BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge, Bioinformatics, vol.22, issue.14, pp.1805-1807, 2006. ,
DOI : 10.1093/bioinformatics/btl172
URL : https://hal.archives-ouvertes.fr/hal-01431364
Petri net modelling of biological networks, Briefings in Bioinformatics, vol.8, issue.4, pp.210-219, 2007. ,
DOI : 10.1093/bib/bbm029
Inferring reaction systems from ordinary differential equations, Theoretical Computer Science, vol.599, pp.64-78, 2015. ,
DOI : 10.1016/j.tcs.2014.07.032
URL : https://hal.archives-ouvertes.fr/hal-01103692
Chemical reaction network structure and the stability of complex isothermal reactors???I. The deficiency zero and deficiency one theorems, Chemical Engineering Science, vol.42, issue.10, pp.2229-2268, 1987. ,
DOI : 10.1016/0009-2509(87)80099-4
Computation of elementary modes: a unifying framework and the new binary approach, BMC Bioinformatics, vol.5, issue.1, p.175, 2004. ,
DOI : 10.1186/1471-2105-5-175
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
Confluent Reductions: Abstract Properties and Applications to Term Rewriting Systems: Abstract Properties and Applications to Term Rewriting Systems, Journal of the ACM, vol.27, issue.4, pp.797-821, 1980. ,
DOI : 10.1145/322217.322230
BioModels: Content, Features, Functionality and Use. CPT: Pharmacometrics & Systems Pharmacology, 2015. ,
A Schematic Method of Deriving the Rate Laws for Enzyme-Catalyzed Reactions, The Journal of Physical Chemistry, vol.60, issue.10, pp.1375-1378, 1956. ,
DOI : 10.1021/j150544a010
Graphical rules of steady-state reaction systems, Canadian Journal of Chemistry, vol.59, issue.4, pp.737-755, 1981. ,
DOI : 10.1139/v81-107
Rule-based modeling of transcriptional attenuation at the tryptophan operon, Transactions on Computational Systems Biology, pp.199-228, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00445565
Attractor Equivalence: An Observational Semantics for Reaction Networks, Formal Methods in Macro-Biology, pp.82-101, 2014. ,
DOI : 10.1007/978-3-319-10398-3_7
URL : https://hal.archives-ouvertes.fr/hal-00990924
Structural simplification of chemical reaction networks in partial steady states, Biosystems, vol.149 ,
DOI : 10.1016/j.biosystems.2016.08.003
URL : https://hal.archives-ouvertes.fr/hal-01350517
Subtiwiki?a comprehensive community resource for the model organism bacillus subtilis. Nucleic acids research, 2011. ,
Uniform confluence in concurrent computation, Journal of Functional Programming, vol.10, issue.5, pp.453-499, 2000. ,
DOI : 10.1017/S0956796800003762
URL : https://hal.archives-ouvertes.fr/inria-00536801
Qualitative Reasoning for Reaction Networks with Partial Kinetic Information, CMSB. 2015 ,
DOI : 10.1007/978-3-319-23401-4_14
Robust simplifications of multiscale biochemical networks, BMC Systems Biology, vol.2, issue.1, p.86, 2008. ,
DOI : 10.1186/1752-0509-2-86
URL : https://hal.archives-ouvertes.fr/inria-00331212
Reduction of dynamical biochemical reactions networks in computational biology, Frontiers in Genetics, vol.3, 2012. ,
DOI : 10.3389/fgene.2012.00131
Graphical reduction of reaction networks by linear elimination of species, Journal of Mathematical Biology, vol.40, issue.73, 2015. ,
DOI : 10.1021/ed069p544
Graphical reduction of reaction networks by linear elimination of species, Journal of Mathematical Biology, vol.40, issue.73, pp.1-43, 2016. ,
DOI : 10.1021/ed069p544
Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system, Proceedings of the National Academy of Sciences, pp.6608-6613, 2008. ,
DOI : 10.1073/pnas.0710134105
On the elimination of intermediate species in chemical reaction networks, 2016. ,