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Logical modelling tutorial at ECCB 2018

Tomas Helikar (University of Nebraska at Lincoln, USA) and Juilee Thakar (University of Rochester, Medical Center, USA) organized a one-day tutorial dedicated to Logical Modelling tools in the context of the European Conference on Computational Biology. This workshop took place in Athens on September 09, before the main ECCB conference (September 09-12). More details are available on the tutorial page.


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.​​​​​​​​​​

The tutorial will begin with an overview of logical modeling, followed by hands-on tutorial sessions on four complementary tools widely used by researchers around the world. Through the tutorials and each tool, you will learn how to construct (manually as well as infer from high-throughput data), simulate, and analyze the dynamics of logical computational models. The objective of the tutorial is that you will be able to begin using logical modeling, and the software tools for your own research. The core logical modeling software tools to be covered in the tutorial include Cell Collective, CellNOpt, GINsim, and the CoLoMoTo notebook.

Schedule and slides

Time Speaker Title
09:00   Introduction (slides)
09:15 Julio Saez-Rodriguez CellNetOpt (slides)
11:00 Tomas Helikar Cell Collective (slides)
12:30   Lunch break
13:30 Denis Thieffry & Aurélien Naldi GINsim (slides)
15:30 Loïc Paulevé The CoLoMoTo notebook (slides)