Reproducibility of research: Issues and proposed remedies, Proc. Natl. Acad. Sci, vol.115, pp.2561-2562, 2018. ,
Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0, Front. Physiol, vol.9, p.646, 2018. ,
The Cell Collective: Toward an open and collaborative approach to systems biology, BMC Syst. Biol, vol.6, p.96, 2012. ,
A cell simulator platform: the cell collective, Clin. Pharmacol. Ther, vol.93, pp.393-395, 2013. ,
BioModels-15 years of sharing computational models in life science, Nucleic Acids Res, 2019. ,
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, vol.19, pp.524-531, 2003. ,
Level 3 package: Qualitative Models, Version 1, Release 1, J. Integr. Bioinforma, vol.12, 2015. ,
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools, BMC Syst. Biol, vol.7, p.135, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00926033
Cooperative development of logical modelling standards and tools with CoLoMoTo, Bioinforma. Oxf. Engl, vol.31, pp.1154-1159, 2015. ,
, SysMod. SysMod Community of Special Interest
, BASEL LIFE, vol.2019, pp.9-12, 2019.
, BaselLife 2019 Workshops and tutorials
, , 2019.
MINERVA-a platform for visualization and curation of molecular interaction networks, NPJ Syst. Biol. Appl, vol.2, p.16020, 2016. ,
UniProt: the universal protein knowledgebase, Nucleic Acids Res, vol.45, pp.158-169, 2017. ,
SIGNOR: a database of causal relationships between biological entities, Nucleic Acids Res, vol.44, pp.548-554, 2016. ,
org: the HGNC and VGNC resources in 2019, Nucleic Acids Res, vol.47, pp.786-792, 2019. ,
, The Gene Ontology Consortium. The Gene Ontology Resource: 20 years and still GOing strong, Nucleic Acids Res, vol.47, pp.330-338, 2019.
The Reactome Pathway Knowledgebase, Nucleic Acids Res, vol.46, pp.649-655, 2018. ,
, The Druglogics Initiative. 21. vsmjs, 2019.
, , 2019.
, MI2CAST, 2019.
BioKB -Text Mining and Semantic Technologies for the Biomedical Content Discovery, p.12, 2019. ,
MINERVA API and plugins: opening molecular network analysis and visualization to the community, Bioinformatics, vol.35, pp.4496-4498, 2019. ,
Closing the gap between formats for storing layout information in systems biology, Brief. Bioinform, 2019. ,
Using process diagrams for the graphical representation of biological networks, Nat. Biotechnol, vol.23, pp.961-966, 2005. ,
BioModels: expanding horizons to include more modelling approaches and formats, Nucleic Acids Res, vol.46, pp.1248-1253, 2018. ,
Minimum information requested in the annotation of biochemical models (MIRIAM), Nat. Biotechnol, vol.23, pp.1509-1515, 2005. ,
, Nucleic Acids Res, 2019.
The NCBI Taxonomy database, Nucleic Acids Res, vol.40, pp.136-143, 2012. ,
ChEBI: a database and ontology for chemical entities of biological interest, Nucleic Acids Res, vol.36, pp.344-350, 2008. ,
,
, Systems Biology Ontology
, BRENDA tissue / enzyme source
Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation, Database J. Biol. Databases Curation, 2018. ,
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks, Front. Physiol, vol.9, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01794294
The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways, BMC Syst. Biol, vol.4, p.65, 2010. ,
A detailed graphical and computational model of the mammalian renal circadian clock, p.795906, 2019. ,
Petri Net-Based Graphical and Computational Modelling of Biological Systems, p.47043, 2016. ,
Automated inference of Boolean models from molecular interaction maps using CaSQ, Bioinformatics Under review ,
URL : https://hal.archives-ouvertes.fr/hal-02590714
Computational Systems Biology Approach for the Study of Rheumatoid Arthritis: From a Molecular Map to a Dynamical Model, Genomics Comput. Biol, vol.4, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02084429
RA-map: Building a state-of-the-art interactive knowledge base for rheumatoid arthritis, Database Under Review ,
Integrating interactive computational modeling in biology curricula, PLoS Comput. Biol, vol.11, p.1004131, 2015. ,
Programmatic access to logical models in the Cell Collective modeling environment via a REST API, Biosystems, vol.139, pp.12-16, 2016. ,
MaBoSS 2.0: an environment for stochastic Boolean modeling, Bioinformatics, vol.33, pp.2226-2228, 2017. ,
PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling, Bioinformatics, vol.35, pp.1188-1196, 2019. ,
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium, Nat. Methods, vol.9, pp.345-350, 2012. ,
The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI), Omics J. Integr. Biol, vol.10, pp.145-151, 2006. ,
Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data, Nat. Commun, vol.6, pp.1-11, 2015. ,
From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL, Npj Syst. Biol. Appl, vol.5, pp.1-10, 2019. ,
OmniPath: guidelines and gateway for literature-curated signaling pathway resources, Nat. Methods, vol.13, pp.966-967, 2016. ,
Bringing data from curated pathway resources to Cytoscape with OmniPath, Bioinformatics ,
A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks, Front. Physiol, vol.9, 2018. ,
Pint: A Static Analyzer for Transient Dynamics of Qualitative Networks with IPython Interface, 2017. ,
The Kappa platform for rule-based modeling, Bioinformatics, vol.34, pp.583-592, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01962663
Rule-Based Modeling of Biochemical Systems with BioNetGen, Syst. Biol, pp.113-167, 2009. ,
,
A simple scheme for annotating SBML with references to controlled vocabularies and database entries, vol.13, 2005. ,
Harmonizing semantic annotations for computational models in biology, Brief. Bioinform, vol.20, pp.540-550, 2019. ,