1. Summary of Embrace WP3 meeting
Nicolas Jacq (CNRS) on behalf of Vincent Breton

2. Reminder: WP3 goals and structure
WP3 goal: initiate a grid-based infrastructure for bioscientists
Making available most of the popular databases and software products
Taking away the need for maintaining local copies of databases and software
Taking advantage of the existing european national and international grid infrastructures and the services they provide
WP3 structured in 3 sub work packages
WP3.1 Technology recommendation and watch
WP3.2 test problems analysis, deployment and evaluation
WP3.3 technology adoption and application deployment

3. WP3.1 Technology recommendation and watch
Objectives
Recommendation for technological choice to the Content Integration work packages and to the Tools Integration work package at project month 18
Technology watch during the project lifetime as grid technology is in constant and quick evolution
Description of work
Evaluation of existing technologies for data and tools integration and deployment
Evaluation of existing technologies against user/provider requirements

4. WP3.2 test problems analysis, deployment and evaluation
Objectives: user driven technology recommandation
Test problems will be deployed before WP4 test cases
They will be used to evaluate existing technologies
List of test cases
Distribution and update of biological data bases in a grid environment, led by BMC
grid portal BioASP, led by CMBI
Computer intensive applications, led by SIB
Description of work
Analysis of test cases
Deployment of test cases
Methodologies for evaluation
Evaluation

5. WP3.3 technology adoption and application deployment
Objectives
To stand at the interface between the project and the grid infrastructures.
To evaluate existing infrastructures for the deployment of EMBRACE gridifed tools and data bases
Provide support to the technology adopted within the project
Description of work
Evaluation of Grid infrastructures for bio-informatics applications
Security
Support to creation of virtual organisations and/or virtual services
Support to technology adoption

6. WP3 roadmap Due Date Number Title Partners involved PM12 (1/2/06)
Initial technological analysis of test problems
CNRS, SIB, CMBI, Uppsala
PM18
D3.1.1 & M3.1.1 & D3.3.1
report on technology & network infrastructure survey & technology recommendation
All WP3 partners
PM24
M3.2.1
First implementation of test cases
D3.2.2
Second technological analysis of test problems
PM36
D3.2.3
First evaluation of test problem implementations

7. Meeting agenda
Evaluation of underlying middlewares deployed on grid infrastructures in Europe
Identification of middlewares where WP3 partners have expertise
High level services and tools
Presentation of high level tools and services for end users
Interfacing high level services and tools with underlying middlewares
Presentation of experiences with high level services and tools as well as attempts to interface them with underlying middlewares
WP3 test cases
Presentation of the test cases
Open discussion

8. Session on underlying middleware evaluation
Goal: evaluation of underlying grid middlewares that will be used to deploy data & integration tools on grid infrastructures
Encourage WP3 partners (particularly test cases) to deploy applications on their local/national infrastructure and report on their experience
From the list of partners, the main middlewares should be tested:
LPC: EGEE( LCG2,gLite), SRB
SIB: Swiss BioGrid (GT2 & GT4)
Uppsala: Swegrid (Globus)
Cineca: national Grid ( tbd)
CSC: Nordugrid, DEISA
CMBI: based on Globus, delayed
CNB: EGEE
EBI: Globus (GT4) / LSF
Need for common evaluation criteria

9. Session on high level services and tools
Integration tools
Presentation of Soaplab (M. Senger, EBI)
SOAP-based Analysis Web Services
Further developments in Embrace WP2 in collaboration with Martin
Presentation of BioMart (A. Kasprzyk, EBI)
A join project (EBI, Cold Spring Harbor Laboratory) to develop a simple and scalable data management system capable of integrating distributed data sources
Further developemnts within BioMart and Embrace WP1
High level services
Presentation of TAVERNA (T. Oinn, EBI)
Taverna is a workflow development and enactment environment
Taverna acts as a client for several systems, Embrace being one of them
Taverna expectation: Embrace is providing data sources
Taverna tutorial for Embrace partners July 25th
Are there other tools and high level services needed/requested ?
Biomoby
Interest to integrate biomoby standards
specific interest for the BioMoby use cases which could be used as a model for Embrace use cases
Hitkeeper, Blast

10. Interfacing Taverna with EGEE (T. Glatard, CNRS)
Session on Interfacing high level services and tools with underlying middlewares
Interfacing Taverna with EGEE (T. Glatard, CNRS)
User experience with Taverna and Soaplab (E. Rossi, CINECA)
Discussion on issues related to asynchronous web services (E. Deandres, CNB)
Issues raised
Some present limitations of Taverna for multithreading and pipelining will be addressed by moving to 2.0 with new workflow core by end 2005
Dedicated component between Taverna and EGEE to optimize job submission and handle fault-tolerance

11. WP3 test problems Test problem SIB
4 applications requiring heavy CPU
Access to more computing power to increase the size of the database
Issue: to optimize job partition and have it submitted to the best infrastructure
To be demonstrated on swiss Biogrid / EGEE
Contact point: Marco Pagni (SIB)
Test problem Uppsala: replication of databases
To be demonstrated on Swegrid
Use of specific ports for xNDT protocol
Contact point: Ann-Charlotte Berglund (Uppsala)
Test problem CMBI: enable a developing bioinformatician in a small lab to make easily a simple in silico experiment and use existing servers in Europe
Have access to a registry of resources
Have libraries (perhaps for different languages) allowing to access remote resources
Clients: students with basic knowledge (Python or Perl)
Deadline for deployment: end of third year

12. Test problems: issues
The three test problems cover nicely service providers and end users needs on Embrace
Important to get them deployed
Local deployment on european/national/regional grid
Evaluation of these infrastructures and their mw
Important to express requirements and to list services needed for future deployment on Embrace Grid
No need expressed to ask for deployment of Embrace test problems on existing infrastructures
SIB test case to be deployed on Swiss BIoGrid / EGEE
Uppsala test case to be deployed on SweGrid

13. Requirements database
EGEE applications have generated a very large database of requirements
Possibility to contribute to this database as a project
Avoid reinventing the wheel and creating a tool
A lot of information already available
Contact point: CNRS
Need to have people familiar with this database to identify relevant requirements for each test case
WP3 partners proposing test problems are encouraged to have one expert to learn how to use the database
One Embrace representative to add new requirements to EGEE database if needed

14. Open discussion / Issues
Need to define a common language
Common understanding of words like grids, middleware, services
Need for an Embrace architecture
Hard to design an architecture without use cases on which to validate it
First attempt by T. Oinn (EBI)
WP3 should promote Life Science Analysis Engine (OMG standard)
Credit: T. Oinn (EBI)

15. Conclusion
Important meeting to set the scene and agree on the way forward
Priority given to the description and deployment of test problems
Good representation of WP3 partners
CINECA (x1), CMBI(x1), CNB (x2), CNRS (x3), CSC (x2), EBI (x6), SIB (x2), Uppsala (x3)
Presentations available online soon from Embrace web site 
Next meeting in Clermont-Ferrand July 25-27th
Tutorial on Taverna and application deployment on EGEE

16. What WP3 can offer to WP4 Now Soon, help to formalize test cases
tutorials (tools, application deployment on grids)
Help to access to grid infrastructures if needed
Soon, help to formalize test cases
Templates & models
At PM18, technology recommendation

17. What WP3 needs from WP4 Description of test case Requirements
Absolutely necessary to have a formalized description of WP4 test cases to use them in WP3
Recommended template: Biomoby use cases online at
Requirements
Prerequisite: a description of the test case according ot BIomoby template
WP3 will help WP4 partners to express requirements
Feedback on high level services and tools needed
Taverna
Soaplab
Hitkeeper, BLAST

18. Joint Embrace / EGEE Tutorial
Where? Clermont-Ferrand (France)
When? 25th-27th July 2005
How to register? soon available from Embrace web site
Registration fees? NO
Preliminary agenda:
Monday (Noon – 19:00)
Taverna Tutorial
Tuesday – Wednesday (noon)
EGEE (Introduction to Grid, LCG2.x.x, gLite, Hands-on)
Who? Embrace Post-docs, EGEE Biomed People
July 11th: 16 registered participants