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 validator.xml-cml.org
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