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Logical modelling tutorial at ECCB 2018

Anna Niarakis and Denis Thieffry organized a one-day workshop dedicated to Logical Modelling in the context of the European Conference on Computational Biology. This workshop took place in Athens on September 08, before the main ECCB conference (September 09-12). More details are available on the workshop page.

Group picture of the participants


Logical models have long been used to explore the dynamical behaviours of regulatory networks. This workshop provides an overview of recent methodological developments and applications on the use of the logical formalism for the modelling of regulatory networks, covering the following main topics:

  • Computational methods: attractor identification, model-checking, reduction techniques, network inference
  • Modelling tools: GINsim, CellNetOpt, boolSim, MaBoSS, CellCollective, EpiLog, ...
  • Biological applications: signalling networks, cell differentiation, cell reprogramming

The workshop was split in two sessions: the first session is dedicated to recent methodological developments, the second session to biological case studies. Each of these sessions includes one introductory talk. It is further articulated with a tutorial organized by Tomas Helikar and Juilee Thakar on Sept 9th, 2018, thereby forming a two-days long SIG meeting devoted to logical modelling of cellular networks.

Schedule and slides

Time Speaker Title
09h00 A Niarakis Welcome and introduction to the workshop
Session I: Methods and tools Chair: C Chaouiya (Oieras)
09h10 L Tournier (Jouy en Josas) Analyzing interconnections of asynchronous Boolean networks with biological applications (slides)
09h40 E Gjerga (Aachen) Advances in computational methods for the modelling of signalling networks (slides)
10h00 L van der Zee (Amsterdam) Deciphering yeast physiology by a multi‐scale framework integrating cell cycle and metabolism
10h20 L Paulevé (Saclay) Boolean Networks: Beyond Generalized Asynchronicity (slides)
10h40 Coffee/tea break
Session II: Methods and tools. Chair: I Xenarios (Lausanne)
11h10 L Sun (Berlin) Logical modelling: Inferring structure from dynamics (slides)
11h30 A Niarakis (Evry) Automated pipeline for the inference of Boolean models from molecular interaction maps (slides)
11h50 C Réda & B Wilczynski (Warsow) Automated Inference of Gene Regulatory Networks Using Explicit Regulatory Modules (slides)
12h10 Lunch break
Session III: Applications. Chair: M Barberis (Amsterdam)
13h30 I Koch (Frankfort) Concepts for functional analysis of signaling pathways in complex networks based on Manatee invariants (slides)
14h00 C Hernandez (Paris) Dynamical modelling of T cell co-inhibitory pathways to predict anti-tumour responses to checkpoint inhibitors (slides)
14h20 J Dorier (Lausanne) Integrative logical and experimental modeling: application to macrophage phenotype transition
14h40 G Selvaggio (Oieras) Logical modelling and analysis of cell adhesion properties along Epithelial to Mesenchymal Transition (slides)
15h00 Coffee/tea break
Session IV: Applications. Chair: A Niarakis (Evry)
15h20 FM Khan (Rostock) Identification of Diagnostic and Therapeutic Markers in Tumor Invasion using Logic-based Modeling (slides)
15h40 A Montagud (Paris) Patient-specific prostate logical models allow clinical stratification of patients and personalized drug treatment (slides)
16h00 L Benoodt (Rochester) Dysregulated signaling networks implicated in vascular aging of HIV+ subjects investigated by logical modeling
16h20 A Siegel (Rennes) Learning Boolean regulations of a metabolic network: a case-study (slides)
Conclusions, discussion & drinks