1. West-Life VRE for Structural Biology Overview and Impact
Martyn Winn, STFC

2. Structural Biology Diverse expt techniques. Large and diverse datasets
Solution NMR: calmodulin (2k61)
MX: FO ATPase (2w5j)
MS: lipid binding to AmtB
Diverse expt techniques.
Large and diverse datasets
EM: GroEL / GroES
SAXS: EGFR ectodomain
ET: EFF-1 in membrane vesicles

3. Challenges in Structural Biology
Increased use of combined techniques:
Multiple facilities visited for one project
Data management challenges including provenance
New algorithms for integrative approaches
More processing online or in the Cloud
Introduction to SB for the e-infrastructure people
"The aim of Instruct is to encourage the integrative use of technology and methodologies."

4. Connecting Structural Biology with e-infrastructure
e-infrastructure landscape:
Grid, Cloud and Storage resources
WeNMR has been heavy user of EGI
GPGPUs coming available via EGI
AAI services
generic standards
specific standards for SB data
EGI, EUDAT, EOSC, Indigo DataCloud
Introduction to e-infrastructure for the SB people

5. High level objectives
Objective 1: Provide analysis solutions for the different Structural Biology approaches
Objective 2: Provide automated pipelines to handle multi-technique datasets in an integrative manner
Objective 3: Provide integrated data management for single and multi-technique projects, based on existing e-infrastructure
Original concept for West-Life

6. West-Life offerings
West-Life pilots an infrastructure that supports the growing use of combined techniques. 
West-Life enables structural biologists to get the benefit of the generic services provided by e-Infrastructures
West-Life pilots an infrastructure for storing and accessing data 
West-life pilots an infrastructure for processing data
Drilling down to specific outputs

7. Project focus Mature landscape for computational structural biology
Aim to enhance rather than replace
West-Life VRE can provide entry point for multi-technique studies
West-Life technologies also under-the-hood of individual services
Major focus on helping developers
What West-Life is not.

8. What is a VRE? VRE = Virtual Research Environment
Whole environment or ecosystem
West-Life are developing components of VRE:
Portal
Scientific services
Access mechanisms to e-infrastructure
Data standards
Multiple providers, one user experience
What West-Life is not.

10. Scientific coverage of West-Life
Nuclear Magnetic Resonance (NMR)
Sustainability for WeNMR
Single particle cryo electron microscopy (EM)
Nature Method of the Year 2015
Supporting development of Scipion / CCP-EM
Macromolecular X-ray Crystallography (MX)
Coordination with CCP4, ARP/wARP etc
SAXS
Partner MU developing service
Combined techniques

11. Contributing web services

12. User base WeNMR running 100,000s Grid jobs per month through enmr VO.
CCP4 ~20,000 users of downloadable software; ~2,000 users of CCP4Online
Other heavily used services, e.g. ARP/wARP, PDB_REDO, Scipion, HADDOCK
Users total
Users 2016
Job submissions
2016
Grid/cloud jobs
AMPSNMR
390 90
185
3655
ARP/wARP
4418
666
3466
AutoRickshaw
2550
430
4357
CCD
4000
CCP4-AMPLE*
187
535
CCP4-BALBES
1521
700
3148
CCP4-Crank2* 94
587
CCP4-MORDA*
202
790
CCP4-MRBUMP
874
453
1721
CCP4-SHELX*
151
656
CCP4-ZANUDA
196
598
CS-ROSETTA3 59 9 33
263871
DISVIS* 39 38
172 64
GROMACS
121
107
368
HADDOCK
8320
1621
27291
PDB_REDO
1200
500
4400
POWERFIT* 21 34 13
SCIPION -
418
30446
UNIO 80 72
280
VICI
417
131
SB community large:
move to online services
move to use of grid / cloud
2016 Portal statistics for services offered by the West-Life partners

13. Development strategy Don't migrate services to central portal
user familiarity
long-term maintenance
Focus on (user-visible):
single sign-on
data management
Focus on (for developers):
supporting use of back-end resources
promoting data standards

14. Main Concepts

15. Core developments

16. WP4 highlights Single Sign-On WP4 IdP/SdP proxy (MU)
ARIA ID Provider (Instruct)
Accepted by PDB_REDO, ARP/wARP, etc
Run in parallel with old logins
Accepted by B2ACCESS (EUDAT)
Compatibility with EGI / EOSC roadmap
Migration to DIRAC4EGI
GPGPU services with gLite
SLA negotiated with EGI
60M CPU hours, 60 dedicated cloud CPUs, 250 TB storage

17. WP5 highlights Customized end user VMs 3 use cases New services:
DISVIS: assessing information content of distance restraints
POWERFIT: rigid-body fitting into cryo-EM density
PDBe API: new API for search PDBe
Customized end user VMs
3 use cases

18. WP6 highlights D6.1 – Virtual Folder – Web components, Settings
configure connection to data provider,
B2DROP (provided by EUDAT – default 20 GB space - single, WEBDAV)
Dropbox (multiple, proprietary API, 2GB default, up to 1TB commercial),
Filesystem (multiple, local scratch disk space, mounted facility storage, USB)

19. WP7 Joint Research Activities
Exploring new ways to use existing or close to existing services, so that broader communities will be reached
1) Extending and benchmarking existing services
2) Combining services into new workflows
e.g. Scipion-Powerfit, NMR-Refmac
3) Studying large sets with Big Data
4) Assessing and extending metadata standards

20. WP2/3 Networking
WP3 Interaction with other European and Global infrastructures
EGI, EUDAT, RDA
Round Table with other ESFRIs
WP2 Training, dissemination, and outreach
60 lectures, 16 conferences, 10 papers
5 user workshops, 3 developer workshops

21. Where will we be at the end of the project?
Enhanced scientific services
maintained by Partners and under continual improvement
Central portal with links to services, per-user Virtual Folders, user support
maintained by Instruct, seek follow-on funding
Core technologies for service developers
job submissions, data storage, SSO
maintained by e-infrastructure providers

22. Goals for Reporting Period 2
Enhanced scientific services
ProteinCCD with construct scoring and ranking (D7.3 , m24)
A REFMAC server for EM and NMR (D7.4 , m24)
A HADDOCK server for EM (D7.5 , m24)
EM quality assurance workflow (D7.6 , m24)
Quality analysis workflow for predicted complexes (D7.7, m30)
Report on prototypes constructed using Big Data approaches. (D7.8, m30)
Output from CCP4Online available to external services, submission of jobs to EGI.

23. Goals for Reporting Period 2
Central portal with links to services, per-user Virtual Folders, user support
Increased coverage of services and support
Repositories (D6.2, m24)
enabling the provision of new data repositories
overview of experiment at different facilities
Assembly queries (D6.3, m32)
search and query interface for modeled assemblies (including CAPRI models)
Provenance (D6.4, m33)
capturing metadata reflecting the history of the project.
Reports on access usage and helpdesk (D5.7, D5.8, D5,9)

24. Goals for Reporting Period 2
Core technologies for service developers
Reports on deployment of consolidated platform (D4.5, D4.6)
Report on available VMs with associated documentation/use case for each of them (D5.6, m24)
Collate list of existing metadata standards, identify gaps, propose for new vocabularies (report due D7.9, m30)
Negotiate and connect with additional grid and cloud resources
Standards: wwPDB PDBx/mmCIF Working Group on Monday 17th & Tuesday 18th July at EMBL-EBI

25. Agenda 8:45 Reviewers meeting Reviewers and PO only 9:15
Start of review for the consortium
Welcome and presentation of the Participants (all)
9:30
Project overview and impact + Demo
Martyn Winn
10:15
West-Life services
WP5 Virtual Research Environment,
WP4 Operation and maintenance of infrastructures
 Alexandre: Bonvin intro
Alexandre Bonvin
Ales Krenek
11:10
Coffee break
11:25
WP6 Data Provenance, compliance,exchange, and integrity
Chris Morris / Tomas Kulhanek
12:00
WP7 Joint Research Activity
Jose Maria Carazo
12:35
Lunch
14:00
Networking
WP3 Interaction with other European and Global infrastructures,
WP2 Training, dissemination, and outreach
 Lucia Banci intro
Lucia Banci
Susan Daenke
14:55
WP1 Management and Finances
Chris Morris
15:30
Panel’s deliberations
16:00
Feedback from panel
All
16:30
Meeting ends