 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?
nicesims
PINathan Kaib
OrganizationUniversity of Oklahoma
DepartmentPhysics and Astronomy
Field of SciencePhysics and astronomy
SponsorCG OSG Connect
Date Registered11/23/2016
Abstract of workThe 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.
Nipyperegtest
PISatrajit Ghosh
OrganizationMassachusetts Institute of Technology
DepartmentMcGovern Institute for Brain Research
Field of ScienceNeuroscience
SponsorCG OSG Connect
Date Registered03/13/2017
Abstract of workRegression testing of various brain imaging tools
NRELMatDB
PIPeter Graf
OrganizationNREL - National Renewable Energy Laboratory, Golden CO
DepartmentComputational Science Center
Field of ScienceMaterials Science
SponsorCG OSG Connect
Date Registered10/01/2013
Abstract of workAb initio calculation of the physical properties of 10^4 to 10^6 materials, database of results, and web site for access.
NSLS2ID
PIDean Andrew Hidas
OrganizationBrookhaven National Laboratory
DepartmentNational Synchrotron Light Source II
Field of ScienceHigh Energy Physics
SponsorCG OSG Connect
Date Registered09/02/2015
Abstract of workUsing 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.
NSNM
PIVadim Apalkov
OrganizationGeorgia State University
DepartmentDepartment of Physics and Astronomy
Field of SciencePhysics
SponsorCG OSG Connect
Date Registered01/04/2016
Abstract of workThis model uses Matlab parallel programming to predict noise sensitive neuronal model.
numfpi
PIJerry Tessendorf
OrganizationClemson University
DepartmentComputer Science
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG Connect
Date Registered08/03/2015
Abstract of workWe 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.
NWChem
PIManish Parashar
OrganizationRutgers University
DepartmentElectrical & Computer Engineering
Field of ScienceComputer and Information Science and Engineering
SponsorVO OSG
Date Registered11/07/2013
Abstract of workThe 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.
oclab
PIDave OConnor
OrganizationUniversity of Wisconsin
DepartmentSchool of Medical and Public Health
Field of ScienceMedical Sciences
SponsorCG OSG Connect
Date Registered07/30/2015
Abstract of workImmunology at OConner's lab
Orbiter
PIAnton Betten
OrganizationColorado State University
DepartmentDepartment of Mathematics
Field of ScienceMathematical Sciences
SponsorCG OSG Connect
Date Registered05/23/2014
Abstract of workThe 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.
OSG-CSC00100
PIGeorge Rudolph
OrganizationThe Citadel
DepartmentMathematics and Computer Science
Field of ScienceComputer and Information Science and Engineering
SponsorVO OSG
Date Registered08/14/2013
Abstract of workDevelop 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.
OSG-Staff
PIChander Sehgal
OrganizationFermilab
DepartmentComputing Sector
Field of ScienceComputer and Information Science and Engineering
SponsorVO OSG
Date Registered08/15/2013
Abstract of workIntegration and testing of science applications for new users
OSGOpsTrain
PIRob Quick
OrganizationOpen Science Grid
DepartmentGOC
Field of ScienceCommunity Grid
SponsorCG OSG Connect
Date Registered06/05/2014
Abstract of workTraining project for OSG Operations staff.
P0-LBNE
PIMaxim Potekhin
OrganizationBrookhaven National Laboratory
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorVO OSG
Date Registered02/03/2014
Abstract of workLBNE 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.
PainDrugs
PIPei Tang
OrganizationUniversity of Pittsburgh
DepartmentAnesthesiology
Field of ScienceMedical Sciences
SponsorCG OSG Connect
Date Registered04/14/2015
Abstract of workVirtual screening for novel anesthetic compounds.
Paniceae-trans
PIJacob Washburn
OrganizationUniversity of Missouri
DepartmentBiological Sciences
Field of ScienceEvolutionary Sciences
SponsorCG OSG Connect
Date Registered10/16/2015
Abstract of workProcessing of Transcriptome data from many species across the grass tribe Paniceae
PathSpaceHMC
PIFrank Pinski
OrganizationUniversity of Cincinnati
DepartmentPhysics
Field of ScienceComputational Condensed Matter Physics
SponsorCG OSG Connect
Date Registered09/25/2013
Abstract of workThe 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.
PBOSD
PIYong Li
OrganizationUC San Diego
DepartmentStructural Engineering
Field of ScienceCivil Engineering
SponsorCG OSG Connect
Date Registered09/15/2016
Abstract of workProbability-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.
PCFOSGUCSD
PIFrank Wuerthwein
OrganizationUniversity of California San Diego
DepartmentPhysics Department
Field of SciencePhysics
SponsorCG UCSD
Date Registered10/03/2016
Abstract of workWork submitted as part of the physics computing facility (PCF) at the physics department at UCSD
peers
PIJessica Sidler Folsom
OrganizationFlorida State University
DepartmentFlorida Center for Reading Research
Field of ScienceEcological and Environmental Sciences
SponsorCG OSG Connect
Date Registered09/02/2015
Abstract of workThis 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.
PegasusTraining
PIMats Rynge
OrganizationUSC
DepartmentISI
Field of ScienceComputer and Information Science and Engineering
SponsorCG ISI
Date Registered10/20/2015
Abstract of workProject used for Pegasus tutorials and training
Perchlorate
PIJustin M Hutchison
OrganizationUniversity of Illinois
DepartmentCivil and Environmental Engineering
Field of ScienceEngineering
SponsorCG OSG Connect
Date Registered04/12/2016
Abstract of workAssessment of costs and environmental impacts of drinking water technologies for the removal of perchlorate
Pheno
PIStefan Hoeche
OrganizationSLAC
DepartmentTheory Group
Field of ScienceHigh Energy Physics
SponsorVO OSG
Date Registered01/20/2014
Abstract of workThe 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
Phylo
PISiavash Mirarab
OrganizationUC San Diego
DepartmentElectrical and Computer Engineering
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered08/28/2015
Abstract of workIn 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.
Phylogenomics
PINathan G Swenson
OrganizationUniversity of Maryland
DepartmentDepartment of Biology
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered05/11/2015
Abstract of workThe 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.
pipediffusion
PIPanthea Sepehrband
OrganizationSanta Clara University
DepartmentMechanical
Field of ScienceMaterials Science
SponsorCG OSG Connect
Date Registered11/03/2015
Abstract of workA molecular dynamics study (LAMMPS) of diffusion along the core of a screw dislocation is to be studied.
PlantBio
PIJoy Bergleson
OrganizationUniversity of Chicago
DepartmentEcology and Evolution
Field of SciencePlant Biology
SponsorCG OSG Connect
Date Registered10/01/2013
Abstract of workInvestigation of plant-pathogen interactions using genome-wide association mapping.
POLARBEAR
PIBrian Keating
OrganizationUniversity of California - San Diego
DepartmentPhysics
Field of ScienceAstrophysics
SponsorCG OSG Connect
Date Registered04/14/2016
Abstract of workThe 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.
polyHERV
PIGkikas Magiorkinis
OrganizationUniversity of Oxford
DepartmentZoology
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered02/01/2016
Abstract of workFine-mapping of human endogenous retrovirus polymorphisms
poromech
PIStephen Moysey
OrganizationClemson University
DepartmentEnvironmental Engineering and Earth Sciences
Field of ScienceEcological and Environmental Sciences
SponsorCG OSG Connect
Date Registered06/02/2016
Abstract of workIn 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.
PreBioEvo
PIJ. Woods Halley
OrganizationUniversity of Minnesota
DepartmentPhysics
Field of ScienceBiophysics
SponsorCG OSG Connect
Date Registered02/11/2016
Abstract of workWe 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)
ProbTracx
PIDr. Bruce P. Hermann
OrganizationUniversity of Wisconsin
DepartmentDepartment of Neurology
Field of ScienceNeuroscience
SponsorCG OSG Connect
Date Registered08/03/2015
Abstract of workGraph 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.
Proteomics
PISam Volchenboum
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered05/27/2014
Abstract of workBioinformatics methods for different proteomic applications in life sciences. Algorithm development for improving mass-spectrometry based proteomic techniques.
ProtEvol
PIPremal Shah
OrganizationUniversity of Pennsylvania
DepartmentBiology
Field of ScienceEvolutionary Sciences
SponsorCG OSG Connect
Date Registered02/23/2015
Abstract of workHow 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.
ProtFolding
PIJinbo Xu
OrganizationToyota Technological Institute at Chicago
DepartmentComputer Science
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered06/06/2014
Abstract of workStudy statistical machine learning and optimization algorithms for data-driven protein structure prediction, by learning sequence-structure relationship from existing protein sequence and structure data.
PRTH
PIEndre Takacs
OrganizationClemson University
DepartmentAstronomy and Physics
Field of SciencePhysics
SponsorCG OSG Connect
Date Registered04/28/2016
Abstract of workModeling 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
psims
PIJoshua Elliott
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of ScienceEarth Sciences
SponsorCG OSG Connect
Date Registered10/21/2014
Abstract of workA 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.
PTMC
PIDerek Dolney
OrganizationUniversity of Pennsylvania
DepartmentRadiation Oncology
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG Connect
Date Registered01/04/2016
Abstract of workWe 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.
QEvolBiol
PIJeremy Van Cleve
OrganizationUniversity of Kentucky
DepartmentBiology
Field of ScienceBiological and Critical Systems
SponsorCG OSG Connect
Date Registered09/22/2015
Abstract of workQuantitative 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.
QGIS
PIPatricia Carbajales-Dale
OrganizationClemson University
DepartmentClemson Center for Geospatial Technologies
Field of ScienceGeographic Information Science
SponsorCG OSG Connect
Date Registered08/03/2016
Abstract of workThis project is created to explore QGIS and analyze solar suitability in South Carolina.
QMC
PIAndrew Powell
OrganizationMissouri University of Science and Technology
DepartmentChemistry
Field of ScienceChemistry
SponsorCG OSG Connect
Date Registered08/24/2016
Abstract of workOur project uses Quantum Monte Carlo (QMC) methods for energy calculations on molecular systems of interest.
RADICAL
PIShantenu Jha
OrganizationRutgers University
DepartmentComputer Science
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG Connect
Date Registered11/26/2013
Abstract of workRADICAL: SAGA / BigJob OSG / XSEDE interoperability and Python APIs for OSG / Condor / iRODS.
RDCEP
PIIan Foster
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of ScienceEconomics
SponsorCG OSG Connect
Date Registered09/25/2013
Abstract of workRobust 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.
REDTOP
PICorrado Gatto
OrganizationFermi National Accelerator Lab
DepartmentParticle Physics
Field of ScienceHigh Energy Physics
SponsorCG OSG Connect
Date Registered07/22/2016
Abstract of workHigh intensity frontier experiment searching for physics beyond the Standard Model
RicePhenomics
PIHarkamal Walia
OrganizationUniversity of Nebraska Lincoln
DepartmentAgronomy
Field of ScienceBiological Sciences
SponsorCG OSG Connect
Date Registered05/28/2015
Abstract of workAnalysis of salinity tolerance in rice.
RIT
PIStanisław P. Radziszowski
OrganizationRochester Institute of Technology
DepartmentComputer Science
Field of ScienceComputer and Information Science and Engineering
SponsorVO OSG
Date Registered08/19/2013
Abstract of workRamsey 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.
SbGenome
PIDave Denlinger
OrganizationOhio State University
DepartmentDepartment of Evolution, Ecology, and Organismal Biology
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered09/15/2014
Abstract of workThe Sarcophaga bullata Genome Project seeks to assemble and annotate the genome of Sarcophaga bullata, an important model for cold tolerance and diapause.
SBGrid
PIPiotr Sliz
OrganizationHarvard Medical School
DepartmentBiological Chemistry and Molecular Pharmacology
Field of ScienceBiochemistry
SponsorCG OSG Connect
Date Registered04/18/2014
Abstract of workSBGrid work using OSG Connect
scicomp-analytics
PIRobert William Gardner Jr
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of ScienceMulti-Science Community
SponsorCG OSG Connect
Date Registered06/18/2014
Abstract of workDevelopment of collection, aggregation, filtering and analysis of probes and metrics as related to distributed computation on the Open Science Grid.
SciSim
PIAmit Goel
OrganizationUniversity of Central Florida
DepartmentAdvanced Research Computing Center
Field of ScienceMulti-Science Community
SponsorCG OSG Connect
Date Registered09/24/2015
Abstract of workThe 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.
SDEalgorithms
PIHarish S. Bhat
OrganizationUniversity of California, Merced
DepartmentApplied Mathematics
Field of ScienceMathematical Sciences
SponsorCG OSG Connect
Date Registered05/12/2015
Abstract of workThe 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.
selfassembly
PIEddie Tysoe
OrganizationUniversity of Wisconsin Milwaukee
DepartmentChemistry
Field of ScienceChemistry
SponsorCG OSG Connect
Date Registered03/23/2017
Abstract of workThe 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.
seq2fun
PIPeter Freddolino
OrganizationUniversity of Michigan
DepartmentBiological Chemistry
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered02/05/2016
Abstract of workWe 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.
SFCphases
PIPaul Siders
OrganizationUniversity of Minnesota Duluth
DepartmentChemistry and Biochemistry
Field of ScienceChemistry
SponsorCG OSG Connect
Date Registered10/03/2016
Abstract of workMolecular-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.
snada
PIWei Wang
OrganizationUniversity of Central Florida
DepartmentPsychology
Field of ScienceMulti-Science Community
SponsorCG OSG Connect
Date Registered03/07/2016
Abstract of workSimulate social networks to analyze statistical properties.
SNOplus
PIJoshua R Klein
OrganizationUniversity of Pennsylvania
DepartmentPhysics and Astronomy
Field of ScienceHigh Energy Physics
SponsorVO OSG
Date Registered09/03/2013
Abstract of workSNO+ 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.
Snowmass
PIMeenakshi Narain
OrganizationBrown University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorVO OSG
Date Registered08/16/2013
Abstract of workSimulate 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.
SO10GU
PIshaikh saad
OrganizationOklahoma State University
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG OSG Connect
Date Registered08/24/2016
Abstract of worksearching for different realistic SO(10) GUT models that are able to reproduce the experimentally observed fermion masses and mixings
SOL
PITyson Swetnam
OrganizationUniversity of Arizona
DepartmentGeosciences
Field of ScienceGeographic Information Science
SponsorVO OSG
Date Registered03/10/2017
Abstract of workThe 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).
SourceCoding
PIDavid Mitchell
OrganizationNew Mexico State University
DepartmentElectrical Engineering
Field of ScienceEngineering
SponsorCG OSG Connect
Date Registered11/12/2015
Abstract of workLossy 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).
SouthPoleTelescope
PIJohn Carlstrom
OrganizationUniversity of Chicago
DepartmentKavil Institute for Cosmological Physics
Field of ScienceAstrophysics
SponsorCG OSG Connect
Date Registered09/24/2013
Abstract of workThe 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.
SoyKB
PIDong Xu
OrganizationUniversity of Missouri
DepartmentChristopher S. Bond Life Sciences Center
Field of SciencePlant Biology
SponsorVO OSG
Date Registered05/06/2014
Abstract of workThe 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.
sPHENIX
PIMartin Purschke
OrganizationBrookhaven National Laboratory
DepartmentPhysics Department
Field of ScienceNuclear Physics
SponsorVO OSG
Date Registered08/20/2013
Abstract of workCollaboration 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.
SPLINTER
PISamy Meroueh
OrganizationIndiana University
DepartmentIndiana Univseristy School of Medicine
Field of ScienceMedical Sciences
SponsorVO CSIU
Date Registered08/19/2013
Abstract of workSPLINTER (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.
srccoding
PIJoerg Kliewer
OrganizationNew Jersey Institute of Technology
DepartmentElectronic Engineering
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG Connect
Date Registered01/30/2017
Abstract of workStudying coding schemes for lossy source compression under privacy constraints
StanfordRCC
PIRuth Marinshaw
OrganizationStanford University
DepartmentRCC
Field of ScienceCommunity Grid
SponsorCG OSG Connect
Date Registered05/02/2014
Abstract of workThis project is for simulation work in the Stanford research community.
SWC-OSG-IU15
PIRobert William Gardner Jr
OrganizationIUPUI
DepartmentOSG
Field of ScienceCommunity Grid
SponsorCG OSG Connect
Date Registered02/23/2015
Abstract of workJoint Software Carpentry/OSG Workshop at IUPUI, March 3rd-6th 2015.
SWC-OSG-UC14
PIRobert William Gardner Jr
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG Connect
Date Registered12/09/2014
Abstract of workSoftware Carpentry/OSG Workshop at University of Chicago. Date Dec 15-17 2014.
Swift
PIMichael Wilde
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG Connect
Date Registered09/25/2013
Abstract of workSoftware development and systems testing for the parallel scripting language.
SWITCHHawaii
PIMatthias Fripp
OrganizationUniversity of Hawaii, Manoa
DepartmentElectrical Engineering
Field of ScienceEngineering
SponsorCG OSG Connect
Date Registered12/01/2015
Abstract of workWe 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.
sykclusters
PIJohn McGreevy
OrganizationUniversity of California San Diego
DepartmentPhysics
Field of SciencePhysics
SponsorCG OSG Connect
Date Registered04/17/2017
Abstract of workDMRG simulation of many body fermion system
SysBioEdu
PIStephen Ficklin
OrganizationWashington State University
DepartmentHorticulture
Field of ScienceBiological and Critical Systems
SponsorCG OSG Connect
Date Registered09/01/2016
Abstract of workA project for teaching analysis of large data sets for construction of models (i.e. graphs) of biological systems.
TAMUpheno
PIBhaskar Dutta
OrganizationTexas A&M University
DepartmentDepartment of Physics & Astronomy
Field of ScienceHigh Energy Physics
SponsorCG OSG Connect
Date Registered10/13/2014
Abstract of workThe 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.
TCGAPartCorr
PIChad Shaw
OrganizationBaylor College of Medicine
DepartmentMolecular and Human Genetics
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered02/14/2017
Abstract of workThis is a project to characterize partial correlation relationships within and between data types in the data available from The Cancer Genome Atlas (TCGA).
TDAstats
PIDavid Meyer
OrganizationUniversity of California San Diego
DepartmentMathematics
Field of ScienceMathematical Sciences
SponsorCG OSG Connect
Date Registered05/24/2016
Abstract of workTopological data analyses on various datasets
Teamcore
PIAmulya Yadav
OrganizationUniversity of Southern California
DepartmentComputer Science
Field of ScienceComputer and Information Science and Engineering
SponsorCG ISI
Date Registered06/16/2015
Abstract of workSolving 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.
TechEX15
PIRobert William Gardner Jr
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of ScienceMulti-Science Community
SponsorCG OSG Connect
Date Registered10/08/2015
Abstract of workInternet2 -TechEX15 Workshop on High Throughput Computing October 8th 2015
TextLab
PIJames Evans
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of ScienceMulti-Science Community
SponsorCG OSG Connect
Date Registered09/14/2015
Abstract of workData analytics on available text with python programs
TG-ASC130043
PIDavid Rogers
OrganizationUniversity of South Florida
DepartmentChemistry
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG-XSEDE
Date Registered10/22/2013
Abstract of workThe 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.
TG-AST140088
PIFrancis Halzen
OrganizationUniversity of Wisconsin-Madison
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG OSG-XSEDE
Date Registered05/07/2015
Abstract of workThe 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.
TG-AST150012
PIGregory Snyder
OrganizationSpace Telescope Science Institute
DepartmentUnknown
Field of ScienceMathematical Sciences
SponsorCG OSG-XSEDE
Date Registered04/23/2015
Abstract of workWe 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.
TG-AST150033
PIJuliette Becker
OrganizationUniversity of Michigan
DepartmentAstronomy
Field of ScienceAstrophysics
SponsorCG OSG-XSEDE
Date Registered06/26/2015
Abstract of workThe 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.
TG-AST150044
PIJennifer Lotz
OrganizationSpace Telescope Science Institute
DepartmentAstronomical Sciences
Field of ScienceAstrophysics
SponsorCG OSG-XSEDE
Date Registered10/22/2015
Abstract of workWe 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.
TG-AST150046
PISuzanne Hawley
OrganizationUniversity of Washington
DepartmentAstronomy
Field of SciencePhysics
SponsorCG OSG-XSEDE
Date Registered01/27/2016
Abstract of workWe 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.
TG-AST160036
PIJames Davenport
OrganizationWestern Washington University
DepartmentPhysics
Field of ScienceAstrophysics
SponsorCG OSG-XSEDE
Date Registered08/17/2016
Abstract of workStarspots 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.
TG-AST160046
PILeslie Hebb
OrganizationHobart and William Smith Colleges
DepartmentPhysics
Field of SciencePhysics
SponsorCG OSG-XSEDE
Date Registered11/07/2016
Abstract of workOur 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.
TG-AST170008
PIStephanie Hamilton
OrganizationUniversity of Michigan
DepartmentPhysics
Field of ScienceAstrophysics
SponsorCG OSG-XSEDE
Date Registered03/14/2017
Abstract of workThe 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.
TG-ATM130009
PIPhillip Anderson
OrganizationUniversity of Texas at Dallas
DepartmentPhysics
Field of ScienceAtmospheric Sciences
SponsorCG OSG-XSEDE
Date Registered10/15/2013
Abstract of workThe 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.
TG-ATM130015
PIPhillip Anderson
OrganizationUniversity of Texas at Dallas
DepartmentPhysics
Field of ScienceAtmospheric Sciences
SponsorCG OSG-XSEDE
Date Registered10/22/2013
Abstract of workThe 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.
TG-BCS110002
PIThomas
OrganizationPurdue University
DepartmentComputer & Information Technology
Field of ScienceBiological and Critical Systems
SponsorCG OSG-XSEDE
Date Registered10/22/2013
Abstract of workThe 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.
TG-CCR130001
PIRuth Marinshaw
OrganizationStanford University
DepartmentResearch Computing
Field of ScienceTraining
SponsorCG OSG-XSEDE
Date Registered05/07/2014
Abstract of workI am applying for a renewal of campus champion allocations for Stanford.
TG-CCR140028
PIShantenu Jha
OrganizationRutgers, the State University of New Jersey
DepartmentComputer Engineering
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG-XSEDE
Date Registered07/17/2015
Abstract of workThis allocation request is as the Rutgers Campus Champion to help serve the Rutgers Academic Community better.
TG-CDA080011
PIVikram Gazula
OrganizationUniversity of Kentucky
DepartmentCenter for Computational Sciences
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG-XSEDE
Date Registered04/11/2014
Abstract of workAllocation needed for Campus Champion Activities
TG-CDA100013
PIMark Reed
OrganizationUniversity of North Carolina, Chapel Hill
DepartmentITS Research Computing
Field of ScienceMathematical Sciences
SponsorCG OSG-XSEDE
Date Registered06/13/2014
Abstract of workCampus Champion renewal to support the University of North Carolina at Chapel Hill.
TG-CHE130091
PIPaul Siders
OrganizationUniversity of Minnesota, Duluth
DepartmentChemistry and Biochemistry
Field of ScienceChemistry
SponsorCG OSG-XSEDE
Date Registered10/10/2013
Abstract of workCompressed 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.
TG-CHE130103
PIJeremy Moix
OrganizationMassachusetts Institute of Technology
DepartmentChemistry
Field of ScienceChemistry
SponsorCG OSG-XSEDE
Date Registered11/01/2013
Abstract of workEnergy 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.
TG-CHE140094
PIJohn Stubbs
OrganizationUniversity of New England
DepartmentChemistry and Physics
Field of ScienceChemistry
SponsorCG OSG-XSEDE
Date Registered07/14/2014
Abstract of workHybridization 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.
TG-CHE140098
PIPaul Siders
OrganizationUniversity of Minnesota, Duluth
DepartmentChemistry and Biochemistry
Field of ScienceChemistry
SponsorCG OSG-XSEDE
Date Registered12/16/2014
Abstract of workThe 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.
TG-CHE140110
PIJohn Stubbs
OrganizationUniversity of New England
DepartmentChemistry and Physics
Field of ScienceChemistry
SponsorCG OSG-XSEDE
Date Registered12/03/2014
Abstract of workMonte 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.
TG-CHE150012
PIChristopher Fennell
OrganizationOklahoma State University
DepartmentChemistry
Field of ScienceChemistry
SponsorCG OSG-XSEDE
Date Registered03/16/2016
Abstract of workThe 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.
TG-DEB140008
PIRobert Toonen
OrganizationUniversity of Hawaii, Manoa
DepartmentUnknown
Field of ScienceBiological Sciences
SponsorCG OSG-XSEDE
Date Registered04/11/2014
Abstract of workWe 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.
TG-DMR130036
PIEmanuel Gull
OrganizationUniversity of Michigan
DepartmentPhysics
Field of ScienceMaterials Science
SponsorCG OSG-XSEDE
Date Registered10/10/2013
Abstract of workWe 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.
TG-DMR140072
PIAdrian Del Maestro
OrganizationUniversity of Vermont
DepartmentPhysics
Field of ScienceMaterials Science
SponsorCG OSG-XSEDE
Date Registered12/19/2014
Abstract of workWhen 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.
TG-DMS120024
PIBenjamin Ong
OrganizationMichigan State University
DepartmentInstitute for Cyber Enabled Research
Field of ScienceMathematical Sciences
SponsorCG OSG-XSEDE
Date Registered04/11/2014
Abstract of workThis allocation will be used to help MSU users transition from local HPC resources to XEDE resrouces.
TG-DMS150022
PIShahriar Afkhami
OrganizationNew Jersey Institute of Technology
DepartmentMathematical Science
Field of ScienceMathematical Sciences
SponsorCG OSG-XSEDE
Date Registered02/18/2016
Abstract of workThis 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.
TG-GEO150003
PIJon Pelletier
OrganizationUniversity of Arizona
DepartmentGeosciences
Field of ScienceGeographic Information Science
SponsorCG OSG-XSEDE
Date Registered01/14/2016
Abstract of workThe 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.
TG-IBN130001
PIDonald Krieger
OrganizationUniversity of Pittsburgh
DepartmentNeurological Surgery
Field of ScienceBiological Sciences
SponsorCG OSG-XSEDE
Date Registered10/10/2013
Abstract of workThe 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.
TG-IRI130016
PIJoseph Cohen
OrganizationUniversity of Massachusetts, Boston
DepartmentComputer Science
Field of ScienceInformation, Robotics, and Intelligent Systems
SponsorCG OSG-XSEDE
Date Registered10/10/2013
Abstract of workAnalysis 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).
TG-IRI160006
PIVictor Hazlewood
OrganizationNational Institute for Computational Sciences
DepartmentNone
Field of ScienceInformation, Robotics, and Intelligent Systems
SponsorCG OSG-XSEDE
Date Registered01/30/2017
Abstract of workStaff 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.
TG-MCB060061N
PIJeffry D. Madura
OrganizationDuquesne University
DepartmentChemistry & Biochemistry
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG-XSEDE
Date Registered01/07/2016
Abstract of workThis 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.
TG-MCB090163
PIMichael Hagan
OrganizationBrandeis University
DepartmentPhysics
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG-XSEDE
Date Registered10/10/2013
Abstract of workThis 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).
TG-MCB090174
PIShantenu Jha
OrganizationRutgers, the State University of New Jersey
DepartmentNone Stated
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG-XSEDE
Date Registered10/22/2013
Abstract of workWe 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.
TG-MCB100109
PILillian Chong
OrganizationUniversity of Pittsburgh
DepartmentChemistry
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG-XSEDE
Date Registered10/10/2013
Abstract of workThe 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.
TG-MCB130072
PIBenjamin Ong
OrganizationMichigan State University
DepartmentInstitute for Cyber Enabled Research
Field of ScienceMathematical Sciences
SponsorCG OSG-XSEDE
Date Registered10/22/2013
Abstract of workThis allocation will be used to help MSU users transition from local HPC resources to XEDE resrouces
TG-MCB130135
PIAshok Mudgapalli
OrganizationUniversity of Nebraska Medical Center
DepartmentResearch IT Office
Field of ScienceMathematical Sciences
SponsorCG OSG-XSEDE
Date Registered12/29/2014
Abstract of workMeta-genomics and Cancer research data
TG-MCB140088
PIJason Key
OrganizationHarvard Medical School
DepartmentBCMP / SBGrid
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG-XSEDE
Date Registered03/09/2016
Abstract of workThe 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.
TG-MCB140160
PIDavid Rhee
OrganizationAlbert Einstein College of Medicine
DepartmentGenetics
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG-XSEDE
Date Registered05/19/2014
Abstract of workDescription: 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.
TG-MCB140211
PIHong Qin
OrganizationSpelman College
DepartmentBiology
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG-XSEDE
Date Registered01/13/2015
Abstract of workWhy 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
TG-MCB140232
PIAlan Chen
OrganizationSUNY at Albany
DepartmentChemistry
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG-XSEDE
Date Registered03/03/2015
Abstract of workA 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.
TG-MCB140268
PIGraziano Vernizzi
OrganizationSiena College
DepartmentPhysics and Astronomy
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG-XSEDE
Date Registered05/24/2015
Abstract of workThe 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)
TG-MCB150090
PIEmiliano Brini
OrganizationSUNY at Stony Brook
DepartmentLaufer Center
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG-XSEDE
Date Registered10/26/2015
Abstract of workSolvation 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.
TG-MCB160027
PIYang Zhang
OrganizationUniversity of Michigan
DepartmentDepartment of Computational Medicine and Bioinformatics
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG-XSEDE
Date Registered05/18/2016
Abstract of workKnowledge 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.
TG-MCB160069
PIEdward O'Brien
OrganizationPennsylvania State University
DepartmentChemistry
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG-XSEDE
Date Registered12/06/2016
Abstract of workExperiments 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.
TG-MCB160192
PISamuel Thompson
OrganizationUniversity of California, San Francisco
DepartmentBioengineering and Therapeutics
Field of ScienceMolecular and Structural Biosciences
SponsorCG OSG-XSEDE
Date Registered01/30/2017
Abstract of workProteins 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.
TG-OCE130029
PIYvonne Chan
OrganizationUniversity of Hawaii, Manoa
DepartmentHawaii Institute of Marine Biology
Field of ScienceOcean Sciences
SponsorCG OSG-XSEDE
Date Registered10/10/2013
Abstract of workMethods 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.
TG-OCE140013
PIYvonne Chan
OrganizationUniversity of Hawaii, Manoa
DepartmentHawaii Institute of Marine Biology
Field of ScienceOcean Sciences
SponsorCG OSG-XSEDE
Date Registered10/27/2014
Abstract of workMethods 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.
TG-PHY110015
PIPran Nath
OrganizationNortheastern University
DepartmentPhysics
Field of SciencePhysics and astronomy
SponsorCG OSG-XSEDE
Date Registered10/22/2013
Abstract of workWe 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.
TG-PHY120014
PIQaisar Shafi
OrganizationUniversity of Delaware
DepartmentPhysics and astronomy
Field of SciencePhysics and astronomy
SponsorCG OSG-XSEDE
Date Registered10/10/2013
Abstract of workThe 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.
TG-PHY150040
PIFrancis Halzen
OrganizationUniversity of Wisconsin-Madison
DepartmentPhysics
Field of SciencePhysics and astronomy
SponsorCG OSG-XSEDE
Date Registered01/14/2016
Abstract of workIceCube 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.
TG-PHY160001
PITerrance Figy
OrganizationWichita State University
DepartmentMathematica, Statistics, and Physics
Field of SciencePhysics
SponsorCG OSG-XSEDE
Date Registered01/29/2016
Abstract of workXSEDE 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.
TG-PHY160031
PINepomuk Otte
OrganizationGeorgia Institute of Technology
DepartmentSchool of Physics & Center for Relativistic Astrophysics
Field of ScienceMathematical Sciences
SponsorCG OSG-XSEDE
Date Registered08/16/2016
Abstract of workWe 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.
TG-SEE140006
PISheila Kannappan
OrganizationUniversity of North Carolina, Chapel Hill
DepartmentPhysics & Astronomy
Field of SciencePhysics and astronomy
SponsorCG OSG-XSEDE
Date Registered07/08/2014
Abstract of workDescription: 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.
TG-SES090019
PIShaowen Wang
OrganizationUniversity of Illinois at Urbana-Champaign
DepartmentGeography and Geographic Information Science
Field of ScienceGeographic Information Science
SponsorCG OSG-XSEDE
Date Registered02/27/2015
Abstract of workGeographic 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).
TG-STA110011S
PIStephen McNally
OrganizationUniversity of Tennessee, Knoxville
DepartmentNICS
Field of ScienceOther
SponsorCG OSG-XSEDE
Date Registered08/18/2014
Abstract of workrenewing project
TG-STA110014S
PINancy Wilkins-Diehr
OrganizationUniversity of California-San Diego
DepartmentSan Diego Supercomputer Center
Field of ScienceTraining
SponsorCG OSG-XSEDE
Date Registered10/22/2013
Abstract of workStaff Account for Training
TG-TRA100004
PIAndrew Ruether
OrganizationSwarthmore College
DepartmentITS
Field of ScienceTraining
SponsorCG OSG-XSEDE
Date Registered10/22/2013
Abstract of workSwarthmore College Campus Champion Renewal
TG-TRA110013
PIHadrian Djohari
OrganizationCase Western Reserve University
DepartmentITS
Field of ScienceChemistry
SponsorCG OSG-XSEDE
Date Registered07/27/2014
Abstract of workDescription: Campus Champions for Case Western Reserve University, helping faculty to start onboarding XSEDE resources. Some research work on Macromolecular Science and Materials Science.
TG-TRA120004
PIRob Lane
OrganizationColumbia University in the City of New York
DepartmentColumbia University Information Techonology
Field of ScienceOther
SponsorCG OSG-XSEDE
Date Registered02/02/2017
Abstract of workThis allocation will be used to help researchers at Columbia University understand how to use XSEDE resources.
TG-TRA120014
PIPol Llovet
OrganizationMontana State University
DepartmentResearch Computing Group
Field of ScienceEvolutionary Sciences
SponsorCG OSG-XSEDE
Date Registered04/11/2014
Abstract of workThis is the allocation for my Montana State University Campus Champion account.
TG-TRA120041
PIHanning Chen
OrganizationGeorge Washington University
DepartmentChemistry
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG-XSEDE
Date Registered04/11/2014
Abstract of workcampus Champion at GWU
TG-TRA130007
PIDavid Monismith
OrganizationNorthwest Missouri State University
DepartmentMathematics, Computer Science, and Information Systems
Field of ScienceTraining
SponsorCG OSG-XSEDE
Date Registered09/30/2014
Abstract of workThis is a renewal request for the Campus Champion allocation for Northwest Missouri State University.
TG-TRA130011
PIJohn Chrispell
OrganizationIndiana University of Pennsylvania
DepartmentMathematics
Field of ScienceOther
SponsorCG OSG-XSEDE
Date Registered05/13/2015
Abstract of workThis 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.
TG-TRA130030
PINeranjan Edirisinghe Pathirannehelage
OrganizationGeorgia State University
DepartmentInformation Technology
Field of ScienceMathematical Sciences
SponsorCG OSG-XSEDE
Date Registered09/11/2015
Abstract of workI 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.
TG-TRA140029
PIScott Hampton
OrganizationUniversity of Notre Dame
DepartmentCenter for Research Computing
Field of ScienceOther
SponsorCG OSG-XSEDE
Date Registered04/06/2016
Abstract of workThe 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.
TG-TRA140043
PIIgor Yakushin
OrganizationPennsylvania State University
DepartmentInstitute for CyberScience
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG-XSEDE
Date Registered03/31/2016
Abstract of workCampus Champion allocation
TG-TRA150018
PIStephen Wolbers
OrganizationOregon State University
DepartmentInformation Services
Field of ScienceOther
SponsorCG OSG-XSEDE
Date Registered12/03/2015
Abstract of workA request for initial campus champion resources for Oregon State University researchers.
TPOT
PIJason H. Moore
OrganizationUniversity of Pennsylvania
DepartmentInstitute for Biomedical Informatics
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered01/29/2016
Abstract of workProject 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
TrappedOrbits
PIKathryne J Daniel
OrganizationBryn Mawr College
DepartmentPhysics
Field of ScienceAstrophysics
SponsorCG OSG Connect
Date Registered06/20/2016
Abstract of workComputing 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.
TRNG
PIAsia Aljahdali
OrganizationFlorida State University
DepartmentComputer Science
Field of ScienceComputer and Information Science and Engineering
SponsorCG OSG Connect
Date Registered03/15/2017
Abstract of workTesting Random number Generators via parallel Testu01 package.
UADataAnalytics
PINirav Merchant
OrganizationUniversity of Arizona
DepartmentArizona Research Laboratories
Field of ScienceMulti-Science Community
SponsorCG OSG Connect
Date Registered11/22/2016
Abstract of workEnabling scalable data analytics for University of Arizona researchers
uchicago
PIRobert William Gardner Jr
OrganizationUniversity of Chicago
DepartmentComputation Institute
Field of ScienceMulti-Science Community
SponsorCG OSG Connect
Date Registered09/15/2014
Abstract of workGeneral use Project for the University of Chicago
UChicago-RCC
PIBirali Runesha
OrganizationUniversity of Chicago
DepartmentResearch Computing Center
Field of ScienceTraining
SponsorCG OSG Connect
Date Registered09/25/2013
Abstract of workUniversity of Chicago Research Computing Center (http://rcc.uchicago.edu) supporting the computational requirements of multiple science domains.
UCSDEngEarthquake
PIFrank Wuerthwein
OrganizationUCSD
DepartmentPhysics
Field of ScienceEngineering
SponsorCG UCSD
Date Registered05/15/2014
Abstract of workEarthquake Engineering from UCSD supported users
UCSDPhysAstroExp
PIFrank Wuerthwein
OrganizationUCSD
DepartmentPhysics
Field of ScienceAstrophysics
SponsorCG UCSD
Date Registered05/15/2014
Abstract of workExperimental Astrophysics from UCSD supported users
UCSDPhysAstroTheo
PIFrank Wuerthwein
OrganizationUCSD
DepartmentPhysics
Field of ScienceAstrophysics
SponsorCG UCSD
Date Registered05/15/2014
Abstract of workTheoretical Astrophysics from UCSD supported users
UCSDPhysBio
PIFrank Wuerthwein
OrganizationUCSD
DepartmentPhysics
Field of ScienceBiophysics
SponsorCG UCSD
Date Registered05/16/2014
Abstract of workBiological Physics from UCSD supported users
UCSDPhysPart
PIFrank Wuerthwein
OrganizationUCSD
DepartmentPhysics
Field of ScienceHigh Energy Physics
SponsorCG UCSD
Date Registered05/15/2014
Abstract of workNon-CMS Particle Physics from UCSD supported users
UMich
PIPaul Wolberg
OrganizationUniversity of Michigan
DepartmentMicrobiology and Immunology
Field of ScienceMicrobiology
SponsorVO OSG
Date Registered08/14/2013
Abstract of workTo use a systems biology approach to directly and significantly impact our understanding and treatment of tuberculosis.
UNC-RESOLVE-photometry
PIDavid Stark
OrganizationUNC Chapel Hill
DepartmentDepartment of Physics and Astronomy
Field of SciencePhysics and astronomy
SponsorVO OSG
Date Registered10/08/2013
Abstract of workAstronomy image manipulation
UNH-IMD
PIDequan Xiao
OrganizationUniversity of New Haven
DepartmentChemistry
Field of ScienceChemistry
SponsorCG OSG Connect
Date Registered01/03/2017
Abstract of workWe are interested in developing new quantum chemistry methods and chemical structure optimization algorithms to design green heterogeneous catalysts.
UNLbcrf
PIJean-Jack M. Riethoven
OrganizationUniversity of Nebraska-Lincoln
DepartmentCenter for Biotechnology
Field of ScienceBioinformatics
SponsorCG OSG Connect
Date Registered03/02/2017
Abstract of workThe 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.
unlcpass
PIAdam Caprez
OrganizationUniversity of Nebraska - Lincoln
DepartmentBioinformatics
Field of ScienceBioinformatics
SponsorVO HCC
Date Registered07/08/2014
Abstract of workThe 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.
UPRRP-MR
PISteven Massey
OrganizationUniversidad de Puerto Rico, Rio Piedras Campus (UPRRP)
DepartmentPhysics / Biology
Field of ScienceBioinformatics
SponsorVO OSG
Date Registered10/18/2013
Abstract of workIn 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).
UserSchool2014
PITim Cartwright
OrganizationOSG
DepartmentOSG
Field of ScienceMulti-Science Community
SponsorCG OSG Connect
Date Registered06/11/2014
Abstract of workTraining project for OSG User School 2014.
UserSchool2015
PITim Cartwright
OrganizationUniversity of Wisconsin - Madison
DepartmentComputer Science
Field of ScienceEducation
SponsorCG OSG Connect
Date Registered07/28/2015
Abstract of workUser School 2015 at University of Wisconsin - Madison
UserSchool2016
PITim Cartwright
OrganizationUniversity of Wisconsin Madison
DepartmentComputer Science
Field of ScienceEducation
SponsorCG OSG Connect
Date Registered07/20/2016
Abstract of workTraining project for OSG User School 2016
velev
PIJulian Velev
OrganizationUniversity of Puerto Rico
DepartmentPhysics
Field of ScienceComputational Condensed Matter Physics
SponsorCG OSG Connect
Date Registered07/15/2014
Abstract of workElectronic structure of solids. Electron and spin transport in nanoscale devices.
VERITAS
PINepomuk Otte
OrganizationGeorgia Institute of Technology
DepartmentSchool of Physics & Center for Relativistic Astrophysics
Field of ScienceAstrophysics
SponsorCG OSG Connect
Date Registered08/24/2016
Abstract of workVERITAS 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
WheatGenomics
PIGhana Challa
OrganizationSouth Dakota State University
DepartmentBiology
Field of ScienceBioinformatics
SponsorCG CMS Connect
Date Registered04/17/2017
Abstract of workAnalysis of wheat genome and transcriptome datasets
XENON
PIAlfio Rizzo
OrganizationColumbia University
DepartmentAstrophysics
Field of ScienceAstrophysics
SponsorVO OSG
Date Registered09/18/2013
Abstract of workThe 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.
xenon1t
PILuca Grandi
OrganizationUniversity of Chicago
DepartmentPhysics
Field of ScienceAstrophysics
SponsorCG OSG Connect
Date Registered09/02/2015
Abstract of workThe 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.
XeTPC
PIAdam Para
OrganizationFermilab
DepartmentScientific Computing Simulation
Field of ScienceHigh Energy Physics
SponsorVO Fermilab
Date Registered12/29/2014
Abstract of workInvestigate the physics potential of high pressure Xenon TPC for detection of rare processes and develop reconstruction techniques for extremely high granularity detectors.
z2dqmc
PISnir Gazit
OrganizationUniversity of California Berkeley
DepartmentPhysics
Field of SciencePhysics
SponsorCG OSG Connect
Date Registered12/15/2015
Abstract of workWe 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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