Structural Biology on the GRID

Dr. Tsjerk A. WassenaarBiomolecular NMR - Utrecht University

(NL)tsjerkw@gmail.com

2nd largest VO in life sciences236 dedicated CPU (473

kSI2K)2.87 Tb storage

3290 CPU at supporting sites35.25 Tb of storage

8 web portals115 registered users~450 server requests

~375k jobs~110 normalized CPU

years

2007: e-Infrastructure grant contract no. 213010 - e-NMR:

Streamline and automate NMR structure determination

2009:

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

GRIDUser InterfaceServer

Security

For services offer usage, don’t offer access

Users can use eNMR services either with a certificate loaded

orUsers 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

HADDOCK: Structure Prediction of Protein-Protein Complexes

CYANA: NMR Structure CalculationsXPLOR-NIH: NMR Structure CalculationscsRosetta: NMR Structure Calculations

TALOS+: Backbone Torsion Angle PredictionMDD NMR: Processing of non-uniformly sampled

nD spectraCCPNmr: Format Conversion

eNMR Database

The eNMR Web Services

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 registrationThe 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

UtrechtUniversity

Thank you for your attention!

Dr. Tsjerk A. WassenaarBiomolecular NMR - Utrecht University

(NL)tsjerkw@gmail.com

http://skriptic.wordpress.com/