Formal molecular biology, Theoretical Computer Science, vol.325, issue.1, pp.69-110, 2004. ,
DOI : 10.1016/j.tcs.2004.03.065
URL : https://hal.archives-ouvertes.fr/hal-00164591
Gkappa: a library to generate site graphs with graphviz ,
Scalable Simulation of Cellular Signaling Networks, Proc. APLAS'07, pp.139-157, 2007. ,
DOI : 10.1007/978-3-540-76637-7_10
URL : https://hal.archives-ouvertes.fr/inria-00528409
Internal coarse-graining of molecular systems, Proceedings of the National Academy of Sciences, vol.83, issue.2-3, 2009. ,
DOI : 10.1016/j.biosystems.2005.06.014
URL : https://hal.archives-ouvertes.fr/inria-00528330
Abstracting the Differential Semantics of Rule-Based Models: Exact and Automated Model Reduction, 2010 25th Annual IEEE Symposium on Logic in Computer Science, pp.362-381, 2010. ,
DOI : 10.1109/LICS.2010.44
URL : https://hal.archives-ouvertes.fr/hal-00520112
GNU Octave version 4.0.0 manual: a high-level interactive language for numerical computations, 2015. ,
BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains, Bioinformatics, vol.20, issue.17, pp.20-3289, 2004. ,
DOI : 10.1093/bioinformatics/bth378
Rule-Based Modeling of Biochemical Systems with BioNetGen, Methods Mol Biol, vol.500, pp.113-67, 2009. ,
DOI : 10.1007/978-1-59745-525-1_5
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core, Nature Precedings, 2010. ,
DOI : 10.1038/npre.2010.4959.1
ERODE: A Tool for the Evaluation and Reduction of Ordinary Differential Equations, Proc. TACAS'17, pp.310-328, 2017. ,
DOI : 10.1007/978-3-319-34096-8_7
SBML2LATEX: Conversion of SBML files into human-readable reports, Bioinformatics, vol.25, issue.11, pp.1455-1456, 2009. ,
DOI : 10.1093/bioinformatics/btp170
CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks, Proc. of the IEEE 96, 2008. ,
DOI : 10.1109/JPROC.2008.925458
Incremental Update for Graph Rewriting, Proc. ESOP'17, pp.201-228, 2017. ,
DOI : 10.1073/pnas.0809908106
Efficient modeling, simulation and coarse-graining of biological complexity with NFsim, Nature Methods, vol.104, issue.2, pp.177-183, 2011. ,
DOI : 10.1021/jp993732q
Formal Reduction for Rule-based Models, Proc. MFPS XXVII, pp.29-59, 2011. ,
DOI : 10.1016/j.entcs.2011.09.014
URL : https://hal.archives-ouvertes.fr/inria-00636850
Combining Model Reductions, Proc. MFPS XXVI, pp.73-96, 2010. ,
DOI : 10.1016/j.entcs.2010.08.006
URL : https://hal.archives-ouvertes.fr/inria-00527536
An Algebraic Approach for Inferring and Using Symmetries in Rule-based Models, Proc. SASB'14, pp.45-65, 2015. ,
DOI : 10.1016/j.entcs.2015.06.010
URL : https://hal.archives-ouvertes.fr/hal-01098556
Bisimulation relations for weighted automata, Theoretical Computer Science, vol.393, issue.1-3, pp.109-123, 2008. ,
DOI : 10.1016/j.tcs.2007.11.018
Stochastic fragments: A framework for the exact reduction of the stochastic semantics of rule-based models, International Journal of Software and Informatics, vol.7, issue.4, pp.527-604, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01098561
Exact and ordinary lumpability in finite Markov chains, Journal of Applied Probability, vol.1, issue.01, pp.59-75, 1994. ,
DOI : 10.1016/0166-5316(88)90031-4
KaDE: a tool to compile kappa rules into (reduced) ode models: Supplementary information ,
Reconstructing species-based dynamics from reduced stochastic rule-based models, Proceedings Title: Proceedings of the 2012 Winter Simulation Conference (WSC), 2012. ,
DOI : 10.1109/WSC.2012.6465241
URL : https://hal.archives-ouvertes.fr/hal-00734483
Canonical Labelling of Site Graphs, Proc. CompMod'13, pp.13-28, 2013. ,
DOI : 10.4204/EPTCS.116.3
Forward and backward bisimulations for chemical reaction networks, Proc. CONCUR'15, pp.226-239, 2015. ,
Efficient Syntax-Driven Lumping of Differential Equations, Proc. TACAS'16, pp.93-111, 2016. ,
DOI : 10.1007/978-3-662-49674-9_6