Transcript 090923-eNMR-Barcelona

Structural Biology on the GRID
Dr. Tsjerk A. Wassenaar
Biomolecular NMR - Utrecht University (NL)
[email protected]
2007:
e-Infrastructure grant contract no. 213010 - e-NMR:
Streamline and automate NMR structure determination
2009:
2nd largest VO in life sciences
236 dedicated CPU (473 kSI2K)
2.87 Tb storage
3290 CPU at supporting sites
35.25 Tb of storage
8 web portals
115 registered users
~450 server requests
~375k jobs
~110 normalized CPU years
Structural Biology on the GRID
Function and Mechanism
of Action
Design of Experiments
Understand Effects
of Mutations
Drug Design
NMR: Nuclear Magnetic Resonance
NMR data processing
NMR data processing
• Many programs
• Expertise required
• Demanding in terms of
CPU and data storage
eNMR: Objectives
Develop and provide integrated protocols
and interoperability of NMR applications
Offer easy access web interfaces for NMR data processing
Exploit GRID technology for computationally
demanding structure calculations
Lower the access level to GRID technology in life sciences
eNMR: Challenges
Porting applications to the GRID
Interoperability of applications
Automated data processing and error handling
User access
Security
Porting applications to the GRID
Call for simple and effective application control:
From UI or SE
To UI or SE
Porting applications to the GRID
A Building Block Based Implementation Approach
From GRID application to Web service
Server
User Interface
GRID
Security
For services offer usage, don’t offer access
Users can use eNMR services either with a certificate loaded
or
Users register with a certificate to obtain a login and password
(jobs can then be run with a robot certificate)
Users can only run prefabricated jobs with limited control
http://www.enmr.eu/webportal
The eNMR Web Services
HADDOCK: Structure Prediction of Protein-Protein Complexes
CYANA: NMR Structure Calculations
XPLOR-NIH: NMR Structure Calculations
csRosetta: NMR Structure Calculations
TALOS+: Backbone Torsion Angle Prediction
MDD NMR: Processing of non-uniformly sampled nD spectra
CCPNmr: Format Conversion
eNMR Database
The HADDOCK Web Portal
A protocol for every user:
Easy Interface: Minimal choice, simple to use
Expert Interface: Many options for tailored runs
Guru Interface: Almost full control
File upload: Complete control
Use of the server requires registration
The service is GRID enabled when run through eNMR
http://www.enmr.eu/
http://haddock.chem.uu.nl/enmr
Behind the Portal
Behind the Portal
Challenges
From simple services to complete workflows
Making services available as web services (WSDL)
Critical Assessment of Structure Determination by NMR
Nature Methods 6, 625-626 (2009)
Meet up to business requirements, regarding security,
provenance and accounting
Beat BioMed as the largest VO in life sciences ;)
Conclusions
eNMR has become established, including
infrastructure, services and a growing user base.
eNMR has yielded innovative solutions to bridge
user needs, user friendliness and GRID resources
eNMR is lowering the barriers
between life sciences and NMR and
between life sciences and GRID computing
Utrecht
University
Thank you for your attention!
Dr. Tsjerk A. Wassenaar
Biomolecular NMR - Utrecht University (NL)
[email protected]
http://skriptic.wordpress.com/