Other Materials
Contents |
Proposed SBML extension for logical models and Petri-net
- Pre-meeting draft is available here : L3F extention draft 1.1.pdf (Updated on 11 of August)
- Some suggestions for this draft by Gwenael Kervizic : L3F_Gwenael_Kervizic.pdf
- A new proposal is available here: L3F Proposal
Existing File formats
Logical models
- GINML - the GINsim's format
Petri nets
Petri Net Markup Language (PNML)
- pnml.org
- hu-berlin.de
- PNML view is a simple, open source, cross-platform viewer for PNML files.
Pi-calculus
Websites
Logical models
Petri nets
- Petri Nets World - introduction, software, publications, community.
- Petri Nets Tools in Java - applets for simple PN simulations
Pi-Calculus
- BIOSPI
- SPiM
- C Kuttler, J Niehren, R Blossey. Gene regulation in the pi calculus: Simulating cooperativity at the lambda switch. Transactions on Computational Systems Biology VII, 2006 - Springer. Kuttler_TCSB_2006.pdf