Structural Biology on the Grid

Christophe Schmitz

Bijvoet Center for Biomolecular Research

Faculty of Science, Utrecht University

The Netherlands

c.p.f.schmitz@uu.nl

e-BioGrid Workshop 2011

e-Infrastructure projectVirtual OrganizationVirtual Research Community

The scientific objectivesThe scientific objectives

The molecular machines and network of lifeThe molecular machines and network of life

# Number of dimensions 2# INAME 1 1H# INAME 2 1H 12 2.137 2.387 1 T 0.000e+00 0.00e+00 - 0 2756 2760 0 14 2.387 4.140 1 T 0.000e+00 0.00e+00 - 0 2760 2752 0 32 1.849 4.432 1 T 0.000e+00 0.00e+00 - 0 2259 2257 0 36 1.849 3.143 1 T 0.000e+00 0.00e+00 - 0 2259 2587 0 39 1.760 4.432 1 T 0.000e+00 0.00e+00 - 0 2260 2257 0 40 1.760 1.849 1 T 0.000e+00 0.00e+00 - 0 2260 2259 0 43 1.760 3.143 1 T 0.000e+00 0.00e+00 - 0 2260 2587 0 46 1.649 4.432 1 T 1.035e+05 0.00e+00 r 0 2583 2257 0 47 1.649 1.849 1 T 0.000e+00 0.00e+00 - 0 2583 2259 0

assign ( resid 501 and name OO ) ( resid 501 and name Z ) ( resid 501 and name X ) ( resid 501 and name Y )

( resid 2 and name CA ) -0.1400 0.15000

assign ( resid 501 and name OO ) ( resid 501 and name Z ) ( resid 501 and name X ) ( resid 501 and name Y )

( resid 3 and name CA ) -0.0100 0.15000

Datainterpretation

Structure, dynamics & interactionsStructure, dynamics & interactions impact on research and health:impact on research and health:

- origin of diseaseorigin of disease- design of new experiments- design of new experiments

- drug design- drug design……

Exploiting GRID resources in structural biology…Exploiting GRID resources in structural biology…

Computations

NMR data collection and processing SAXS data analysis

The institute and the usersThe institute and the users

The InstitutePartner Institute

BCBR Utrecht, The NetherlandsBMRZ Frankfurt, GermanyCIRMMP Florence, ItalyINFN Padova, ItalyRUN Nijmegen, The NetherlandsUCAM Cambridge, United KingdomEMBL Hamburg, Germany

Partner Institute

BCBR Utrecht, The NetherlandsBMRZ Frankfurt, GermanyCIRMMP Florence, ItalyINFN Padova, ItalyRUN Nijmegen, The NetherlandsUCAM Cambridge, United KingdomEMBL Hamburg, Germany

Alexandre Bonvin, WeNMR coordinator

BCBR institute resources• LB• CREAM-CE• SITE-BDII• TOP-BDII• APEL• UI• SE• WMS• 22 NODES (8 CPUs each) + 4 NODES (16 CPUs)• 240 CPUs• 1.8 Tb of data

Vitual Machines (XEN) with Glite 3.2

Australia: 2Brazil: 5Canada: 2China: 1Germany: 48France: 12Italy: 59Netherlands: 41Turkey: 21United Kingdom: 40United States: 37South Africa: 4

The users

Today: 352 Users, growth ~ 10 users per month

The usersBCBR Utrecht, The NetherlandsBMRZ Frankfurt, GermanyCIRMMP Florence, ItalyINFN Padova, ItalyRUN Nijmegen, The NetherlandsUCAM Cambridge, United KingdomEMBL Hamburg, Germany

BCBR Utrecht, The NetherlandsBMRZ Frankfurt, GermanyCIRMMP Florence, ItalyINFN Padova, ItalyRUN Nijmegen, The NetherlandsUCAM Cambridge, United KingdomEMBL Hamburg, Germany

Structural biologists

http://www.wenmr.eu/wenmr/user-survey

The softwareThe software

Software packagesAMBER -> Molecular dynamicsGROMACS -> Molecular Dynamics

CSROSETTA -> Structure CalculationCNS -> Structure CalculationXPLOR -> Structure calculation

ROSETTA -> protein folding prediction

HADDOCK-> protein-protein docking + =

The Web Portals

Haddock web portal

Software characteristics• CPU intensive• Possibly parallel jobs• Small internet transfer (except for software deployment)• Usually low I/O• Usually no storage required

Typical use case

3. User obtains a grid certificate3. User obtains a grid certificate

4. User joins enmr.eu VO4. User joins enmr.eu VO

5. User registers for a software (HADDOCK)5. User registers for a software (HADDOCK)

2. User wants to use a GRID enabled software of our VO (HADDOCK)2. User wants to use a GRID enabled software of our VO (HADDOCK)

1. A scientific problem requires protein-protein docking calculation (HADDOCK)1. A scientific problem requires protein-protein docking calculation (HADDOCK)

6. User provides calculation parameters6. User provides calculation parameters

Behind the sceneBehind the scene 7. User gets results7. User gets results

Behind the scene: the grid

Required resources

Lots of CPUs!Short queues

WeNMR platform operational and well used!• Largest global VO in the life sciences• Over 352 registered users from 38 nationalities, and growing• >33 000 CPUs• >700 (normalized) CPU years over the last 12 months• 1.4 million jobs over the last 12 months• 150Tb of storage space• ~20% of Life Sciences on the Grid• User-friendly access to e-Infrastructure via web portals

AcknowledgmentsAcknowledgments

Utrecht University, Bijvoet Center for Biomolecular Research, NLJohann Wolfgang Goethe Universität Frankfurt a.M., Center for Biomolecular Magnetic Resonance DEUniversity of Florence, Magnetic Resonance Center, ITIstituto Nazionale di Fisica Nucleare , Padova, ITRaboud University, Nijmegen, NLUniversity of Cambridge UKEuropean Molecular Biology Laboratory, Hamburg, DESpronk NMR Consultancy, LT

Prof. Alexandre Bonvin (WeNMR coordinator)All the Bijvoet Center in Utrecht