Selected Publications

In recent years Systems Biology has become a rich field of study, trying to encompass all the information that has become available thanks to the new high-throughput techniques of biologists. Fifteen years ago, a fundamental breakthrough was the publication of Kurt Kohn’s map of the cell cycle control in mammals. Its similarity with electronic circuits was crucial in both making it impossible for humans to comprehend fully, and in prompting the use of formal methods […]
Habilitation à diriger des recherches, Université Paris Sud - Orsay, December, 2016.

Biochemical reaction networks grow bigger and bigger, fed by the high-throughput data provided by biologists and bred in open repositories of models allowing merging and evolution. Nevertheless, since the available data is still very far from permitting the identification of the increasing number of kinetic parameters of such models, the necessity of structural analyses for describing the dynamics of chemical networks appears stronger every day. Using the structural information, notably from the stoichiometric matrix, of a biochemical reaction system, we state a more strict version of the famous Thomas’ necessary condition for multistability […]
Bulletin of Mathematical Biology, 75 (11):2289-2303, November, 2013.

Background We present a way to compute the minimal semi-positive invariants of a Petri net representing a biological reaction system, as resolution of a Constraint Satisfaction Problem. The use of Petri nets to manipulate Systems Biology models and make available a variety of tools is quite old, and recently analyses based on invariant computation for biological models have become more and more frequent, for instance in the context of module decomposition. Results In our case, this analysis brings both qualitative and quantitative information on the models, in the form of conservation laws, consistency checking, etc […]
Algorithms for Molecular Biology, 7 (1):15, December, 2012.

interpretation is a theory of abstraction that has been introduced for the analysis of programs. In particular, it has proved useful for organizing the multiple semantics of a given programming language in a hierarchy corresponding to different detail levels, and for defining type systems for programming languages and program analyzers in software engineering. In this paper, we investigate the application of these concepts to systems biology formalisms […]
Theoretical Computer Science, 403 (1):52–70, August, 2008.

Other Recent Publications

More Publications

. Graphical Requirements for Multistationarity in Reaction Networks and their Verification in BioModels. Journal of Theoretical Biology, 459:79–89, 2018.

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. Executable Disease Networks: Adding dynamics to molecular maps. ECCB 2018, 17th European Conference on Computational Biology, 2018.

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. On Robustness Computation and Optimization in BIOCHAM-4. In 16th Int. Conf. on Computational Methods in Systems Biology, 2018.

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. Probably Approximately Correct Learning of Regulatory Networks from Time-Series Data. In J. Feret, H. Koeppl, editor, CMSB’17 - 15th International Conference on Computational Methods for Systems Biology, pages 74-90, 2017.

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. Model-based Investigation of the Circadian Clock and Cell Cycle Coupling in Mouse Embryonic Fibroblasts: Prediction of RevErb-α Up-regulation During Mitosis. In Dynamics Days 2017 - XXXVII Dynamics Days Europe International Conference, 2017.

HAL

Projects

ANR BioPSy

Hybrid Formal Modelling of Time for Circadian Clock Biology and Chronopharmacology

ANR HyClock

Hybrid Formal Modelling of Time for Circadian Clock Biology and Chronopharmacology

French-German PROCOPE Mobility Grant

O. Radulescu, Univ. Montpellier, France, Andreas Weber, Univ. Bonn, Germany

Teaching

I teach/taught in the following frameworks:

  • in the Paris Computer Science Masters (M2 Research), I am in charge of the Constraint Programming course;

    • class 1 - Introduction to CLP, operational semantics, examples
    • class 2 - CLP: fixpoint semantics
    • class 3 - CLP: logical semantics, CSP: solving by simplification and domain reduction
    • class 4 - CLP: the Warren Abstract Machine, CSP: Symmetries
    • class 5 - CLP: typing; CHR; Programming project discussion; MiniZinc and CLPZinc
    • class 6 - CC: examples, operational and denotational semantics
    • class 7 - CC: linear logic semantics; LCC
    • class 8 - LCC: logical semantics, links with CHR; EMoP: modules for LCC/CC/CLP
  • at École Polytechnique, I’m co-coordinator of the INF555 – Constraint-based Modeling & Algorithms for Decision Making 3rd year (M1) class from the Master AI & Advanced Visual Computing;

    Course material (partial, since François Fages is also teaching, you can find everything together on our wiki):

    • class 1 - MiniZinc, Jupyter and friends…
    • TD1 - You can access it with docker pull registry.gitlab.inria.fr/soliman/inf555/td1
    • class 2 - Boolean satisfiability, SAT solvers (part 1)
    • TD2 - You can access it with docker pull registry.gitlab.inria.fr/soliman/inf555/td2
    • TD4 - You can access it with docker pull registry.gitlab.inria.fr/soliman/inf555/td4
  • I used to be for several years teaching assistant for Java classes corresponding to the Informatique Fondamentale lessons of Jean-Jacques Levy in that same École Polytechnique.

I also supervize some internships on the dedicated page of the Lifeware team.

Recent Posts

More Posts

CellDesigner model to SBML-Qual encoded logical model converter

   ______      _____ ____ 
  / ____/___ _/ ___// __ \
 / /   / __ `/\__ \/ / / /
/ /___/ /_/ /___/ / /_/ / 
\____/\__,_//____/\___\_\ 
                          

This page allows you to convert a CellDesigner model to a logical model with default logical rules.

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This is a set of reasonable guidelines for formatting Prolog programs, freely adapted from Caml guidelines and M. Covington’s Prolog coding guidelines. They aim at reflecting the consensus among the programmers of the Lifeware team. Nevertheless, all detailed notifications of possible errors or omissions will be noted with pleasure. To send your comments: Sylvain.Soliman@inria.fr.

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Nontransitive dice

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.ode to reaction model converter

This page allows you to convert a system of ordinary differential equations in the .ode format of XPPAUT to a reaction model.

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CellDesigner model to influence graph converter

This page allows you to convert a CellDesigner model to a supposedly meaningful influence model.

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