W6 – Logical modelling of cellular networks



Date: Saturday September 8, 2018
Time: 9:00 – 17:00
Venue: Stavros Niarchos Foundation Cultural Center
Room: A2.00.127

Download the abstract booklet here




Logical models have long been used to explore the dynamical behaviours of regulatory networks.

This workshop will provide an overview of recent methodological developments and applications on the use of the logical formalism for the modelling of regulatory networks.

Relying on a community effort with the Consortium for Logical Models and Tools (CoLoMoTo – http://colomoto.org​) to promote the exchange of models and to improve existing methods, this workshop will cover 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 is articulated with a tutorial proposal (Sept 9th, 2018) organized by Tomas Helikar and Juilee Thakar, thereby forming a two-days long SIG meeting devoted to logical modelling of cellular networks.

The workshop day (Sept 8th, 2018) will be split in two sessions: the first session will be dedicated to recent methodological developments, the second session to biological case studies.
Each of these sessions will include one introductory talk.

At the end of the day, a round table with all speakers and the audience will be devoted to global discussions.



09h00-09h10 A Niarakis Welcome and introduction to the workshop
09h10-10h40 C Chaouiya (Oieras) – Chair Session I: Methods and tools (1)
09h10-09h40 L Tournier (Jouy en Josas ) Analyzing interconnections of asynchronous Boolean networks with biological applications
09h40-10h00 E Gjerga et al (Aachen) Advances in computational methods for the modelling of signalling networks
10h00-10h20 L van der Zee et al (Amsterdam) Deciphering yeast physiology by a multi‐scale framework integrating cell cycle and metabolism
10h20-10h40 T Chatain et al (Saclay) Boolean Networks: Beyond Generalized Asynchronicity
10h40-11h10 Coffee/tea break
11h10-12h40 I Xenarios (Lausanne) – Chair  Session II: Methods and tools (2)
11h10-11h30 L Sun et al (Berlin) Logical modelling: Inferring structure from dynamics
11h30-11h50 S Pankaew et al (Evry) Automated pipeline for the inference of Boolean models from molecular interaction maps
11h50-12h10 C Réda & B Wilczynski (Warsow) Automated Inference of Gene Regulatory Networks Using Explicit Regulatory Modules
12h10-13h30 Lunch break
13h30-15h00  M Barberis (Amsterdam) – Chair Session III: Applications (1)
13h30-14h00 I Koch (Frankfort) Concepts for functional analysis of signaling pathways in complex networks based on Manatee invariants
14h00-14h20 C Hernandez et al (Paris) Dynamical modelling of T cell co-inhibitory pathways to predict anti-tumour responses to checkpoint inhibitors
14h20-14h40 J Dorier et al (Lausanne) Integrative logical and experimental modeling: application to macrophage phenotype transition
14h40-15h00 G Selvaggio et al (Oieras) Logical modelling and analysis of cell adhesion properties along Epithelial to Mesenchymal Transition
15h00-15h20 Coffee/tea break
15h20-17h00 A Niarakis (Evry) – Chair Session IV: Applications (2)
15h20-15h40 FM Khan (Rostock) Identification of Diagnostic and Therapeutic Markers in Tumor Invasion using Logic-based Modeling
15h40-16h00 A Montagud et al (Paris) Patient-specific prostate logical models allow clinical stratification of patients and personalized drug treatment
16h00-16h20 L Benoodt et al (Rochester) Dysregulated signaling networks implicated in vascular aging of HIV+ subjects investigated by logical modeling
16h20-16h40 A Cornet et al (Rennes) Learning Boolean regulations of a metabolic network: a case-study
16h40- Conclusions, discussion & drinks





This workshop targets students and researchers interested in learning about the recent developments on modelling regulatory networks, ranging from recent biological applications, to the development of methods and tools. This workshop will be a unique opportunity for participants to discover and discuss state of the art methods in logical modelling and their applications to biological problems.



  • Ina Koch, Molecular Bioinformatics, Institute of Computer Science, Goethe-University Frankfurt am Main, Germany
  • Laurent Tournier,  MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France



  • Matteo Barberis, University of Amsterdam, Netherlands
  • Claudine Chaouiya, Instituto Gulbenkian de Ciência, Portugal
  • Benjamin Hall, MRC Cancer Unit, University of Cambridge
  • Tomas Helikar, University of Nebraska – Lincoln, USA
  • Anna Niarakis, Univ Evry, Université Paris-Saclay, France
  • Julio Saez-Rodriguez, RWTH-Aachen University, Germany
  • Denis Thieffry, École Normale Supérieure, Paris, France
  • Ioannis Xenarios, Vital IT / Swiss Bioinformatics Institute, Switzerland
  • Juilee Thakar, University of Rochester Medical Center, Rochester, New York, USA



Abstract submissions for oral and poster presentations should be send to the following addresses anna.niaraki@univ-evry.fr, thieffry@ens.fr with the indication: ECCB18 Workshop Submission.

Abstracts should include title, author affiliation and contact information and a summary of the work that should not exceed 600 words.



Registration to the workshop is done through the ECCB registration page.



Submission Opening date: April 24, 2018
Submission Deadline (abstract): June 20, 2018
Notification: July 05, 2018
Workshop Date: September 8, 2018