ELIXIR Competence Center teleconference meeting

Tuesday 3 May 2016, 13:00 → 15:00 Europe/Amsterdam

AGENDA: 1. ELIXIR Compute Infrastructure status and related deliverable: D6.10: Infrastructure tests and best usage practices for life science service providers 2. Status reports of the use cases by the use case representatives: - cBioPortal replication (Miroslav Ruda) - Marine metageniomics (Kimmo Mattila) - Insyght Comparative Genomics (Christophe Blanchet, Jean-françois Gibrat) - PhenoMeNal project (Steven Newhouse, Enol Fernandez) - JetStream interoperability (Robert Quick) 3. New opportunities: - BioShaDock: a community driven bioinformatics shared Docker-based tools registry 4. Events: - Data Node Network workshop (Apr 13-14) - EXCELERATE WP4 meeting (May) CONNECTION DETAILS (NEW SYSTEM!): Please join my meeting from your computer, tablet or smartphone. https://www.gotomeeting.com/join/924248133 You can also dial in using your phone. Access Code: 924-248-133 Australia (Long distance): +61 3 9008 7863 Austria (Long distance): +43 7 2088 1033 Belgium (Long distance): +32 (0) 28 93 7001 Canada (Long distance): +1 (647) 497-9379 Denmark (Long distance): +45 69 91 89 33 Finland (Long distance): +358 (0) 942 41 5770 France (Long distance): +33 (0) 170 950 585 Germany (Long distance): +49 (0) 692 5736 7303 Ireland (Long distance): +353 (0) 19 030 050 Italy (Long distance): +39 0 693 38 75 50 Netherlands (Long distance): +31 (0) 208 080 208 New Zealand (Long distance): +64 9 925 0481 Norway (Long distance): +47 21 54 82 21 Spain (Long distance): +34 911 82 9890 Sweden (Long distance): +46 (0) 853 527 817 Switzerland (Long distance): +41 (0) 435 0167 65 United Kingdom (Long distance): +44 (0) 330 221 0099

 

Participants:

Kimmo Mattila, CSC
Miroslav Ruda, CESNET
Olivier Collin, IRISA (INRIA)
Olivier Sallou, IRISA (INRIA)
Steven Newhouse, EBI
Jean-Francois Gibrat, CNSR
Christoph Blanchet, IFB
Gergely, Peter, Enol - EGI

Discission points

1. D6.10:

- New structure:

* Section 1 (or in Intro) Describe What is the ELIXIR Compute Platform, What is the role of infrastructure service providers.

* Section 2: A 'Summary dashboard about where are the sites are in terms of integration' (Already integrated, Under integration, Planning to integrate - When? What are the next steps?)

* Section 3: Guidelines for integration, based on experience of partners covered in Section 2. Technology specific details can be added by CESNET (OpenNebula), EBI (OpenStack), GRNET (Synnefo). 

- Status of integration:

* EBI is still testing - in the week or so  on pre-production introduction. Software integration is going well. We are waiting for the hardware team

* CSC: Team is re-organised. First contacts to EGI FedCloud experts have been made. For CSC running  and developing the local IAAS cloud is the primary target and EGI Fededrated Cloud will be an additional feature.  Steven pointed out that there is misunderstanding at CSC about what's required to integrate into the FedCloud. In addition to technical issues the user polices of the EGI Federated Cloud and CSC should be in non-conflicting. CSC will get back to EGI.eu to get more detailed view about the what is needed to join EGI Federeted Cloud.

* CNRS: Currently building the national bioinformatics infrastructure. The work is complex, we cannot yet tell how and when this will 'meet' with ELIXIR Compute Platform. IFB is the coordinator of this effort. Some FranceGrid institutes are already part of EGI FedCloud. Maybe some of these CNRS members (e.g. Strasbourg) can offer capacity in the ELIXIR Compute platform? Gergely pointed out that desipte every CC member was stated as resource provider in the CC workplan, there is no need to join in the ELIXIR Compute Platform unless you see the benefits. But in D6.10 all partners should describe their position and conditions about joining.

- Keep the scope of D6.10 on 'low-level services': Cloud provisioning, data storage provisioning --> So the document directly links to EXCELERATE WP4

- Action about D6.10: Gergely to restructure the last version based on the above discussion, then send out a new version to the CC list. Members to add their own contributions. Deadline for submitting the document to the EC is end of May. We need also external review before that.

2. Use cases:

- cBioPortal replication (Miroslav Ruda) - no update

- Marine metageniomics (Kimmo Mattila) - CSC has given to the MetaPIPE developers  isntructions about using Spark environmnet and gridFTP servers in the cloud environmnet of CSC, but the pipeline construction in the CSC environment has not started yet.

- Insyght Comparative Genomics (Christophe Blanchet, Jean-françois Gibrat) - analysis of application is ongoing. Planning to start using the FedCloud in next month.

- PhenoMeNal project (Steven Newhouse, Enol Fernandez) - Enol created a pilot integration of Terraform with the EGI FedCloud. More work is needed on this to release it. CESNET can help with this. Enol to discuss this offline with Miroslav.

- JetStream interoperability (Robert Quick) - No representative in the meeting

Gergely encouraged Use case owners to organise 'side meetings' for any of the use cases, with relevant partners from the CC. Gergely can help booking the Gotomeeting teleconference system, setting up agenda in Indico

 

3. BioShaDock:

Registry of docker containers including tools/software for bioinformatics. Already offered as a service by IFB for ELIXIR. The EGI Fedcloud  already includes an Ubuntu image with Docker Engine pre-installed, so a FedCloud user can use these containers. After the ELIXIR VO is populated with cloud sites, then we should create a short guideline for users on how to use BioShaDock containers on the ELIXIR compute platform.

4. Events
- Data Node Network workshop (Apr 13-14): Miroslav will check for minutes/notes from this event and circulate to the CC members.
- EXCELERATE WP4 meeting (8-10 June, CSC): Intended mostly to ELIXIR WP4 members.

Next meeting: Before the EXCELERATE WP4 meeting. Kimmo to open a doodle.