BioCoRE Submits, Runs, and Visualizes Your Simulation · PDF fileresearch process zIncrease...
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BioCoRE BioCoRE Submits, Runs, and Visualizes Submits, Runs, and Visualizes Your Simulation From Afar Your Simulation From Afar Presenter: Kirby Vandivort K. Schulten (PI), G. Budescu, L. Kalé Development Team: M. Bach, D. Brandon, R. Brunner, J. DeSouza, S. Kumar, K. Vandivort, H. Wang NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois at Urbana/Champaign
Transcript of BioCoRE Submits, Runs, and Visualizes Your Simulation · PDF fileresearch process zIncrease...
BioCoRE BioCoRE Submits, Runs, and Visualizes Submits, Runs, and Visualizes
Your Simulation From AfarYour Simulation From AfarPresenter: Kirby Vandivort
K. Schulten (PI), G. Budescu, L. Kalé
Development Team: M. Bach, D. Brandon, R. Brunner, J. DeSouza, S. Kumar, K. Vandivort, H. Wang
NIH Resource for Macromolecular Modeling and BioinformaticsBeckman Institute for Advanced Science and Technology
University of Illinois at Urbana/Champaign
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
BioCoRE OverviewBioCoRE OverviewBioCoRE is a collection of web-based tools
that:Forms a complete environment for biomedical researchAllows single password loginIs freely available
BioCoRE consists of Java servlets accessed through secure Apache with a database back end
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
BioCoRE GoalsBioCoRE Goals((BioBiological logical CoCollaborative llaborative RResearch esearch EEnvironment)nvironment)
Enhance the research processIncrease researcher effectivenessImprove collaborations
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Accessing BioCoREAccessing BioCoREStandard web browser– BioCoRE applets require Java support
WindowsUnixMac OSPocketPC PDAs
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
BioCoRE ProjectsBioCoRE ProjectsOrganized around ProjectsProjects are secure (only project members can see project data)
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
BioCoRE Tool AreasBioCoRE Tool AreasWorkbenchConferencesNotebookDocuments
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Workbench ToolsWorkbench ToolsSimulation Configuration File GeneratorSupercomputer Job ManagementVMD* Save/Load stateJMV** – Java Molecular Viewer – Java3D applet
*http://www.ks.uiuc.edu/Research/vmd/**http://www.ks.uiuc.edu/Development/jmv/
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Configuration File GeneratorConfiguration File GeneratorSimplifies creation of NAMD* input filesChecks for common input errorsJava applet
*http://www.ks.uiuc.edu/Research/namd/
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
BioFSBioFS File SystemFile SystemWeb-based File systemHigh bandwidth utilizedWebDAV support
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Supercomputer Job Supercomputer Job ManagementManagement
Submits and monitors supercomputer jobsAccesses multiple supercomputers from a single web pageHandles system-specific aspects (queues, file directories, etc.) automatically
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Supercomputer Job Supercomputer Job ManagementManagement
Single-screen summary of jobs
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Registering Supercomputer Registering Supercomputer Accounts with BioCoREAccounts with BioCoRE
User needs account on desired supercomputerNo need to remember supercomputer passwords
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
BioCoRE Account RegistrationBioCoRE Account RegistrationUser selects supercomputerSC account accessed via Globus or SSH
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Globus SupportGlobus SupportUses standard BioCoRE user interface Supports Alliance machinesCertificates set up by usersBioCoRE obtains user certificates via theMyProxy credential server
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Account Details (Globus)Account Details (Globus)
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Account Details (SSH)Account Details (SSH)
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Job Submission via BioCoREJob Submission via BioCoRESubmit a new job based on previous job parameters
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Job Submission via BioCoREJob Submission via BioCoRESubmit a new job based on previous job parameters(or create a new one)
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Job Submission via BioCoREJob Submission via BioCoRESelect account Check queue status
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Job Submission via BioCoREJob Submission via BioCoRESet the job parameters
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Job Submission via BioCoREJob Submission via BioCoRESet the job parametersSubmit job
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Monitor Running JobsMonitor Running JobsThe new job has been submitted
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
BioCoRE Job DetailsBioCoRE Job DetailsDetails of running jobs can be displayed
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
BioCoRE Job DetailsBioCoRE Job DetailsStandard output of the job
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Job Details Saved To Job Details Saved To BioFSBioFSAccessible to all project members
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
BioCoRE Job DetailsBioCoRE Job DetailsGraphical capabilities when running NAMD
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Launching VMDLaunching VMD
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Interactive MDInteractive MDReal-time interaction between VMD/NAMD
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
JMV Support Within BioCoREJMV Support Within BioCoREJMV: Web-based Java3D molecular viewerCan view PDB files straight from the BioFS
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Collaboration ToolsCollaboration ToolsCollaborative VMDMessage BoardProject-wide Bookmarks fileControl Panel
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Collaborative VMDCollaborative VMDLoad/save visualization statesSaved in Message Board
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
BioCoRE Message BoardBioCoRE Message BoardAsynchronousThreaded SortableSearchable
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Website Link LibraryWebsite Link LibraryProject-wide BookmarksfileRanked by popularity
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
BioCoRE Control PanelBioCoRE Control Panel“Always-on”Automatic event notificationJava Swing
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Control Panel ChatControl Panel ChatSaved to Message Board
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Publication ToolsPublication ToolsBioFS support for seamless file transport across platformsFile conversions planned (Word→TeX, TeX →Word, etc.)WebDAV for easy access
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
EvaluationEvaluationTracking BioCoRE usage patterns, analysis of BioCoRE users’ feedback and needsSupport of development process (product design, integration of user preferences and input)Assessment of BioCoRE impact and benefits to research efforts and outcomes
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Local BioCoRE ServersLocal BioCoRE ServersResearch groups can install own serverTracking data sent to central server
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
User StatisticsUser StatisticsInitial release : March 2000Registered Users: 299Logins: 2,553Registered Projects: 50Job Submissions (since March 2001): 1,114
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
Questions?Questions?
http://www.ks.uiuc.edu/Research/biocore/
Theoretical Biophysics Group,Beckman Institute, University of Illinois at Urbana/Champaignhttp://www.ks.uiuc.edu/Research/biocore/
