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The MoSGrid Portal – A workflow-enabled Grid Portal for Molecular Simulations. Sandra Gesing Center for Bioinformatics, University of Tübingen sandra.gesing@uni-tuebingen.de 28.04.2010. Outline. Motivation MoSGrid (Molecular Simulation Grid) The MoSGrid portal
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The MoSGrid Portal – A workflow-enabled Grid Portal for Molecular Simulations Sandra Gesing Center for Bioinformatics, University of Tübingen sandra.gesing@uni-tuebingen.de 28.04.2010
Outline • Motivation • MoSGrid (Molecular Simulation Grid) • The MoSGrid portal • Domain specific workflows • MSML (Molecular Simulation Markup Language) • Future work • MoSGrid Portal
Motivation • Numerousapplicationsformolecularsimulationsanddocking, e.g. • Materials science • Structuralbiology • Drug design • Sophisticatedtoolsandalgorithmssupportscientists • High-performancecomputingfacilitiesareavailable • MoSGrid Portal
Motivation • Drawbacks of using molecular simulations and docking • Usability of tools is limited • Complexity of methods • Lack of graphical user interfaces • Complexity of infrastructures • Many end users lack computer science background • ⇒ Need for self-explanatory and intuitive user interfaces • ⇒ A portalformolecularsimulationsanddocking • MoSGrid Portal
Portals • Single point of entry • Possibility to customize views and tools • Store user preferences • No installation of software on the user’s side • No firewall issues • MoSGrid Portal
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MoSGrid • Molecular Simulation Grid (D-Gridproject) • Goal • Providing users with Grid access to molecular simulation tools and docking tools via a workflow-enabledportal • Implementation of high-performance computing • Workflows • Annotations of results • Data mining • Use of the D-Grid-infrastructure • MoSGrid Portal
MoSGrid Partners • Universitätzu Köln • Eberhard-Karls-UniversitätTübingen • Universität Paderborn • Konrad-Zuse-ZentrumfürInformationstechnik Berlin • TechnischeUniversitätDresden • TechnischeUniversität Dortmund • Bayer Technology Services GmbH, Leverkusen • Origines GmbH, Martinsried • GETLIG&TAR, Falkensee • BioSolveIT, Sankt Augustin • COSMOlogicGmbH&Co. KG, Leverkusen • MoSGrid Portal
MoSGrid in a Nutshell Portal WS-PGRADE Workflow Structure Recipe Result High-levelmiddlewareservicelevel gUSE Cloud File System Gridresources UNICORE 6 XtreemFS Result • MoSGrid Portal
Credential Management • User management based on Liferay features • Community management • Organization management • X.509 user certificates • SAML (Security Assertion Markup Language) • Minimize credential data transfers • Set of maximum hops for trust delegation • Usable for single sign-on infrastructures (e.g., Shibboleth) • MoSGrid Portal
Credential Management • MoSGrid Portal
WS-PGRADE • MoSGrid Portal
WS-PGRADE • MoSGrid Portal
WS-PGRADE • MoSGrid Portal
gUSE Architecture grid User Support Environment User interface WS-PGRADE High-levelmiddlewareservicelayer gUSE Workflow storage Application repository Information system Workflow engine Submitters Logging Gridresources middlewarelayer UNICORE 6 • MoSGrid Portal
gUSE Submitter Interface GridService • actionJobSubmit • actionJobAbort • actionJobOutput • actionJobStatus • actionJobResource JOB1 JOB3 JOB4 JOB2 Workflow engine JOBn Submitter GridService • MoSGrid Portal
gUSE Submitter for UNICORE gUSE UNICORE 6 Resources UNICORE Atomic Services actionJobSubmit JOB1 JOB3 JOB4 JOB2 1 - Security 2 - Registry 3 - Submitjob 5 - Start job Workflow engine JOBn UNICORE submitter (UCC lib) Uspace 4 - Upload data • MoSGrid Portal
ASM (ApplicationSpecific Module) • Library formanaging WS-PGRADE workflows • Listing of users and workflows in the local repository • Import of Workflows in the user space • Upload/download of input and output files • Setting the parameters of a job in a workflow • Submission of workflows • Monitoring of workflows • Deletion of workflows • Usable in portlets und Java tools ⇒ ImplicituseofgUSE submitter • MoSGrid Portal
Distributed Data Management • XtreemFS is an object-basedgridandcloudfilesystem • Abilitytominimizedatatransfer • Low latency, localavailabilitythroughreplication • Grid Security Infrastructure (GSI) support • MoSGrid Portal
Distributed Data Management • XtreemFSintegration • Portlet • UNICORE • GSI support • Data flow • WS-PGRADE • XtreemFS • Frontend nodes • Computenodes • UNICORE mediates datatransfers XtreemFS UNICORE TSI • MoSGrid Portal
Domain Molecular Dynamics • Study and simulation of molecular motion • Provide a molecular dynamics service on multiple levels • Direct upload of job descriptions • Workflows and standard recipes for repeating tasks • Analysis of relevant properties • MoSGrid Portal
Equilibration of Proteins • Proteins from databases (e.g., the Protein Data Bank, PDB) do not necessarily represent a near-native conformation/configuration • For all kind of production runs a minimization and an equilibration is an indispensable prerequisite • Eases the work of experienced users • Lowers the hurdle for novice users • MoSGrid Portal
UseCase: Gromacs_EQ structure (pdb/gro) pdb2gmx structure (pdb) topology (top/itp) editconf genbox box (pdb) EM.mdp (mdp) Solvated (pdb) adj. Top. (top/itp) grompp topol.tpr mdout.mdp • MoSGrid Portal
mdrun xmgrace g_energy ener.edr traj.trr traj.xtc state.cpt md.log SYSTEM_EM.pdb Analysis.jpg grompp topol.tpr mdout.mdp FULL.mdp (mdp) mdrun xmgrace g_energy ener.edr traj.trr traj.xtc state.cpt md.log SYSTEM_EQ. pdb Analysis.jpg • MoSGrid Portal
MD Portlet • MoSGrid Portal
Domain Quantum Chemistry • Study and simulation of molecular electronic behavior relative to their chemical reactivity • Survey - MoSGrid Community • First implementation for Gaussian • Then support for • Turbomole • GAMESS-US • Further relevant QC applications • MoSGrid Portal
Domain Quantum Chemistry Gaussian Jobs • Single input file • Defines molecular geometry and task • Result • Not structured output • Platform dependent checkpoint file • Integrated multi-step job option • Not usable for generalized workflows • MoSGrid Portal
Domain Quantum Chemistry First prototype • Workflow controlled by portlet • Three phases • Pre-processing • Job execution • Post-processing • MoSGrid Portal
Assisted job creation Guiding GUI Most common options available Domain Quantum Chemistry Workflows • Pre-created job description • Upload of Gaussian job description file • Monitoring of jobs • Post-processing and presentation of results • MoSGrid Portal
Domain Quantum Chemistry Preprocessing • Portlet (GUI) supports common options • Automatic generation of job description • Submission of job • MoSGrid Portal
Domain Quantum Chemistry Post-processing • Parsing of result file • Python scripts executed by portlet • Relevant information about molecular properties • Data in CSV-Format saved and accessible • MoSGrid Portal
Domain Docking • CADDSuite(Computer-aided Drug Design) • MoSGrid Portal
Domain Docking • Galaxy available for local ressources in Tübingen • MoSGrid Portal
MolDB • Stores molecules in binary format, which allows for fast export • Automatically creates and stores can. smiles, fingerprints, and functional groups counts for imported molecules • Automatically saves and restores docking-/rescoring-results • DB can be filtered to all stored molecule properties before exporting molecules • Current speed for import/export: ~100 compounds/sec. • MoSGrid Portal
MSML Molecular Simulation Markup Language • Based on CML (Chemical Markup Language) • Common interpretation by humans and computers • Follows the minimum information principle • Description: http://xml-cml.org/convention/dictionary • XSL transformation • Usedforvalidationpurposesvalidator.xml-cml.org • MoSGrid Portal
Future Work • WS-PGRADE • Integration of the UNICORE IDB to offer drop-down boxes of available tools • MD- and QC-Portlet • Adoption to gUSE workflow engine via the ASM libraries • CADDSuite • Export of workflows from Galaxy to WS-PGRADE • MSML • Further development • MoSGrid Portal
Involved Projects SHIWA (SHaring Interoperable Workflows for Large Scale Scientific Simulations on Available DCIs) • EU project • Duration: 01.07.2010 – 30.06.2012 • Tübingen participates via Galaxyworkflowexport CompChem Virtual Organization • EGEE project • Availableressources MoSGridPortal
Future Projects SCI-BUS (SCIentific gateway Based User Support) • EU project • Duration: 01.10.2011 – 30.09.2014 • Pan-European ressources • Tübingen participateswiththeextensionoftheMoSGridportalwith an interactivemoleculeeditoranda semanticsearch MoSGridPortal
Acknowledgements • Oliver Kohlbacher • ÁkosBalaskó • Georg Birkenheuer • Sebastian Breuers • Richard Grunzke • Sonja Herres-Pawlis • Valentina Huber • Miklos Kozlovszky • Jens Krüger • IstvánMárton • Patrick Schäfer • Bernd Schuller • Johannes Schuster • Anna SzikszayFabri • Klaus-Dieter Warzecha • Martin Wewior • MoSGrid Portal