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Systems Biology Data Management Foundry: A meeting for practitioners

6th – 7th October 2014 - Heidelberg, Germany

About the workshop

Data management is generally recognized as a crucially important but challenging part of Systems Biology. Data management systems that are useful, usable and used are difficult to get right. It is not easy to find out about already existing software, or the state of standards that could or should be adopted. Following the outstanding success of the Systems Biology Software Developers Workshop in 2012, we propose the next meeting in the series that enables practitioners in the field to meet like-minded scientists, show their working and upcoming developments, and give opportunities to team up. A meeting to socialize, yes. But also a meeting to figure out how we can improve collaboration of data management practitioners beyond project borders in the light of ESFRI and other, national infrastructure movements, as well as the move from systems biology to systems medicine and synthetic biology. Our end goal is to establish a Foundry for Systems Biology Software development.

  • How do we interlink with other resources and tools with the goal of making more of our own development?
  • How can we have the best of lively development and reliable infrastructures in a world shaped by consensual ESFRI infrastructures?
  • How can we prepare our systems and policies for scientific computing infrastructures to become more dynamic, and data and code to move between computing clouds?
  • How do we make use of standards in our work?
  • How do we shape standards in the interest of sustainable software development for our users?
  • What do we expect from national/international infrastructures for the future of our software?
  • How can we achieve true sustainability of our developments?

To establish a practitioner’s community that the workshop focuses on active participation:

  • Two invited talks about software sustainability (Dr. Neil Chue Hong, director of the Software Sustainability Institute) and infrastructures for warm up and to get us started.
  • A series of innovative interactive show-and-tell sessions that take the best from scientific speed dating and lightning talks. Let us all get to show our software and drill down on others.
  • World café sessions yielding ideas for recommendations to funders and infrastructures
  • Wrap up with collected recommendations for funders and practitioners


The workshop will be held at the Studio Villa Bosch in Heidelberg, Germany. (Google Maps).

Who should come?

Participation is limited to 25 people and the intended participants are software developers working in the field of data management in biology.

If you want to participate you should be:

  • fluent in at least one programming language
  • daily working as either a programmer or as someone concerned with software engineering or code audit.
  • willing to participate in discussions about the (technical) future and extensibility of the software project you are involved with.

Participation in the workshop is free. However, participants have to bear travel and accommodation costs by themselves, and we reserve the right to pick participants.

Preliminary Program


11:00 - 11:15 welcome and outline

11:15 Invited talk about software sustainability. Speaker: Neil Chue Hong, Director of Software Sustainability Institute, Edinburgh.

12:30 lunch

13:30 Start interactive demonstration/discussion 3 groups of 5 parallel sessions, 40 minutes each. Each demo/talk is about 10 minutes and is given several times to varying small groups of people! Each parallel session will see all tables. This way, we get small discussion groups that which facilitates true, interactive discussion.

Questions to be addressed in each lightning demo:

  • what does my tool/data source do?
  • what are the *neighbors* (natural interaction partners) of the tool?
  • what are the *users* of the tool?
  • what is the current sustainability concept?
  • how does this fit in with ELIXIR/ISBE/National efforts?


09:00 Assemble, Coffee, Lee way

09:30 Short introduction: “What is ISBE?” (Carole Goble)

10:00 World café about questions voiced in workshop call, 4 tables

11:00 break

11:15 round 2

12:30 lunch break

13:30 collection session, outcomes: Recommendations for single groups/tools, infrastructure projects, funders.

15:00 end

How to apply

To apply to the workshop, please send an email to

The email should contain the following details:

  • Subject: Foundry workshop

In the message body please provide details about:

  • Address;
  • the project you are involved in;
  • links to software artefacts Function in that project;
  • System you are ready to demo at the meeting.


We (HITS) have blocked rooms in the IBIS right next to the main Heidelberg station, for the time from 5th to 7th of october. Please reserve there on acceptance.

Details about the hotel can be found there: following this link


The workshop is being sponsored by ERASysAPP.

The workshop is organized by

  • Carole Goble, University of Manchester
  • Wolfgang Müller, HITS gGmbH, Heidelberg
  • Bernd Rinn, ETH Zürich and SIB
  • Dagmar Waltemath, University of Rostock
events/foundry_workshop.txt · Last modified: 2016/07/27 16:39 (external edit)