Campus de Luminy, Case 907, 13288 Marseille Cedex 9, France. 3 European Molecular Biology Laboratory Wellcome Trust Genome Campus, European Bioinformatics Institute (EMBL-EBI), vol.6, issue.2 6, pp.2780-156 ,
CH-1015 Lausanne, Switzerland. 10 INRIA Grenoble ? Rhône-Alpes, 655 avenue de l'Europe, Montbonnot, 38334 Saint-Ismier Cedex, France. 11 IAE Grenoble, Université Pierre-Mendès-France, Domaine universitaire BP 47, 12 Instituto de Engenharia de Sistemas e Computadores -Investigação e Desenvolvimento Rua Alves Redol 9, 1000-029 Lisbon, Portugal. 13 Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, D-39106 Magdeburg, Germany. 14 Computing and Mathematical sciences, California Institute of Technology. 15 Institut de Biologie de l'Ecole Normale Supérieure (IBENS) -UMR CNRS 8197 -INSERM 1024 46 rue d ,
Homeostasis and Differentiation in Random Genetic Control Networks, Nature, vol.217, issue.5215, pp.177-185, 1969. ,
DOI : 10.1038/224177a0
Boolean formalisation of genetic control circuits, J Theor Biol, vol.42, pp.565-583, 1973. ,
A Boolean Model of the Cardiac Gene Regulatory Network Determining First and Second Heart Field Identity, PLoS ONE, vol.7, issue.10, p.46798, 2012. ,
DOI : 10.1371/journal.pone.0046798.s003
Digital clocks: simple Boolean models can quantitatively describe circadian systems, Journal of The Royal Society Interface, vol.220, issue.4598, pp.2365-82 ,
DOI : 10.1126/science.220.4598.671
A Boolean Model of the Gene Regulatory Network Underlying Mammalian Cortical Area Development, PLoS Computational Biology, vol.223, issue.9, p.1000936, 2010. ,
DOI : 10.1371/journal.pcbi.1000936.s001
Boolean network-based model of the Bcl-2 family mediated MOMP regulation, Theoretical Biology and Medical Modelling, vol.10, issue.1, p.40, 2013. ,
DOI : 10.1186/1742-4682-10-40
Boolean modeling and fault diagnosis in oxidative stress response, BMC Genomics, vol.13, issue.Suppl 6, p.4 ,
DOI : 10.1109/GENSiPS.2011.6169471
Information Routing Driven by Background Chatter in a Signaling Network, PLoS Computational Biology, vol.135, issue.12, p.1002297, 2011. ,
DOI : 10.1371/journal.pcbi.1002297.s013
Attractor analysis of asynchronous Boolean models of signal transduction networks, Journal of Theoretical Biology, vol.266, issue.4, pp.641-56, 2010. ,
DOI : 10.1016/j.jtbi.2010.07.022
Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling, PLoS Computational Biology, vol.212, issue.9, p.1000912, 2010. ,
DOI : 10.1371/journal.pcbi.1000912.s003
URL : https://hal.archives-ouvertes.fr/inserm-00704876
The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data, PLoS Computational Biology, vol.2, issue.8, p.1000438, 2009. ,
DOI : 10.1371/journal.pcbi.1000438.s007
Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement, PLoS Computational Biology, vol.2006, issue.3, p.1000702, 2010. ,
DOI : 10.1371/journal.pcbi.1000702.s008
URL : https://hal.archives-ouvertes.fr/inserm-00704979
Emergent decision-making in biological signal transduction networks, Proceedings of the National Academy of Sciences, vol.105, issue.6, pp.1913-1918, 2008. ,
DOI : 10.1073/pnas.0705088105
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle, Bioinformatics, vol.22, issue.14, pp.124-155, 2006. ,
DOI : 10.1093/bioinformatics/btl210
Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast, PLoS ONE, vol.11, issue.12, p.1672, 2008. ,
DOI : 10.1371/journal.pone.0001672.t004
Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle, PLoS ONE, vol.7, issue.10, p.45780, 2012. ,
DOI : 10.1371/journal.pone.0045780.g006
Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance, BMC Systems Biology, vol.3, issue.1, p.1, 2009. ,
DOI : 10.1186/1752-0509-3-1
Dynamics of Influenza Virus and Human Host Interactions During Infection and Replication Cycle, Bulletin of Mathematical Biology, vol.26, issue.1, pp.988-1011, 2013. ,
DOI : 10.1007/s11538-012-9777-2
Model-based analysis of an adaptive evolution experiment with Escherichia coli in a pyruvate limited continuous culture with glycerol, EURASIP Journal on Bioinformatics and Systems Biology, vol.2012, issue.1, p.14, 2012. ,
DOI : 10.1186/gb-2003-4-9-r54
Boolean Model of Yeast Apoptosis as a Tool to Study Yeast and Human Apoptotic Regulations, Frontiers in Physiology, vol.3, p.446, 2012. ,
DOI : 10.3389/fphys.2012.00446
The yeast cell-cycle network is robustly designed, Proceedings of the National Academy of Sciences, vol.101, issue.14, pp.4781-4787, 2004. ,
DOI : 10.1073/pnas.0305937101
Modular logical modelling of the budding yeast cell cycle, Molecular BioSystems, vol.97, issue.2, pp.1787-96, 2009. ,
DOI : 10.1109/TCBB.2008.64
The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster, Journal of Theoretical Biology, vol.223, issue.1, pp.1-18, 2003. ,
DOI : 10.1016/S0022-5193(03)00035-3
Segmenting the fly embryo: logical analysis of the role of the Segment Polarity cross-regulatory module, The International Journal of Developmental Biology, vol.52, issue.8 ,
DOI : 10.1387/ijdb.072439ls
Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc, Bioinformatics, vol.24, issue.16, pp.234-274, 2008. ,
DOI : 10.1093/bioinformatics/btn266
Predicting Essential Components of Signal Transduction Networks: A Dynamic Model of Guard Cell Abscisic Acid Signaling, PLoS Biology, vol.34, issue.10, p.312, 2006. ,
DOI : 10.1371/journal.pbio.0040312.sd003
Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis, Bioinformatics, vol.15, issue.7, pp.593-606, 1999. ,
DOI : 10.1093/bioinformatics/15.7.593
A Comprehensive, Multi-Scale Dynamical Model of ErbB Receptor Signal Transduction in Human Mammary Epithelial Cells, PLoS ONE, vol.22, issue.4, p.61757, 2013. ,
DOI : 10.1371/journal.pone.0061757.s002
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms, BMC Systems Biology, vol.6, issue.1, p.133, 2012. ,
DOI : 10.1186/1752-0509-6-133
ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra, BMC Bioinformatics, vol.12, issue.1, p.295, 2011. ,
DOI : 10.1016/j.aam.2006.08.004
BoolNet--an R package for generation, reconstruction and analysis of Boolean networks, Bioinformatics, vol.26, issue.10, pp.1378-80, 2010. ,
DOI : 10.1093/bioinformatics/btq124
Boolean network simulations for life scientists, Source Code for Biology and Medicine, vol.3, issue.1, p.16, 2008. ,
DOI : 10.1186/1751-0473-3-16
A Cell Simulator Platform: The Cell Collective, Clinical Pharmacology & Therapeutics, vol.93, issue.5, pp.393-398, 2013. ,
DOI : 10.1371/journal.pone.0046417
The Cell Collective: Toward an open and collaborative approach to systems biology, BMC Systems Biology, vol.6, issue.1, p.96, 2012. ,
DOI : 10.1186/1752-0509-3-1
Structural and functional analysis of cellular networks with cell NetAnalyzer, BMC Syst Biol, vol.17, issue.2, pp.1752-0509135, 2007. ,
ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists, BMC Systems Biology, vol.3, issue.1, p.58, 2009. ,
DOI : 10.1186/1752-0509-3-58
Logical modelling of regulatory networks with GINsim 2.3, Biosystems, vol.97, issue.2, pp.134-139, 2009. ,
DOI : 10.1016/j.biosystems.2009.04.008
Odefy -- From discrete to continuous models, BMC Bioinformatics, vol.11, issue.1, p.233, 2010. ,
DOI : 10.1186/1471-2105-11-233
SimBoolNet--a Cytoscape plugin for dynamic simulation of signaling networks, Bioinformatics, vol.26, issue.1, pp.141-143, 2010. ,
DOI : 10.1093/bioinformatics/btp617
Dynamic simulation of regulatory networks using SQUAD, BMC Bioinformatics, vol.8, issue.1, p.462, 2007. ,
DOI : 10.1186/1471-2105-8-462
Peled D: Model-checking, p.330, 1999. ,
Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli, Bioinformatics, vol.21, issue.Suppl 1, pp.19-28, 2005. ,
DOI : 10.1093/bioinformatics/bti1048
URL : https://hal.archives-ouvertes.fr/hal-00171939
NuSMV 2: An OpenSource Tool for Symbolic Model Checking, Lect Notes Comp Sci, vol.2404, pp.359-64, 2002. ,
DOI : 10.1007/3-540-45657-0_29
Application of formal methods to biological regulatory networks: extending Thomas??? asynchronous logical approach with temporal logic, Journal of Theoretical Biology, vol.229, issue.3, pp.339-386, 2004. ,
DOI : 10.1016/j.jtbi.2004.04.003
The Biochemical Abstract Machine BIOCHAM, Lect Notes Comp Sci, vol.11, pp.171-91, 2005. ,
DOI : 10.1007/BF03037227
URL : https://hal.archives-ouvertes.fr/inria-00000814
Efficient Verification for Logical Models of Regulatory Networks, Adv Intell Soft Comput, vol.154, pp.259-67, 2012. ,
DOI : 10.1007/978-3-642-28839-5_30
Temporal logic patterns for querying dynamic models of cellular interaction networks, Bioinformatics, vol.24, issue.16, pp.227-260, 2008. ,
DOI : 10.1093/bioinformatics/btn275
URL : https://hal.archives-ouvertes.fr/inria-00357805
An overview of existing modeling tools making use of model checking in the analysis of biochemical networks, Frontiers in Plant Science, vol.3, p.155, 2012. ,
DOI : 10.3389/fpls.2012.00155
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, vol.19, issue.4, pp.524-531, 2003. ,
DOI : 10.1093/bioinformatics/btg015
The Systems Biology Graphical Notation, Nature Biotechnology, vol.267, issue.8, pp.735-776, 2009. ,
DOI : 10.1038/nbt.1558
MODELING AND SIMULATION OF MOLECULAR BIOLOGY SYSTEMS USING PETRI NETS: MODELING GOALS OF VARIOUS APPROACHES, Journal of Bioinformatics and Computational Biology, vol.02, issue.04, pp.595-613, 2004. ,
DOI : 10.1142/S0219720004000764
Petri nets.I nBiol Netw Anal, pp.139-179 ,
URL : https://hal.archives-ouvertes.fr/hal-00697985
Snoopy--a unifying Petri net framework to investigate biomolecular networks, Bioinformatics, vol.26, issue.7, pp.974-979, 2010. ,
DOI : 10.1093/bioinformatics/btq050
LibSBML: an API Library for SBML, Bioinformatics, vol.24, issue.6, pp.880-881, 2008. ,
DOI : 10.1093/bioinformatics/btn051
JSBML: a flexible Java library for working with SBML, Bioinformatics, vol.27, issue.15, pp.2167-2175, 2011. ,
DOI : 10.1093/bioinformatics/btr361
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction, Molecular Systems Biology, vol.41, p.331, 2009. ,
DOI : 10.1038/msb.2009.87
A methodology for the structural and functional analysis of signaling and regulatory networks, BMC Bioinformatics, vol.7, issue.1, p.56, 2006. ,
DOI : 10.1186/1471-2105-7-56
MEIGO: a software suite based on metaheuristics for global optimization in systems biology and bioinformatics. Submitted (available on arXiv, p.1311 ,
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming, Bioinformatics, vol.29, issue.18, pp.2320-2326, 2013. ,
DOI : 10.1093/bioinformatics/btt393
URL : https://hal.archives-ouvertes.fr/hal-00853704
Comparing Signaling Networks between Normal and Transformed Hepatocytes Using Discrete Logical Models, Cancer Research, vol.71, issue.16, pp.5400-5411, 2011. ,
DOI : 10.1158/0008-5472.CAN-10-4453
Integrating literature-constrained and data-driven inference of signalling networks, Bioinformatics, vol.28, issue.18, pp.2311-2317, 2012. ,
DOI : 10.1093/bioinformatics/bts363
Logical Modelling of Gene Regulatory Networks with GINsim, Methods Mol Biol, vol.804, pp.463-79, 2012. ,
DOI : 10.1007/978-1-61779-361-5_23
Dynamical roles of biological regulatory circuits, Briefings in Bioinformatics, vol.8, issue.4, pp.220-225, 2007. ,
DOI : 10.1093/bib/bbm028
Dynamical modeling and analysis of large cellular regulatory networks, Chaos: An Interdisciplinary Journal of Nonlinear Science, vol.23, issue.2, p.25114, 2013. ,
DOI : 10.1063/1.4809783
Dynamically consistent reduction of logical regulatory graphs, Theoretical Computer Science, vol.412, issue.21, pp.2207-2225, 2011. ,
DOI : 10.1016/j.tcs.2010.10.021
URL : https://hal.archives-ouvertes.fr/hal-01284743
Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control, Lect Notes Comp Sci, vol.7605, pp.288-306, 2012. ,
DOI : 10.1007/978-3-642-33636-2_17
Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models, PLoS ONE, vol.7, issue.10, p.46417, 2012. ,
DOI : 10.1371/journal.pone.0046417.s001
State???time spectrum of signal transduction logic models, Physical Biology, vol.9, issue.4, p.45003, 2012. ,
DOI : 10.1088/1478-3975/9/4/045003
CySBGN: A Cytoscape plug-in to integrate SBGN maps, BMC Bioinformatics, vol.14, issue.1, p.17, 2013. ,
DOI : 10.1093/bioinformatics/btm032
Precise generation of systems biology models from KEGG pathways, BMC Systems Biology, vol.7, issue.1, p.15, 2013. ,
DOI : 10.1186/1471-2105-9-399
Path2Models: large-scale generation of computational models from biochemical pathway maps, BMC Systems Biology, vol.7, issue.1, p.116, 2013. ,
DOI : 10.1186/1471-2105-9-399
Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks, Methods Mol Biol, vol.804, pp.439-62, 2012. ,
DOI : 10.1007/978-1-61779-361-5_22
URL : https://hal.archives-ouvertes.fr/hal-00762122
BioModels Database: A Repository of Mathematical Models of Biological Processes, Methods Mol Biol, vol.1021, pp.189-99, 2013. ,
DOI : 10.1007/978-1-62703-450-0_10
The logical analysis of continuous, non-linear biochemical control networks, Journal of Theoretical Biology, vol.39, issue.1, pp.103-132, 1973. ,
DOI : 10.1016/0022-5193(73)90208-7
Hybrid modeling and simulation of biomolecular network, Hybrid Syst Comput Control, pp.19-32, 2001. ,
HSM ??? a hybrid system based approach for modelling intracellular networks, Gene, vol.518, issue.1, pp.70-77, 2013. ,
DOI : 10.1016/j.gene.2012.11.084
A mathematical framework for describing and analysing gene regulatory networks, Journal of Theoretical Biology, vol.176, issue.2, pp.291-300, 1995. ,
DOI : 10.1006/jtbi.1995.0199
Fuzzy Logic Analysis of Kinase Pathway Crosstalk in
TNF/EGF/Insulin-Induced Signaling, PLoS Computational Biology, vol.13, issue.4, p.1000340, 2009. ,
DOI : 10.1371/journal.pcbi.1000340.s007
On timed models of gene networks.I nForm model anal timed syst, pp.38-52 ,
Temporal constraints in the logical analysis of regulatory networks, Theoretical Computer Science, vol.391, issue.3, pp.258-275, 2008. ,
DOI : 10.1016/j.tcs.2007.11.010
Querying quantitative logic models (Q2LM) to study intracellular signaling networks and cell-cytokine interactions, Biotechnology Journal, vol.39, issue.3, pp.374-86, 2012. ,
DOI : 10.1002/biot.201100222
Minimum Information About a Simulation Experiment (MIASE), PLoS Computational Biology, vol.5307, issue.4, p.1001122, 2011. ,
DOI : 10.1371/journal.pcbi.1001122.s002
URL : https://hal.archives-ouvertes.fr/hal-00772491
Controlled vocabularies and semantics in systems biology, Controlled vocabularies and semantics in systems biology, p.543, 2011. ,
DOI : 10.1016/j.jbi.2010.10.003
URL : https://hal.archives-ouvertes.fr/hal-00767736
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language, BMC Systems Biology, vol.5, issue.1, p.198, 2011. ,
DOI : 10.1038/35002125