1. INFN Grid - Referee meeting Bologna, 25 July 2008
The e-NMR project: deploying and unifying the NMR e-Infrastructure in System Biology
Marco Verlato

2. Deploying and unifying the NMR e-Infrastructure in System Biology
An e-infrastructure funded by the European Commission
Project type: I3
Duration: 3 years
Start date: November 1, 2007
Total budget: €
Funding from the EC: €
Total funded effort: 27 person-years
Related EC-funded projects: EU-NMR, NMR-Life

3. Project Participants
Coordinator: Harald Schwalbe, University of Frankfurt
Johann Wolfgang Goethe Universität Frankfurt am Main, Germany Center for Biomolecular Magnetic Resonance (BMRZ)
University of Florence, Italy Magnetic Resonance Center (CERM) Subcontractor: Spronk NMR Consultancy, Vilnius, Lithuania
Utrecht University, The Netherlands Bijvoet Center for Biomolecular Research Subcontractor: European Bioinformatics Institute, Hinxton, UK
Istituto Nazionale di Fisica Nucleare , Italy

4. Objectives
Deploy and support an interoperable Grid infrastructure at the three NMR infrastructures to be later integrated with EGEE
Assess the state-of-the-art in computational bio-NMR and promote knowledge and spreading of best computational practices
Identify and promote a sustainable NMR technical framework for e-Science
Develop an integrated e-NMR computational platform

5. Main Goal Networking Activities Support Activities
Build an interoperable e-NMR Grid infrastructure with EGEE to support the test and deployment of enhanced NMR scientific applications
Project Goal 1
Establish a human collaboration network between the NMR community and the e-Infrastructures ones
Project Goal 2
Assess state-of-the-art in structural biomolecular NMR and promote spreading of knowledge and good practice
Project Goal 3
Deploy and support an
interoperable Grid
infrastructure at the three
NMR facilities to be later
integrated with EGEE
Project Goal 4
Identify and promote a sustainable NMR technical framework for e-Science
Project Goal 5
Assess and implement state-of-the-art in NMR computational methods and develop an integrated computational platform
Networking Activities
Obj. 1: Project organisation and management
Obj. 2: Critical assessment of NMR computational approaches
Obj. 3: Policy study and participation to standardisation efforts
Obj. 4: Training and dissemination
Support Activities
Obj. 1: deploy the e-NMR infrastructure
Obj. 2: support the e-NMR infrastructure
Joint Research Activities
Obj. 1: identify research applications to be ported onto the e-NMR GRID
Obj. 2: enhance grid middleware (gLite) for NMR applications
Obj. 3: develop a unified e-NMR computational platform implementing state-of-the-art
Obj. 4: identify and develop missing applications
WP0: Management
T0.1: Project coordination, monitoring and reporting to EU
T0.2: Financial administration
T0.3: Ensuring long-term self sustainability
WP1: Monitoring, Standardization & Outreach
T1.1: Assessment of the state-of-art in computational aspects of bio-NMR and establishment of software, protocols and data storage standards.
T1.2: Establish tight connections between e-science and bio-NMR communities.
T1.3: Spreading and training.
WP2: e-NMR grid
deployment &
operations
T2.1: deployment of e NMR grid services
T2.2: e-NMR Grid Operation center (GOC)
T2.3: integration of JRA components
WP3: design & development of the e-NMR grid platform
T3.1: Identification of NMR applications suitable for porting to the GRID
T3.2: Enhancement and development of GRID middleware for e-NMR support
T3.3: Development of the e-NMR platform and implementation of state-of-the-art protocols
T3.4: Identification and development of missing NMR applications within the e-NMR platform

7. Objectives
Deploy and support an interoperable Grid infrastructure at the three NMR infrastructures to be later integrated with EGEE
Assess the state-of-the-art in computational bio-NMR and promote knowledge and spreading of best computational practices
Identify and promote a sustainable NMR technical framework for e-Science
Develop an integrated e-NMR computational platform

8. e-NMR gLite Infrastructure
GridICE
HLRmon
SAM
GStat
WMSmon
INFN
INFN
CIRMMP
WMS/ LB
BDII/
RGMA
LFC
VOMS/
MyProxy
BMRZ
BCBR
CIRMMP
CEs, SEs, MON-box
and UI at sites

9. e-NMR gridICE snapshot

10. e-NMR HLRmon snapshot

11. Objectives
Deploy and support an interoperable Grid infrastructure at the three NMR infrastructures to be later integrated with EGEE
Assess the state-of-the-art in computational bio-NMR and promote knowledge and spreading of best computational practices
Identify and promote a sustainable NMR technical framework for e-Science
Develop an integrated e-NMR computational platform

12. PARA restraints toolkit
D3.6, month 36
The e-NMR platform
NMR raw data processing
TopSpin/XwinNMR
NmrPipe
Azara …
Assignment & Bookkeeping
Graphics
Sparky
NMRView
Cara
CCPN Analysis
Backbone
Autoassign
MARS
Pistachio
Match
Garant …
Side-chains
PROSIAS
Pistachio
ASCAN …
Data analysis / restraints generation
e-NMR GRID, EGEE, …
NOEs
QUEEN
AQUA …
Dihedral angles
Talos
CSI
PECAN
RDCs
Pales
Module …
Relaxation data
TENSOR2
ModelFree
HydroNMR
CCPN FormatConverter
Curvefit …
Paramagnetic data
PARA restraints toolkit
Structure calculations / automated NOE assignment
Computation engines
CYANA
CNS
Xplor-NIH
Automated procedures
CANDID
ARIA
RADAR
RECOORD
ABACUS …
Modelling of biomolecular complexes
HADDOCK
Structure validation
Procheck
Whatcheck
PSVS
DNA/RNA toolkit …
e-NMR raw
and processed
data storage
PDB
BMRB

13. e-NMR website: www.enmr.eu
Will become the access point to the platform

14. the HADDOCK web portal

15. The HADDOCK Software web portal
Accessible from:
Registration required (but free for non profit)
Four interfaces:
Easy: simple docking from list of residues to define interfaces
Expert: more control on docking parameters. Allow the user to input restraint files (e.g. NOEs, Hbonds, dihedral angles)
GURU: full control, addition support for RDCs and diffusion anisotry restraints
Parameter file upload

16. The server output ...... Cluster statistics for the best 10 clusters
Best 4 structures from each cluster.
Full docking run as gzipped tar file.
Visualization using Jmol

17. Xplor-NIH in GENIUS

18. Xplor-NIH in GENIUS

19. Xplor-NIH in GENIUS

20. INFN activities in e-NMR
INFN is responsible of the Work Package 2, which aims to:
deploy at the 3 NMR sites the gLite grid services
establish the e-NMR Grid Operation Centre (GOC) for management, control and support of the infrastructure
certify and integrate in e-NMR the newly developed JRA-WP3 components
2 FTEs funded (3,65 persons) + myself unfunded:
S.Dalpra (Jun’08-Apr’10) + E.Frizziero +65%*S.Traldi (May’08-Apr’10) + P.Solagna (Oct’08-Apr’10) + M.Verlato (uf)
3 deliverables under INFN responsibility before end of 2009:
D3.1: Release of first set of use-cases – PM6 (Apr’08)
D1.1: e-NMR database model – PM8 (June’08)
D0.1: Organisation of First Annual Meeting - PM12 (Oct’08)
D2.1: e-NMR grid operational – PM12 (Oct’08)
D1.2: Test data sets – PM15 (Jan’09)
D3.2: Overview of software for nucleic acids – PM15 (Jan’09)
D1.3: First assessment of state-of-art – PM18 (Apr’09)
D2.2: Assessment of e-NMR infrastructure and GOC report – PM18 (Apr’09)
D3.3: Enhanced gLite version for NMR – PM18 (Apr’09)
D3.5: Online tutorials – PM18 (Apr’09)
D2.3: New components’ integration and deployment report – PM21 (Jul’09)
D0.2: Organisation of second annual meeting – PM24 (Oct’09)

21. Plans for
Supporting operations with monitoring (gridICE, SAM, gStat) and accounting (DGAS, HLRMon):
enabling VO/group based views on HLRMon
following EGEE-III evolution on monitoring/operations (e.g. Nagios)
Application support/gridification, middleware development for e-NMR:
Bio-NMR applications from Genius portal evaluated: they don’t like the need of users’ unix accounts on the server and the proxy creation mechanism
Robot certificates approach with certificate-based web access is preferred
The development of a certificate-based web access for servers is planned
We were asked for a location for the “bio-NMR software workshop” (D1.3) to be delivered in April/May’09  INFN-CNAF Centre proposed
WP1 coordination activity - 46k€ planned per workshop in T.A.
Requests for 2009:
MI: 7 k€ (3 meetings + User Forum/OGF x 3 persons)
ME=18.5 k€ (2 meetings + EGEE’09 + Annual Workshop x 3 persons)
 Total = 25,5 k€