TheoBioR

Computational methods for modelling and analysing biological networks

Axis: SciLex
Coordinators : Stefan Haar (Inria Saclay-Île-de-France/LSV) , Sabine Peres, LRI, Loïc Paulevé (CNRS/LRI)
Objective: Seminar series and collaborative work on computational methods for biological networks.
Labex funding: 2016/2019
Mailing-list: gt-theobior@lists.lri.fr

The Workging Group TheoBioR focuses on computational methods for modelling and analysing biological networks.
It includes work around the following type of modelling:

static models: reaction networks, regulation networks;
qualitate models of dynamics of networks: Boolean and multivalued networks;
hybrid models: time and/or stochastic aspects.

The analyses usually focus on:

dynamical features: steady states (fixed points, attractors), temporal properties, critical components/transitions;
fundamental links between network architecture and it dynamical properties;
model identification and synthesis from logical specifications and experimental data;
network comparison and reduction.

These analyses have direct applications in systems biology and synthetic biology, for example for the prediction of steady states and their reachability; the identification of targets for controlling the cell; in-silico conception of articial networks; evolution of biological networks.
These analyses typically rely on the following computational principles:

model checking;
abstract interpretation;
concurrency theory;
constraint solving;
combinatorics and discrete mathematics.

Involved teams

I2BC (CNRS, Université Paris-Sud, CEA), équipe Bio-informatique moléculaire (Olivier Lespinet)
IBISC (Université d’Evry), équipe COSMO (Franck Delaplace)
INRA Jouy-en-Josas, unité MaIAGE (Vincent Fromion)
Inria Saclay-Île-de-France, EPI LifeWare (François Fages)
LRI (CNRS, Université Paris-Sud), équipe BioInfo (Christine Froidevaux et Alain Denise)
LSV (CNRS, ENS Cachan), équipe Mexico (Stefan Haar)
MAS (École Centrale Paris), équipe LogiMAS (Pascale Le Gall)

Scientific production:

Publications: 3 high-rank journals et 3 international conferences:
- journals: TCS 2018 on abstract interpretation of parametric Boolean networks; Frontiers in Physiology 2018a and Frontiers in Physiology 2018b on a software environment to foster reproducibility for analysis of qualitative models of biological systems, relying on Docker and Jupyter technologies.
- conferences: AUTOMATA 2018 on semantics of Boolean networks; CONCUR 2017 on unfolding of Petri nets guided by static analysis; CMSB 2017 on temporal reprogramming of Boolean networks.
WG meetings allowed to identify a new joint research thematic on Boolean network reprogramming with teams from LRI, LSV, and IBISC; it has resulted in a CNRS/INS2I PEPS project in 2017.

Projects funded by Digicosme through the WG

Engineer contract (1y)

Leader: Philippe Dague (LRI/LaHDAK)
Selected candidate: Eva Dechaux
Period: Sept 2017/Sept 2018)
Result: implementing and validating softwares package in Python for the computation of extremal elementary fluxes in a metabolic network ( « minimal » metabolic paths from which all possible paths at steady state may be reconstructed). This package uses the algorithm of double description by interfacing with the open access tools CDD or efmtool (this last one much more efficient but with more difficult access) which implement it. But it uses it in a totally different way that what are doing bioinformaticians at the origin of the implementation of efmtool. By giving up the certificate guaranteeing that all solutions have been found, we reach a much better efficiency while being able in practice to enumerate all solutions. In addition, this implementation can be massively parallelized, which is not the case of CDD or efmtool. It is thus a totally novel approach in the bioinformatic community, promising for metabolic networks analysis of genome-scale organisms.

Postdoc contract (1y) "DynaRNA"

Leaders: Loïc Paulevé (LRI/bioinfo), Yann Ponty (LIX)
Selected candidate: Christelle Rovetta
Period: Sept 2018/Sept 2019
Objective: stochastic modelling of ARN folding and sampling methods for estimating duration and probability of RNA folding changes.

Communications

Minutes of seminar "Logical models for formal representation of living systems" in bulletin 97 of AfIA (Association française pour l'Intelligence Artificielle)

Seminars

8 November 2018

Misbah Razzaq (LS2N, Nantes)

Title: "Integrating Phosphoproteomic Time Series Data into Prior Knowledge Networks to build Cell Line Specific Boolean Networks"
Time and location: 14:30-15:30 at LRI, Ada Lovelace building, room 465

3 October 2018

RNA Kinetics Day : sampling and abstractions

Speakers:

Christelle Rovetta (LRI)
Ronny Lorenz (University of Vienna)
Frédéric Cazals (Inria Sophia)
Ana Bušić (Inria Paris)
Benoît Delahaye (LS2N, Univ Nantes)
Benoît Barbot (LACL, Univ Paris-Est Créteil)
Bruno Tuffin (Inria Rennes)

More information at RNAKinetics

22-23 June 2017

Modèles logiques pour la représentation formelle des systèmes vivants (Logical models for formal representation of living systems)

Programme
Jeudi 22 juin

14h00 - 15h00: François Fages (Inria) "En quête du logiciel du vivant: succès et difficultés du paradigme de la vérification de programmes en biologie cellulaire"
15h00 - 15h20: Laurent Trilling (Univ Grenoble) "Modélisation déclarative de réseaux de régulation génique. Apport de la programmation logique « non monotone"
15h50 - 16h10: Morgan Magnin (École Centrale Nantes) "Enjeux de l'apprentissage de modèles dynamiques des réseaux biologiques par la programmation logique"
16h10 - 16h30: Anne Siegel (CNRS) "Raisonner sur des abstractions et invariants de systèmes dynamiques en biologie avec ASP"
16h30 - 16h50: Céline Rouveirol (Univ Paris Nord) "Découverte dans les réseaux biologiques hétérogènes : l'expérience Adalab"
17h10 - 17h30: Béatrice Duval (Univ Angers) "Analyse différentielle de réseaux"
17h30 - 17h50: Philippe Dague (Univ Paris-Sud) "Analyse de réseaux métaboliques en présence de contraintes biologiques : approches géométriques, combinatoires et logiques"

Vendredi 23 juin

9h30 - 9h50: Andrei Doncescu (Univ Paul Sabatier Toulouse) "Quel type de modélisation pour des interactions entre composants biologiques ?"
9h50 - 10h50: Pierre Siegel (Univ Aix-Marseille) "Logiques non-monotones pour les réseaux de gênes et les systèmes dynamiques booléens"
11h20 - 11h40: Joëlle Despeyroux (Inria) "Towards a Logical Framework for Systems Biology"
11h40 - 12h00: Loïc Paulevé (CNRS) "Approximations de problèmes PSPACE en SAT pour la reprogrammation cellulaire"
12h00 - 12h20 Exposé Franck Delaplace (Univ Evry) "Abduction based drug target discovery using boolean control network"

27 février 2017: Causal Network Inference for Biology

Lieu: LRI, Bâtiment 660 - Claude Shannon, amphi
Programme

09h45: coffee/welcome
10h00-10h45: Hervé Isambert (CNRS, Institut Curie) "Learning causal networks with latent variables from multivariate information in observational data"
10h45-11h30: Olivier Goudet (Inria, LRI)"Building causal graphs and applications in social science"
11h30: coffee break
11h45-12h30: Loïc Paulevé (CNRS, LRI) "Identification of qualitative dynamical models from perturbation time series data".
12h30-13h: Discussion

Slides

29 novembre 2016: Hétérogénéité et dynamique des flux métaboliques

Lieu: LRI, Bâtiment 650 - Ada Lovelace, salle 435
Voir l'annonce
Programme

10h-12h Exposés invités de
- Sophie Colombié (INRA Bordeaux) "Modélisation et flux métaboliques au cours du développement du fruit"
- Damien Eveillard (LINA, Nantes) "Metabolic Modeling of Microbial Communities: a computational viewpoint"
- Joachim Niehren (Inria Lille) "Predicting Changes of Reaction Networks with Partial Kinetic Information"
14h - 14h45 Exposé invité de
- Thomas Duigou (INRA Jouy) "Dynamique d'un réseau métabolique avec un modèle à base de contraintes : approche par échantillonnage des trajectoires solutions"
15h - 17h Discussions

13 June 2016: Réseaux booléens et reprogrammation cellulaire (Boolean networks and cellular reprogramming)

Lieu: LRI, Bâtiment 650 - Ada Lovelace, salle 435
Programme

10h00 - 12h30
- Wassim Abou-Jaoudé (IBENS)
- Laurence Calzone (Curie)
- Adrien Richard (I3S)
- Sylvain Sené (LIF)
14h - 15h : exposés de
- Célia Biane (IBISC)
- Hugues Mandon (LRI)
15h - 16h : discussions

9 February 2016: Première journée du GT TheoBioR (WG kick-off)