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) - 🌐 Zoom: https://u-bordeaux-fr.zoom.us/j/85420546177?pwd=THRUSHVSU0cvbDhhYmMwWVprellOdz09 (Meeting ID: 854 2054 6177 -- Passcode: 875158) ### 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 - 11h00: *Break* - 11h00 - 11h40: 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* - 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/).