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Center for Bioinformatics, University of Tübingen

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Presentation on theme: "Center for Bioinformatics, University of Tübingen"— Presentation transcript:

1 Center for Bioinformatics, University of Tübingen
The MoSGrid Portal – A workflow-enabled Grid Portal for Molecular Simulations Sandra Gesing Center for Bioinformatics, University of Tübingen

2 Outline Motivation MoSGrid (Molecular Simulation Grid)
The MoSGrid portal Domain specific workflows MSML (Molecular Simulation Markup Language) Future work MoSGrid Portal

3 Motivation Numerous applications for molecular simulations and docking, e.g. Materials science Structural biology Drug design Sophisticated tools and algorithms support scientists High-performance computing facilities are available MoSGrid Portal

4 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 portal for molecular simulations and docking MoSGrid Portal

5 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

6 Unifying Diversity MoSGrid Portal
12181 acatttctac caacagtgga tgaggttgtt ggtctatgtt ctcaccaaat ttggtgttgt cagtctttta aattttaacc tttagagaag agtcatacag tcaatagcct tttttagctt gaccatccta atagatacac agtggtgtct cactgtgatt ttaatttgca ttttcctgct gactaattat gttgagcttg ttaccattta gacaacttca ttagagaagt gtctaatatt taggtgactt gcctgttttt ttttaattgg gatcttaatt tttttaaatt attgatttgt aggagctatt tatatattct ggatacaagt tctttatcag atacacagtt tgtgactatt ttcttataag tctgtggttt ttatattaat gtttttattg atgactgttt tttacaattg tggttaagta tacatgacat aaaacggatt atcttaacca ttttaaaatg taaaattcga tggcattaag tacatccaca atattgtgca actatcacca ctatcatact ccaaaagggc atccaatacc cattaagctg tcactcccca atctcccatt ttcccacccc tgacaatcaa taacccattt tctgtctcta tggatttgcc tgttctggat attcatatta atagaatcaa Slide copied from: Stuart Owen „Workflows with Taverna“ MoSGrid Portal

7 MoSGrid Molecular Simulation Grid (D-Grid project) Goal
Providing users with Grid access to molecular simulation tools and docking tools via a workflow-enabled portal Implementation of high-performance computing Workflows Annotations of results Data mining Use of the D-Grid-infrastructure MoSGrid Portal

8 MoSGrid Partners Universität zu Köln
Eberhard-Karls-Universität Tübingen Universität Paderborn Konrad-Zuse-Zentrum für Informationstechnik Berlin Technische Universität Dresden Technische Universität Dortmund Bayer Technology Services GmbH, Leverkusen Origines GmbH, Martinsried GETLIG&TAR, Falkensee BioSolveIT, Sankt Augustin COSMOlogic GmbH&Co. KG, Leverkusen MoSGrid Portal

9 High-level middleware service level
MoSGrid in a Nutshell Portal WS-PGRADE Workflow Structure Recipe Result High-level middleware service level gUSE Cloud File System Grid resources UNICORE 6 XtreemFS Result MoSGrid Portal

10 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

11 Credential Management
MoSGrid Portal

12 WS-PGRADE MoSGrid Portal

13 WS-PGRADE MoSGrid Portal

14 WS-PGRADE MoSGrid Portal

15 High-level middleware service layer
gUSE Architecture grid User Support Environment User interface WS-PGRADE Application repository Information system Logging Submitters Workflow storage engine High-level middleware service layer gUSE grid User Support Environment Grid resources middleware layer UNICORE 6 MoSGrid Portal

16 gUSE Submitter Interface GridService actionJobSubmit actionJobAbort
actionJobOutput actionJobStatus actionJobResource JOB1 JOB2 JOB3 JOB4 Workflow engine JOBn Submitter GridService MoSGrid Portal

17 gUSE Submitter for UNICORE
Resources actionJobSubmit UNICORE Atomic Services JOB1 JOB2 JOB3 JOB4 1 - Security 2 - Registry 3 - Submit job 5 - Start job Workflow engine JOBn UNICORE submitter (UCC lib) 4 - Upload data Uspace MoSGrid Portal

18 ASM (Application Specific Module)
Library for managing 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 ⇒ Implicit use of gUSE submitter MoSGrid Portal

19 Distributed Data Management
XtreemFS is an object-based grid and cloud filesystem Ability to minimize data transfer Low latency, local availability through replication Grid Security Infrastructure (GSI) support MoSGrid Portal

20 Distributed Data Management
XtreemFS integration Portlet UNICORE GSI support Data flow WS-PGRADE XtreemFS Frontend nodes Compute nodes UNICORE mediates data transfers XtreemFS UNICORE TSI MoSGrid Portal

21 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

22 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

23 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

24 ener.edr state.cpt mdrun xmgrace g_energy traj.trr traj.xtc 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

25 MD Portlet MoSGrid Portal

26 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

27 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

28 Domain Quantum Chemistry
First prototype Workflow controlled by portlet Three phases Pre-processing Job execution Post-processing MoSGrid Portal

29 Domain Quantum Chemistry
Workflows Assisted job creation Guiding GUI Most common options available Pre-created job description Upload of Gaussian job description file Monitoring of jobs Post-processing and presentation of results MoSGrid Portal

30 Domain Quantum Chemistry
Preprocessing Portlet (GUI) supports common options Automatic generation of job description Submission of job MoSGrid Portal

31 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

32 Domain Docking CADDSuite (Computer-aided Drug Design) MoSGrid Portal

33 Domain Docking Galaxy available for local ressources in Tübingen
MoSGrid Portal

34 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

35 MSML Molecular Simulation Markup Language
Based on CML (Chemical Markup Language) Common interpretation by humans and computers Follows the minimum information principle Description: XSL transformation Used for validation purposes MoSGrid Portal

36 Future Work WS-PGRADE MD- and QC-Portlet CADDSuite MSML
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 WS-PGRADE Anstatt MoSGrid Portal

37 Involved Projects SHIWA (SHaring Interoperable Workflows for Large Scale Scientific Simulations on Available DCIs) EU project Duration: – Tübingen participates via Galaxy workflow export CompChem Virtual Organization EGEE project Available ressources MoSGrid Portal

38 Future Projects SCI-BUS (SCIentific gateway Based User Support)
EU project Duration: – Pan-European ressources Tübingen participates with the extension of the MoSGrid portal with an interactive molecule editor and a semantic search MoSGrid Portal

39 Acknowledgements Oliver Kohlbacher Ákos Balaskó Georg Birkenheuer
Sebastian Breuers Richard Grunzke Sonja Herres-Pawlis Valentina Huber Miklos Kozlovszky Jens Krüger István Márton Patrick Schäfer Bernd Schuller Johannes Schuster Anna Szikszay Fabri Klaus-Dieter Warzecha Martin Wewior MoSGrid Portal

40 MoSGrid Portal

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