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Systems Biology Data Management Foundry Workshop
ERASysAPP – ERA-Net on Systems Biology Applications
Monday, October 6, 2014, 11:00 h –19:15 h
Tuesday, October 7, 2014, 9:00 h – 17:45 h
@ Studio Villa Bosch Heidelberg
Schloss-Wolfsbrunnenweg 35
69118 Heidelberg
FAIRDOM
• Findable
• Accessible
• Interoperable
• Reusable
• Data
• Operations
• Models
Organisers & Participants
Organisers:
• Carole Goble (U Manchester, FAIRDOM)
• Wolfgang Müller (HITS Heidelberg, FAIRDOM)
• Bernd Rinn (ETH Zürich, FAIRDOM)
• Dagmar Waltemath (U Rostock)
Participants:
35 people based in 5 nations: UK, USA, Germany,
Switzerland, Slovenia
Topics
• Improve collaboration of Data Management
(DM) practitioners
• Look at opportunities in current landscape
– ESFRIs
– Large projects
– Move from systems bio to synthetic bio and
systems medicine
• Move towards establishment of foundry
Concrete goals for the WS
• Better understanding of >1 systems you‘ve
never seen before
• Generate ideas for cross-integration
• Share ideas about sustainability
• Form group of developers supported through
FAIRDOM
• Contribution to ESFRI ISBE
– Needs?
– What can the community provide?
Day 1: Talk by Neil Chue Hong
Software is
• everywhere
• long-lived
• hard to define
All these matter:
• Context
• Reasons
• People
Hugely inspirational talk. Large set of surprising examples and solution approaches.
Software carpentry, cultivating contributors for long-term maintenance. Hiring hard for old
projects...
Day 1: Show and tell sessions
Everybody sees systems presented by everyone else
Starting point for collaborations
Big topics: Docker, Galaxy + other workflow systems,
data management adapting to changing data, semantics
Day 2: Discussions about landscape
• Highlight ESFRI infrastructures as central entry
point for infrastructure as well as
software/legal/business model/security
advice
• ISBE as data integration facilitator, enabler,
support broker
• People as community and problem solvers
• Teaching: Towards common certificates
Outcomes & suggested improvements
• Outcome
– Positive echo, participants report
• having seen new software
• seeing new collaboration opportunities
– Public wiki for communication
– Plan for next meeting (possibly Slovenia)
• Suggested improvements:
– More time for overall workshop‚
– Fewer, longer presentations in roughly same interactive format
– More breaks for follow-up discussions
– More information about other presentations
up-front
– Means: More selection of talks
Next meetings
• We have funding for meetings held in
Germany or UK. Foundry meetings can be part
of this.
• To internationalize Foundry it would be
desirable if we could use that funding in other
countries, e.g. Slovenia.
• Very desirable would be funding for travel
grants

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Report of the second FAIRDOM foundry

  • 1. Systems Biology Data Management Foundry Workshop ERASysAPP – ERA-Net on Systems Biology Applications Monday, October 6, 2014, 11:00 h –19:15 h Tuesday, October 7, 2014, 9:00 h – 17:45 h @ Studio Villa Bosch Heidelberg Schloss-Wolfsbrunnenweg 35 69118 Heidelberg
  • 2. FAIRDOM • Findable • Accessible • Interoperable • Reusable • Data • Operations • Models
  • 3. Organisers & Participants Organisers: • Carole Goble (U Manchester, FAIRDOM) • Wolfgang Müller (HITS Heidelberg, FAIRDOM) • Bernd Rinn (ETH Zürich, FAIRDOM) • Dagmar Waltemath (U Rostock) Participants: 35 people based in 5 nations: UK, USA, Germany, Switzerland, Slovenia
  • 4. Topics • Improve collaboration of Data Management (DM) practitioners • Look at opportunities in current landscape – ESFRIs – Large projects – Move from systems bio to synthetic bio and systems medicine • Move towards establishment of foundry
  • 5. Concrete goals for the WS • Better understanding of >1 systems you‘ve never seen before • Generate ideas for cross-integration • Share ideas about sustainability • Form group of developers supported through FAIRDOM • Contribution to ESFRI ISBE – Needs? – What can the community provide?
  • 6. Day 1: Talk by Neil Chue Hong Software is • everywhere • long-lived • hard to define All these matter: • Context • Reasons • People Hugely inspirational talk. Large set of surprising examples and solution approaches. Software carpentry, cultivating contributors for long-term maintenance. Hiring hard for old projects...
  • 7. Day 1: Show and tell sessions Everybody sees systems presented by everyone else Starting point for collaborations Big topics: Docker, Galaxy + other workflow systems, data management adapting to changing data, semantics
  • 8. Day 2: Discussions about landscape • Highlight ESFRI infrastructures as central entry point for infrastructure as well as software/legal/business model/security advice • ISBE as data integration facilitator, enabler, support broker • People as community and problem solvers • Teaching: Towards common certificates
  • 9. Outcomes & suggested improvements • Outcome – Positive echo, participants report • having seen new software • seeing new collaboration opportunities – Public wiki for communication – Plan for next meeting (possibly Slovenia) • Suggested improvements: – More time for overall workshop‚ – Fewer, longer presentations in roughly same interactive format – More breaks for follow-up discussions – More information about other presentations up-front – Means: More selection of talks
  • 10. Next meetings • We have funding for meetings held in Germany or UK. Foundry meetings can be part of this. • To internationalize Foundry it would be desirable if we could use that funding in other countries, e.g. Slovenia. • Very desirable would be funding for travel grants