The fourth CoLoMoTo meeting took place in Paris, from the 17th to the 19th of July, 2017. As usual, the meeting covered a wide range of topics related to logical modelling, from methodological and software developments to biological applications. It was hosted by IBENS in the center of Paris (46 rue d'Ulm).
This meeting was organized by Aurélien Naldi (IBENS, Paris), Claudine Chaouiya (IGC, Lisbon), Denis Thieffry (IBENS, Paris), Gautier Stoll (INSERM, IGR, U. Paris Descartes), and Laurence Calzone (Curie Institute, Paris).
Also see the minutes of the discussions.
July 17 - Scientific Presentations
| Time | Speaker | Title |
|---|---|---|
| 13:00 | Introductory remarks | |
| 13:20 | Gautier Stoll | Using MaBoSS for modeling heterogeneous cell behavior |
| 13:40 | Samuel Collombet | Deciphering the regulatory network of blood cells specification and reprogramming |
| 14:00 | Coffee Break | |
| 14:30 | Loïc Paulevé | Modelling and analysis of transient dynamics of qualitative models (tutorial) |
| 14:50 | Enio Gjerga | Efficient modelling of signalling networks derived from mass spectrometry phosphoproteomic data using Integer Linear Programming |
| 15:10 | Ping Zhang | Control and Diagnosis of Boolean Networks |
| 15:30 | Coffee Break | |
| 16:00 | Anna Niarakis | Integrative modelling and analysis of molecular pathways involved in Rheumatoid Arthritis |
| 16:20 | Arnau Montagud | Conceptual and computational framework for logical modelling of deregulated biological networks |
| 16:40 | Claudine Chaouiya | Standards for logical models: current status of SBML qual & SED-ML |
| 17:00 | Discussion - planning workgroups |
July 18 - Working groups and Presentations
| Time | Speaker | Title |
|---|---|---|
| 09:00 | Working group on tooling | |
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Aurélien Naldi | Model conversion, modification, and analysis with bioLQM |
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Loïc Paulevé | Jupyter Notebook |
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Claudine Chaouiya | Future extensions to SBML qual and SED ML |
| 12:30 | Lunch break | |
| 13:30 | Working group on applications | |
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Laurence Calzone | Model composition |
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Gautier Stoll | Modelling the immune system |
| 15:30 | Working group on methods | |
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Pedro T. Monteiro | On the structure and robustness of gene regulatory network Boolean functions |
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Adrien Fauré | A circuit-preserving mapping from multilevel to Boolean dynamics |
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Aurélien Naldi | Trap-spaces and global reachability mapping |
| 17:30 | Wrapping-up |
July 19 - Wrapping up and hacking
| Time | Title |
|---|---|
| 10:00 | MaBoSS Tutorial |
| 10:00 | Docker session |
| 12:00 | Discussion and Wrapping-up |
Participants
- Adrien Fauré (Yamaguchi University)
- Anna Niarakis (Université d'Evry Val d'Essonne)
- Arnau Montagud (Institut Curie)
- Aurélien Naldi (IBENS)
- Célia Biane (UEVE, IBISC Lab)
- Céline Hernandez (IBENS)
- Claudine Chaouiya (Instituto Gulbenkian de Ciência)
- Daniela Ferretti (University of Camerino)
- Delphine Potier (CIML)
- Denis Thieffry (IBENS)
- Élisabeth Remy (CNRS)
- Enio Gjerga (JRC COMBINE, RWTH Aachen University)
- Gautier Stoll (INSERM U1138eq11/Université Paris 5/Gustave Roussy)
- Geoffray Brelurut (IBENS)
- Ghislaine Morvan-Dubois (CNRS)
- Hugues Mandon (INRIA - LSV - LRI)
- Laurence Calzone (Institut Curie)
- Loïc Paulevé (CNRS/LRI)
- Nathalie Lehmann (IBENS)
- Paolo Ballarini (CentraleSupelec)
- Pauline Traynard (Institut Curie)
- Pedro T. Monteiro (INESC-ID/IST - Universidade de Lisboa)
- Ping Zhang (University of Kaiserslautern, Institute of Automatic Control)
- Samuel Collombet (IBENS)
- Samyadeep Basu (IBENS)
- Seraya Maouche (TBi Scientific)
- Swann Flochlay (IBENS)
- Tomas Helikar (University of Nebraska)
- Vidisha Singh (Genhotel, University of Evry val d'essonne)
- Wassim Abou-Jaoude