GT Bioss Days 2024: CoLoMoTo Workshop
===
- Date: **Wednesday 29 May 9h30-12h30**
- Place: **Room 306 (3rd floor), IBENS, ENS Paris** (46 rue d’Ulm, 75005 Paris)
:::info
:information_source: A Zoom link for listening to the talks will be provided soon.
:::
### Objectives
- Review the tools developped by our community and their sharing through the CoLoMoTo suite.
- Discuss on the current state and future of CoLoMoTo Docker distribution.
- Improve the collective organisation of the consortium.
### Program
- 9h15 - 9h30: Welcome
- 9h30 - 10h00: Loïc Paulevé (CNRS/LaBRI, Bordeaux): *Current state of the CoLoMoTo Docker distribution*
- 10h00 - 10h30: Invited talk: Pedro Monteiro (Lisbon, Portugal): *Using ModRev to automatically repair Boolean models with new data*
- 10h30 - 11h10: Flash talks on softwares (5min per talk, no Q&A)
1. Franck Delaplace (IBISC, Evry): *BooN une plateforme pour l'analyse des réseaux Booléens en Python*
2. Clémence Reda (Universität Rostock): *NORDic: drug response simulation and drug repurposing*
3. Tony Ribeiro (LS2N, Nantes): *PyLFIT: package python pour le framework Learning from Interpretation Transition*
4. Mathieu Hemery (Inria Saclay): *Biocham: Python API?*
5. Francisco Planes (Tecnun, University of Navarra): *gMCSpy: computing genetic minimal intervention sets in large integrated metabolic and regulatory models*
6. Maxime Mahout (Inria Saclay): *aspefm: calcul des modes élémentaires de flux avec Answer Set Programming*
7. Marius Kirchner (Goethe University Frankfurt, Germany): *MonaLisa - SBML Extension for Petri nets*
- 11h10 - 11h40: *Break*
- 11h40 - 12h45: Discussion topics
- Tutorial: Use of CoLoMoTo Docker, how to integrate a tool
- Technical aspects: packaging, maintenance, archiving.
- Delimitation of softwares, challenges in the integration of new tools: Biocham, PhysiBoSS?
- SED-ML for SBML-qual, KiSAO terms for logical models, annotations & IDs (FAIRification).
- Communication and organisation: Web sites, github, mailing list, opening to new members, workshops, tutorials, coordination.
- Interactions with COMBINE.
### Organization
- Loïc Paulevé (CNRS, LaBRI, Bordeaux)
- Denis Thieffry (ENS Paris)
- GT Bioss - https://gt-bioss.cnrs.fr
With funding from CNRS [GDR BIMMM](https://www.gdr-bim.cnrs.fr/), [GDR IFM](https://www.gdr-im.fr/), and [GDR RADIA](https://gdr-radia.cnrs.fr/).