SySMO modelers workshop agenda
Tuesday, 8th of March
9:30 – 10:00 Arriving, coffee
10:00 -10:15 Introduction to the workshop (Jacky Snoop)
10:15 – 11:00 Illustration of the functionality of OneStop: new tool for model construction, schema generation, model annotation (Franco Du Preez)
Jacky's and Franco's presentations here
11:00 – 11:30 coffee break
11:30 -12:30 Participants work on:
- Example 1: a mathematical description for a very simple model to learn how to use OneStop (Franco & Jacky & everyone)
- Example 2: work with the own model or with a given realistic model to work with, to obtain an SBML model description, possibly with SBGN schema and MIRIAM annotation
12:30 – 13:00 Standards for computational systems biology: SBML, SBGN, MIRIAM (Jacky & Franco)Talk here
13:00-14:00 Lunch
14:00- 14:40 The workflow of constructing and validating models and its representation in SEEK: examples from SySMO projects:
Maksim Zakhartsev/MOSES and Ulf Liebal/BaCell)
14:40 – 15:40 The workflow of constructing and validating models
examples from JWS online & discussion
15:40 – 16:00 Coffee break
16:00 – 17:00 More standards:
KiSAO (Kinetic Simulation Algorithm Ontology)
Wednesday, 9th of March
10:00 – 11:00 Complexity reduction of nonlinear biochemical networks models.
Irina Surovtsova (Bioquant, Heidelberg)
Talk here
