QualMod2019: Qualitative computational modeling for biological networks Okinawa, Japan, October 31, 2019 |
Conference website | https://www2.aeplan.co.jp/icsb2019/tutorials_satellite.html |
Submission link | https://easychair.org/conferences/?conf=qualmod2019 |
Abstract registration deadline | September 1, 2019 |
Submission deadline | September 1, 2019 |
Program:
Session 1 | Regulatory circuits | Chair: Takeyuki TAMURA | 9h | ||
FAURÉ | Adrien | Yamaguchi | Introduction | 9h | |
KAUFMAN | Marcelline | Brussels | Link between logical structure and dynamics in genetic and (bio)chemical reaction networks | 9h15 | |
FAURÉ | Adrien | Yamaguchi | Circuit functionality: towards a new definition | 10h00 | |
Pause | 10h30 | ||||
Session 2 | Signalling/regulatory networks | Chair: Marcelle KAUFMAN | 11h | ||
KOCH | Ina | Frankfurt | Petri net modelling in the context of big data omics | 11h00 | |
THIEFFRY | Denis | Paris | Computational verification of large logical models - application to the prediction of T cell response to checkpoint inhibitors | 11h45 | |
Discussion | 12h15 | ||||
Lunch | 12h30 | ||||
Session 3 | Hybrid and multiscale models | Chair: Adrien FAURÉ | 14h00 | ||
TAMURA | Takeyuki | Kyoto | Integer linear programming-based methods for controlling Boolean metabolic networks | 14h00 | |
BARBERIS | Matteo | Surrey | Deciphering Yeast Physiology by a Multi‐scale Framework Integrating Cell Cycle and Metabolism | 14h45 | |
Pause | 15h15 | ||||
Session 4 | Tools | Chair: Ina KOCH | 15h45 | ||
NOËL | Vincent | Paris | Stochastic simulations with MaBoSS ecosystem | 16h15 | |
NALDI | Aurélien | Paris | The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks | 16h45 | |
THIEFFRY | Denis | Paris | Wrap-up | 17h15 |
Dear colleagues,
It's our pleasure to invite you to Okinawa for a workshop on Qualitative computational modeling for biological networks.
This workshop is a satellite of ICSB2019.
Applications are now open for oral presentation based on abstract submission.
Submissions will be selected by the workshop's scientific committee.
Motivation and scope
Interactions networks have been used to represent and study biological systems small and large, ranging from genes and metabolites all the way to ecosystems, and from a handful of components to several hundreds and more. Recent technical developments have brought new challenges to the field: more data to exploit, integrate and interpret, multi-scale modeling, larger networks and models to annotate and parametrize, analyze and simulate. Meanwhile, questions regarding fundamental properties of these systems, such as the role of motifs and circuits in the emergence of dynamical properties, are still being actively pursued. Furthermore, although qualitative approaches such as logical models and Petri nets have been used for several decades, new methods and formats and tools keep appearing, calling for the development of common standards to ensure interoperability. In this context, this workshop aims at gathering the network modeling community, sharing progress among its members, and strengthening the links within the community as a whole.
The workshop will consist of three sessions:
- Session 1 will be dedicated to the development of community standards, interoperability, and model curation/annotation.
- Session 2 will be dedicated to methodological aspects, including network inference, model checking and the computation of dynamical propertiess.
- Session 3 will be devoted to the analysis and simulation of large cellular networks.
Submission Guidelines
- Title
- List of authors
- Affiliations
- Abstract (maximum 300 words)
List of Topics
- Boolean and logical modeling
- Petri nets
- community standards development and interoperability
- model composition and modularity
- model checking
- analytical methods
- network inference
- regulatry circuits and their dynamical properties
- model curation and annotation
Committees
Scientific Committee
- Tatsuya Akutsu (Institute for Chemical Research, Kyoto University, Kyoto, Japan)
- Réka Albert (Pennsylvania State University, Pennsylvania)
- Claudine Chaouiya (Aix-Marseille University, France / Gulbenkian Institute, Portugal)
- Thomas Helikar (Department of Biochemistry, University of Nebraska, USA)
- Ina Koch (Institute of Computer Science, Goethe University, Frankfurt, Germany)
- Reinhard Laubenbacher (Jackson Laboratory / UConn School of Medicine, Connecticut)
- Hiroshi Matsuno (Yamaguchi University, Japan)
- Atsushi Mochizuki (Kyoto University, Japan)
- Heike Siebert (Berlin Free University, Germany)
Organizers
- Adrien Fauré (Yamaguchi University, Japan)
- Denis Thieffry (Ecole Normale Supérieure, Paris, France)
Invited Speakers
- Marcelle Kaufman (Université Libre de Bruxelles, Belgium)
- Edda Klipp (Humboldt Universität, Berlin, Germany)
- Takeyuki Tamura (Institute for Chemical Research, Kyoto University, Kyoto, Japan)
Venue
Okinawa Insitute of Science and Technology Graduate University
Contact
All questions about submissions should be emailed to afaure@yamaguchi-u.ac.jp