GT Bioss Days 2024: CoLoMoTo Workshop === - 📅 Date: **Wednesday 29 May 9h30-12h30** - 📌 Place: **Salle Favard (rez-de-chaussé), IBENS, ENS Paris** (46 rue d’Ulm, 75005 Paris) + 🌐 Zoom :::warning - :pencil: Notes for discussion on CoLoMoTo organization https://codimd.math.cnrs.fr/YhKFZIs_RqS00FMhu3cTPA?both Please complete with suggestions, remarks, and put your name for tasks you may be volunteer to help - Slides: - [️🖥️ Status of CoLoMoTo Docker distribution](https://loicpauleve.name/md/p/mKXIXf5Yk#/), including steps to request tool inclusion - [🖥️ ModRev (Pedro Monteiro)](https://mycore.core-cloud.net/index.php/s/xopDImJqVkx6RY5/download?path=%2F&files=ModRev_CoLoMoTo.pdf) - Flash talks: - [🖥️ BooN (F Delaplace)](https://mycore.core-cloud.net/index.php/s/xopDImJqVkx6RY5/download?path=%2F&files=1-delaplace.pdf) - [🖥️ NORDic (C Réda)](https://mycore.core-cloud.net/index.php/s/xopDImJqVkx6RY5/download?path=%2F&files=2-reda.pdf) - [🖥️ PyLFIT (T Ribeiro)](https://mycore.core-cloud.net/index.php/s/xopDImJqVkx6RY5/download?path=%2F&files=3-ribeiro.pdf) - [🖥️ Biocham (M Hemery)](https://mycore.core-cloud.net/index.php/s/xopDImJqVkx6RY5/download?path=%2F&files=4-hemery.pdf) - [🖥️ gMCSpy (F Planes)](https://mycore.core-cloud.net/index.php/s/xopDImJqVkx6RY5/download?path=%2F&files=5-planes.pdf) - [🖥️ aspefm (M Mahout)](https://mycore.core-cloud.net/index.php/s/xopDImJqVkx6RY5/download?path=%2F&files=6-mahout.pdf) - [🖥️ MonaLisa (M Kirchner)](https://mycore.core-cloud.net/index.php/s/xopDImJqVkx6RY5/download?path=%2F&files=7-kirchner.pdf) ::: ### 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 Shared document: https://codimd.math.cnrs.fr/YhKFZIs_RqS00FMhu3cTPA?both ### 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/).