SBI – Department of Systems Biology and Bioinformatics
Faculty of Computer Science and Electrical Engineering
University of Rostock
Ulmenstrasse 69 | 18057 Rostock
Germany
+49 381 498-7571
olaf.wolkenhauer@uni-rostock.de
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.
Schedule
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
Participation
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