Satellite Workshop Tutorial:
Hands-on tutorial on software tools for logical modeling


The objective of this (free) workshop is to provide hands-on experience with several logical modeling software tools. This tutorial will be made accessible to participants with no modeling experience as well as to those who are seasoned modelers.

Logical modeling provides a computational approach to the visualization and analysis of the dynamics of biochemical and biological systems complementary to others such as reaction-based or rule-based modeling. One of the main advantages of logical models is their scalability and the relatively easy method of construction. In part due to these attributes, logical models have become increasingly more popular among the computational biology community. This has, in turn, led to the development of different techniques and software tools that enable the construction, simulation, and analysis of logical models and their variants (Boolean, multilevel, deterministic, stochastic, etc.) to address various biological questions.​​​​​​​​​​

Reflecting the diversity and popularity of the community, the Consortium for Logical Modelling and Tools (CoLoMoTo, has been launched. This open community aims at promoting the logical modeling framework, and at providing scientists with standards as well as repositories for models and methods.​​​​​​​​

This workshop aims at extending the outreach of CoLoMoTo, providing an overview of recent achievements that render possible the modeling and the analysis of large cellular networks, covering intricate signaling pathways, sophisticated transcriptional networks, as well as novel regulatory mechanisms.

Specifically, four hands-on tutorials will cover the following software tools: Cell Collective (, CellNOpt (, GINsim (, and PyBoolNet (



21st September 09:00 – 18:30

Morning Session

 9:00-09:30 Welcomome and Introduction to logical frameworks
 9:30-12:30 CellNOpt: Emanuel Gonçalves (Coffee break 10:30-11:00)
 9:30-12:30 GINsim: Pauline Traynard & Céline Hernandez (Coffee break 10:30-11:00)
 12:30-14.30 Lunch (on your own)

Afternoon Sessioin

 14:30-17:00 Cell Collective: Tomas Helikar
 14:30-17:00 PyBooINet (Command line!): Hannes Klarner
 17:00-18:30 Coffee (or Beer!) + conclusions

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