SED-ML Meeting

The Simulation Experiment Description Markup Language (SED-ML) is an exchange format for simulation experiments in computational biology and related fields.

The first version of the language has been released as SED-ML L1V1 in March 2011. The further development and promotion of SED-ML is one of the project goals of the BMBF-funded SEMS project at the SBI.

The first workshop of the SEMS project aims to evaluate the current status of SED-ML, in particular with respect to:

  • How is SED-ML currently being used by other projects? Which concepts of SED-ML are of most interest to other research groups implementing SED-ML support?
  • What are the applications of SED-ML in systems biology, medicine and the neuro sciences?
  • Which software tools support SED-ML? Which databases offer links to SED-ML descriptions?

We aim close the meeting with an outlook for the year 2013, collecting to-dos for further development of SED-ML.


The meeting will take place from the 19th-22nd of November 2012 at the Department of Systems Biology and Bioinformatics at the University of Rostock (directions).

MON, 19th of November 2012  
12:00 – 13:00 Arrival/self-funded lunch (Mensa)
13:30 – 15:00 Invited Talk: COPASI (Sven Sahle, BIOQUANT)
15:00 – 15:30 Coffee break
15:30 – 17:00 Session I : Plan for days 2 + 3, Nested vote
19:30 Uhr Workshop dinner: Warmbad
TUE, 20th of November 2012  
8:45- 9:00 Welcome & Coffee
09:00 -10:00 Session II: Editors meeting
10:00- 11:30 Session III: Nested / multiple sub-tasks
11:30 – 13:00 Self-funded lunch
13:00 – 14:00 Session IV: Nested/multiple sub-tasks
14:00 – 15:30 Session V: Parameter estimation
15:00 – 15:30 Coffee break
15:30 – 17:00 Session VI: Parameter estimation/post-processing
WED, 21st of November 2012  
8:45 - 9:00 Welcome & Coffee
09:00 -11:00 Session VII: SED-ML specification update
11:00 – 12:30 Self-funded lunch (Mensa)
12:30- 14:30 Session VIII: Discussion further development
14:30 – 15:00 Coffee break
15:00 – 17:00 Session IX: Discussion further development
17:00 Workshop summary

Useful information

You are welcome to join the meeting either in person of remotely through Evo.

Remote attendance
If you wish to attend remotely, please connect to the Evo meeting via Evo gate. We will unfortunately not be able to broadcast the talk by Sven Sahle on Monday, but will be online from 3:00pm.

Meeting dinner
We will meet in the pub "Warmbad", Niklotstrasse 2 (near Doberaner Platz) on Monday evening, 7:30pm.

Meeting documents