HoNs meeting. 3 September 2014

1. European Life Sciences Infrastructure for Biological Information
www.elixir-europe.org
Summary of Technical
Coordinators discussions

2. Technical Coordinator Group (TCG)
The Technical Coordinator Group is formed as an advisory body
to the Heads of Nodes Committee. This group consists of
technical experts representing each ELIXIR Node, appointed by
the Head of Node. The role of the group to share information
and discuss the technical and scientific aspects of ELIXIR as
well as lead the identification and implementation of best
practice.
http://www.elixir-europe.org/system/files/documents/elixir_scientific_programme_1.pdf

3. TCG - Members
Belgium Lieven Sterck Norway Kjell Petersen
Czech Republic David Antos
Jan Paces
Portugal Mario Silva
Denmark Kristoffer Rapacki Slovenia Peter Juvan
Brane Leskosek
Estonia Hedi Peterson Spain Victor de la Torre
Finland Jarno Laitinen Sweden Mikael Borg
France Christophe Blanchet Switzerland Heinz Stockinger
Greece TBC UK Mario Caccamo
Manuel Corpas
Israel Jaime Prilusky EMBL Steven Newhouse
Italy Federico Zambelli ELIXIR Hub Rafael C Jimenez
Netherlands Rob Hooft

4. • Short term working groups
• Driven by ELIXIR technical coordinators
• Participated by experts
• Represent & coordinate a specific technical effort
Task forces
4
Scientific and
funding
strategies
ELIXIR Programme of work
Task forces
Planning Agreement Implementation
Technical strategies
Pilot projects
HoNs
HoNs
HoNs
TCG

5. Task force - members
5
~60

6. ELIXIR Task Forces
6
Task forces Programme of work
Cloud Technical services
Storage Technical services
Authentication and authorization Technical services
Service registry Tools Interoperability and Service Registry
Metrics, monitoring & quality control Data resources and services
Communication Management and Operations
Website Management and Operations
Training portal Training
e-Learning Training
Interoperability Data interoperability, vocabulary and
ontology services

7. Areas of interest & programme of work
7
Domain specific services
Data interoperability, vocabulary and ontology services
Tools interoperability and Service Registry
Data resources & services
Technical Services
Management and operations
Training
Compute
Dat
a
Standards
Tools
Training

8. Task forces - Timeline
6-8 May 2014
ELIXIR HoN
& TCG meeting
Appointment of
ELIXIR TeCs
Creation of
task forces
Task forces
planning
Feb Mar Apr MayJan Jun
Definition and
prioritization of
Task forces
Jul Aug Sep Oct
19 Sep 2014
TCG meeting
Coordination of technical activities
(prioritized and common interest)
7 months old

9. Cloud TF
Use cases
• Infrastructure as a Service (IaaS)
• Platform as a Service (PaaS)
• Virtual Machine Repository or
Marketplace Portal
• Virtual Clusters
• Running Data Analysis Pipelines
• Data Extraction
• Scalable Web Service Hosting
• Shared Environment
• Virtual Desktops for Immediate Use
• Software Development and Testing
• Appliance
Projects
• EMBASSY cloud
• Elixir Competence Centre(CC)
• EGI Federated Cloud
• Cloud portal in collaboration with Bull
• Virtual Machine Library
• Australian Genomics Workbench
• Bioinformatics Tools: Genome Analysis
and Protein Folding (GAPF)
• Elixir Ensembl Pilot
• EYR Pilot
• BBMRI Cloud
• eLearning pilot with Computing pilot

10. Storage TF
• Survey of storage practices in node countries
• Discussions with EUDAT and EGI
• List of use cases
• BioImaging (collaboration agreement)
• Proteomics (pilot)
CSC
BILS
Site B
Site C
EUDAT CDIELIXIR
B2SAFE
B2SAFE
B2SAFE
B2SAFE
PRIDE
EMBL-EBI

11. AAI TF
8. Attributes across services
9. Sharing generic web based resources
10. eLearning platform and Cloud
Use case
Identity and
authentication
Authorisation
Access control
enforcement
1: Guest account service x
2: Bona fide researcher service x
3: Availability service x
4: REMS x
5: EGA x
6: Cloud and EGA x
7: Service Provider x

12. Service registry TF
Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
2013 20142013 2014
Collaboration with
BioMedBridges
started
Workshop in CPH,
critique of the registry
concepts
Registry structure defined:
MODEL - DATA -
UPKEEP
DebianMed/BioLinux
workshop in Stonehaven,
collaboration started
AllBio workshop
in Amsterdam,
collaboration started
Tool description model
completed
Interfaces releasedCollaboration
mechanisms conceived:
- other registries
- major tool providers
- user community
Further registry critique on
two workshops in CPH
REGISTRY RELEASE
Meeting in Lausanne:
starting the
collaboration with SIB

13. Mar
• Implementation
• Service delivery
• Best practice
FebJan
• SAB
DecNov
• 23d HoN
meeting
Oct
• Mail TF
feedback
• Mail TeC HoN
feedback
Sep
Service monitoring TF
Metrics
Workshop
Draft White Paper
+
Metrics Matrix
Discussion
TeCs HoNs

14. Communication TF
• Virtual meetings
• Collaborative writing
• Project management and documentation
• Mailing lists
• ELIXIR main Web Site

15. Website TF
• Web guidelines
• Template

16. Training portal TF - Training e-Support Service platform (TeSS)
Individuals content
providers:
• Lecturers
• Course Organizers
• Students
TeSS
TeSS
Website
Content
Consumer
Consumer’s
Website
TeSS
Bulk content providers:
• Software Carpentry
• GOBLET
• EMBL-EBI Train Online
• iAnn Events
• ELIXIR e-learning
• SysMIC etc
UK

17. e-Learning TF
• ELIXIR eLearning platform – EeLP
• In-depth survey
https://elixir.mf.uni-lj.si

18. Interoperability
Documentation and technologies
Standards
• Development of identifiers best practice
• Development of ontologies best practice
• Development of a registry of database
models
• Development of EDAM ontology (to model
types of identifiers)
• Development of a tools and dataservices
registry
Technical Integration
• Adoption of webservice best practices
• BioJS
• Semantic Web Technologies / RDF
Security
• Integrated security framework (single sign-
on)
• Legal and ethical requirements and
framework
Use cases and projects
• Interoperability of large scale image data sets from different
biological scales
• PhenoBridge - crossing the species bridge between mouse and
human
• Personalized Medicine - integrating complex data sets
• From cells to molecules - integrating structural data
• Integrating disease related data and terminology from samples of
different types
• Biosample information integration and discovery
• Federating biobank queries for translational research
• Sharing protein engineering knowledge
• Sharing and integrating medical imaging data
• Visualising and leveraging ontologies in queries: PLATO Plugin for
• Autocompletion on Ontologies
• Connectivity-Based Searching in UniChem
• Sharing and visualising sequencing data from environmentally-
derived biological samples
• Integrating mouse phenotype data for studying diabetes and
obesity
• Leveraging the utility of compound screening functional assays
• Integrating clinical trials metadata with the genes, drugs, and
publications they reference
• Connect clinical and lab workflows using TranSMART, Galaxy

19. ELIXIR Pilot Projects
1. ELIXIR Facing Cloud Support and Virtual Machines - with SIB
2. ELIXIR Data IO to pilot the continuous transfer of major archive
resources to a remote European location - with CSC, Finland
3. Establishing EGA Distributed authentication - with CSC, Finland
4. Establishing EGA as joint venture – with CRG, Spain
5. Improving links between Human Proteome Atlas (HPA) and EMBL-
EBI resources
6. BILS-ProteomeXchange integration using EUDAT resources
7. Interoperable controlled-access big data transfer technology for
ELIXIR - application to EGA EBI / CRG ELIXIR collaboration and
beyond
8. Harmonising Marine Metagenomics pipelines

20. Process – TCG involvement
Data interoperability,
vocabulary and
ontology services
Tools interoperability
and Service Registry
Data resources & service
s
Technical Services
Training
Ideas
TCG
+
TrCG
Oct 6
Pilots
INFRADEV3
Sep 30

21. Process – INFRADEV3
Data interoperability,
vocabulary and
ontology services
Tools interoperability
and Service Registry
Data resources & service
s
Technical Services
Training
Ideas Proposals
Drafts
WP
Oct 6 Oct 21
TCG
+
TrCG
WS leaders
+
TCG
HoNs
WP
HoNs
Jan 14

22. Pull of ideas (~50)

23. Pull of ideas - stats
• Described – 67%
• Pilots - 67%
• Infradev3 - 36%
1: Data
Resources &
Services
10%
2: Tools
Interoperabilit
y and Service
Registry
18%
3: Technical
Services
26%
4: Data
Interoperabilit
y, Vocabulary
and Ontology
services
16%
5: Training
Programme
23%
6: Domain
Specific
Services
7%
PoW

24. Pull of ideas - stats
Countries
NL
10%
EBI
10%
SI
9%
UK
8%
CH
8%
IT
7%
FI
7%
DK
5%
IL
4%
SE
4%
CZ
4%
EE
4%
PT
4%
NO
4%
FR
3%
ES
2%
SP
1%
FL
1%
GR
1%
CR
1%
SL
1%

25. ELIXIR

26. BD2K

27. References
ELIXIR Scientific Programme 2014-2018
• Official version
• Long version including complete content for work streams
• SAB general report January 2014
• Common challenges in data management, sharing and
integration across scientific disciplines
• Outcomes: Workshop on the current and future needs of
biological and biomedical sciences for infrastructures

28. European Life Sciences Infrastructure for Biological Information
www.elixir-europe.org
Thanks