Cooperative development of logical modelling standards and tools with CoLoMoTo

The identification of large regulatory and signalling networks involved in the control of crucial cellular processes calls for proper modelling approaches. Indeed, models can help elucidate properties of these networks, understand their behaviour, and provide (testable) predictions by performing in silico experiments. In this context, qualitative, logical frameworks have emerged as relevant approaches as demonstrated by a growing number of published models, along with new methodologies and software tools. This productive activity now requires a concerted effort to ensure model reusability and interoperability between tools. Here, we outline the logical modelling framework and present the most important achievements of the Consortium for Logical Models and Tools, along with future objectives. This open community welcomes contributions from all researchers interested in logical modelling or in related mathematical and computational developments.

[1]  Hans A. Kestler,et al.  Attractors in Boolean networks: a tutorial , 2012, Computational Statistics.

[2]  Stuart A. Kauffman,et al.  The origins of order , 1993 .

[3]  Stephan Merz,et al.  Model Checking , 2000 .

[4]  H. Siebert.  Analysis of Discrete Bioregulatory Networks Using Symbolic Steady States , 2011, Bulletin of mathematical biology.

[5]  Michel Dumontier,et al.  Controlled vocabularies and semantics in systems biology , 2011, Molecular systems biology.

[6]  Nicolas Le Novère,et al.  BioModels Database: a repository of mathematical models of biological processes. , 2013, Methods in molecular biology.

[7]  Julio Saez-Rodriguez,et al.  Integrating literature-constrained and data-driven inference of signalling networks , 2012, Bioinform..

[8]  Hidde de Jong,et al.  Modeling and Simulation of Genetic Regulatory Systems: A Literature Review , 2002, J. Comput. Biol..

[9]  Giovanni De Micheli,et al.  Synchronous versus asynchronous modeling of gene regulatory networks , 2008, Bioinform..

[10]  Edward R. Dougherty,et al.  Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks , 2002, Bioinform..

[11]  Giovanni De Micheli,et al.  Dynamic simulation of regulatory networks using SQUAD , 2007, BMC Bioinformatics.

[12]  R. Thomas,et al.  Boolean formalization of genetic control circuits. , 1973, Journal of theoretical biology.

[13]  Michael Hucka,et al.  The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core (Release 1 Candidate) , 2010 .

[14]  Aurélien Naldi,et al.  The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1 , 2015, J. Integr. Bioinform..

[15]  Aurélien Naldi,et al.  Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling , 2010, PLoS Comput. Biol..

[16]  Claudine Chaouiya,et al.  A Discrete Model of Drosophila Eggshell Patterning Reveals Cell-Autonomous and Juxtacrine Effects , 2014, PLoS Comput. Biol..

[17]  Michael Hucka,et al.  LibSBML: an API Library for SBML , 2008, Bioinform..

[18]  Steffen Klamt,et al.  SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools , 2013, BMC Systems Biology.

[19]  Denis Thieffry,et al.  Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module. , 2003, Journal of theoretical biology.

[20]  H. Othmer,et al.  The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. , 2003, Journal of theoretical biology.

[21]  Aurélien Naldi,et al.  Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle , 2006, ISMB.

[22]  Morgan Magnin,et al.  Static analysis of Biological Regulatory Networks dynamics using abstract interpretation , 2012, Math. Struct. Comput. Sci..

[23]  Pedro T. Monteiro,et al.  Dynamical modeling and analysis of large cellular regulatory networks. , 2013, Chaos.

[24]  Andreas Zell,et al.  JSBML: a flexible Java library for working with SBML , 2011, Bioinform..

[25]  Stefan Bornholdt,et al.  Boolean network models of cellular regulation: prospects and limitations , 2008, Journal of The Royal Society Interface.

[26]  H. Kestler,et al.  A Boolean Model of the Cardiac Gene Regulatory Network Determining First and Second Heart Field Identity , 2012, PloS one.

[27]  Isabelle S. Peter,et al.  Predictive computation of genomic logic processing functions in embryonic development , 2012, Proceedings of the National Academy of Sciences.

[28]  R. Thomas.  Remarks on the Respective Roles of Logical Parameters and Time Delays in Asynchronous Logic: An Homage to El Houssine Snoussi , 2013, Bulletin of mathematical biology.

[29]  Jacky L. Snoep,et al.  Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language , 2011, BMC Systems Biology.

[30]  Gary D Bader,et al.  A travel guide to Cytoscape plugins , 2012, Nature Methods.

[31]  Alex Madrahimov,et al.  The Cell Collective: Toward an open and collaborative approach to systems biology , 2012, BMC Systems Biology.

[32]  Sui Huang.  Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery , 1999, Journal of Molecular Medicine.

[33]  L. Glass,et al.  The logical analysis of continuous, non-linear biochemical control networks. , 1973, Journal of theoretical biology.

[34]  Assieh Saadatpour,et al.  Boolean modeling of biological regulatory networks: a methodology tutorial. , 2013, Methods.

[35]  Andreas Zell,et al.  Path2Models: large-scale generation of computational models from biochemical pathway maps , 2013, BMC Systems Biology.

[36]  Denis Thieffry,et al.  Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement , 2010, PLoS Comput. Biol..

[37]  Hans A. Kestler,et al.  BoolNet - an R package for generation, reconstruction and analysis of Boolean networks , 2010, Bioinform..

[38]  Aurélien Naldi,et al.  Logical modelling of regulatory networks with GINsim 2.3 , 2009, Biosyst..

[39]  Réka Albert,et al.  Modeling Systems-Level Regulation of Host Immune Responses , 2007, PLoS Comput. Biol..

[40]  Adrien Richard,et al.  Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic. , 2004, Journal of theoretical biology.

[41]  Steffen Klamt,et al.  Structural and functional analysis of cellular networks with CellNetAnalyzer , 2007, BMC Systems Biology.

[42]  Q. Ouyang,et al.  The yeast cell-cycle network is robustly designed. , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Monika Heiner,et al.  A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets , 2007, CMSB.

[44]  Guy Karlebach,et al.  Modelling and analysis of gene regulatory networks , 2008, Nature Reviews Molecular Cell Biology.

[45]  Steffen Klamt,et al.  Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling , 2009, BMC Systems Biology.

[46]  Tomáš Helikar,et al.  A Comprehensive, Multi-Scale Dynamical Model of ErbB Receptor Signal Transduction in Human Mammary Epithelial Cells , 2013, PloS one.

[47]  François Robert,et al.  Discrete iterations - a metric study , 1986, Springer series in computational mathematics.

[48]  Claudine Chaouiya,et al.  Composition and abstraction of logical regulatory modules: application to multicellular systems , 2013, Bioinform..

[49]  Tomáš Helikar,et al.  Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle , 2012, PloS one.

[50]  Abdul Salam Jarrah,et al.  Polynomial algebra of discrete models in systems biology , 2010, Bioinform..

[51]  Emmanuel Barillot,et al.  Continuous time boolean modeling for biological signaling: application of Gillespie algorithm , 2012, BMC Systems Biology.

[52]  T. Helikar,et al.  Dynamics of Influenza Virus and Human Host Interactions During Infection and Replication Cycle , 2013, Bulletin of mathematical biology.

[53]  D. Thieffry,et al.  A logical analysis of the Drosophila gap-gene system. , 2001, Journal of theoretical biology.

[54]  Denis Thieffry,et al.  Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision , 2013, PLoS Comput. Biol..

[55]  Adrien Richard,et al.  On Circuit Functionality in Boolean Networks , 2013, Bulletin of mathematical biology.

[56]  Julio Saez-Rodriguez,et al.  CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms , 2012, BMC Systems Biology.

[57]  Alexander Bockmayr,et al.  Incorporating Time Delays into the Logical Analysis of Gene Regulatory Networks , 2006, CMSB.

[58]  R. Albert,et al.  Network model of survival signaling in large granular lymphocyte leukemia , 2008, Proceedings of the National Academy of Sciences.

[59]  Réka Albert,et al.  An effective network reduction approach to find the dynamical repertoire of discrete dynamic networks. , 2013, Chaos.

[60]  Steffen Klamt,et al.  Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction , 2008, BMC Systems Biology.

[61]  René Thomas.  Regulatory networks seen as asynchronous automata: A logical description , 1991 .

[62]  Rainer Breitling,et al.  What is Systems Biology? , 2010, Front. Physiology.

[63]  Edda Klipp,et al.  Systems Biology , 1994 .

[64]  Carsten Peterson,et al.  Random Boolean network models and the yeast transcriptional network , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[65]  Jay Pedersen,et al.  Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models , 2012, PloS one.

[66]  A. Bockmayr,et al.  Computing Symbolic Steady States of Boolean Networks , 2014, ACRI.

[67]  Steffen Klamt,et al.  Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks , 2010, J. Comput. Biol..

[68]  Fabian J. Theis,et al.  Odefy -- From discrete to continuous models , 2010, BMC Bioinformatics.

[69]  Joshua E. S. Socolar,et al.  Global control of cell-cycle transcription by coupled CDK and network oscillators , 2008, Nature.

[70]  S. Klamt,et al.  Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks , 2013, Cell Communication and Signaling.

[71]  M. Kaufman,et al.  From structure to dynamics: frequency tuning in the p53-Mdm2 network. II Differential and stochastic approaches. , 2010, Journal of theoretical biology.

[72]  Laurence Calzone,et al.  Correction: Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision , 2013, PLoS Computational Biology.

[73]  Hans A. Kestler,et al.  Multiscale Binarization of Gene Expression Data for Reconstructing Boolean Networks , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[74]  René Thomas.  On the Relation Between the Logical Structure of Systems and Their Ability to Generate Multiple Steady States or Sustained Oscillations , 1981 .

[75]  Claudine Chaouiya,et al.  Efficient Verification for Logical Models of Regulatory Networks , 2012, PACBB.

[76]  D. Thieffry,et al.  Segmenting the fly embryo: logical analysis of the role of the segment polarity cross-regulatory module. , 2008, The International journal of developmental biology.

[77]  Denis Thieffry,et al.  Dynamical roles of biological regulatory circuits , 2007, Briefings Bioinform..

[78]  Aurélien Naldi,et al.  Dynamically consistent reduction of logical regulatory graphs , 2011, Theor. Comput. Sci..

[79]  S. Bornholdt,et al.  Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast , 2007, PloS one.

[80]  Denis Thieffry,et al.  Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework , 2008, Adv. Appl. Math..

[81]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[82]  Aurélien Naldi,et al.  Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks , 2007, CMSB.

[83]  Stefan Bornholdt,et al.  Less Is More in Modeling Large Genetic Networks , 2005, Science.

[84]  Steffen Klamt,et al.  A Logical Model Provides Insights into T Cell Receptor Signaling , 2007, PLoS Comput. Biol..

[85]  Martine Labbé,et al.  Identification of all steady states in large networks by logical analysis , 2003, Bulletin of mathematical biology.

[86]  S. Kauffman.  Metabolic stability and epigenesis in randomly constructed genetic nets. , 1969, Journal of theoretical biology.

[87]  Denis Thieffry,et al.  Logical modelling of cell cycle control in eukaryotes: a comparative study. , 2009, Molecular bioSystems.

[88]  Maxim Teslenko,et al.  A SAT-Based Algorithm for Finding Attractors in Synchronous Boolean Networks , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[89]  Jim A. Rogers,et al.  ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists , 2009, BMC Systems Biology.

[90]  Steffen Klamt,et al.  A methodology for the structural and functional analysis of signaling and regulatory networks , 2006, BMC Bioinformatics.

[91]  Ilya Shmulevich,et al.  Binary analysis and optimization-based normalization of gene expression data , 2002, Bioinform..

[92]  Radu Mateescu,et al.  Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli , 2005, ISMB.

[93]  J. Demongeot,et al.  On the number of different dynamics in Boolean networks with deterministic update schedules. , 2013, Mathematical biosciences.

[94]  Hidde de Jong,et al.  Genetic Network Analyzer: qualitative simulation of genetic regulatory networks , 2003, Bioinform..