M Hucka

Summary

Affiliation: California Institute of Technology
Country: USA

Publications

  1. pmc Path2Models: large-scale generation of computational models from biochemical pathway maps
    Finja Büchel
    European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Syst Biol 7:116. 2013
  2. pmc SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
    Claudine Chaouiya
    Instituto Gulbenkian de Ciencia, Rua da Quinta Grande 6, 2780 156 Oeiras, Portugal
    BMC Syst Biol 7:135. 2013
  3. pmc Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language
    Dagmar Waltemath
    Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, D 18051 Rostock, Germany
    BMC Syst Biol 5:198. 2011
  4. pmc BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
    Chen Li
    European Bioinformatics Institute, Hinxton, UK
    BMC Syst Biol 4:92. 2010
  5. pmc Software that goes with the flow in systems biology
    Michael Hucka
    Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA
    BMC Biol 8:140. 2010
  6. ncbi request reprint Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project
    M Hucka
    Control and Dynamical Systems, California Institute of Technology, Pasadena 91125, USA
    Syst Biol (Stevenage) 1:41-53. 2004
  7. ncbi request reprint The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    M Hucka
    Control and Dynamical Systems, MC 107 81, California Institute of Technology, Pasadena, CA 91125, USA
    Bioinformatics 19:524-31. 2003
  8. pmc MathSBML: a package for manipulating SBML-based biological models
    Bruce E Shapiro
    Jet Propulsion Laboratory, California Institute of Technology, Mail Stop 126 347, 4800 Oak Grove Drive, Pasadena, CA 91109, USA
    Bioinformatics 20:2829-31. 2004
  9. pmc LibSBML: an API library for SBML
    Benjamin J Bornstein
    NASA Jet Propulsion Laboratory, Biological Network Modeling Center, California Institute of Technology, Pasadena, CA, USA
    Bioinformatics 24:880-1. 2008
  10. pmc Escalating model sizes and complexities call for standardized forms of representation
    Michael Hucka
    Mol Syst Biol 1:2005.0011. 2005

Collaborators

Detail Information

Publications16

  1. pmc Path2Models: large-scale generation of computational models from biochemical pathway maps
    Finja Büchel
    European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Syst Biol 7:116. 2013
    ..However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data...
  2. pmc SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
    Claudine Chaouiya
    Instituto Gulbenkian de Ciencia, Rua da Quinta Grande 6, 2780 156 Oeiras, Portugal
    BMC Syst Biol 7:135. 2013
    ..While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing...
  3. pmc Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language
    Dagmar Waltemath
    Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, D 18051 Rostock, Germany
    BMC Syst Biol 5:198. 2011
    ..The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools...
  4. pmc BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
    Chen Li
    European Bioinformatics Institute, Hinxton, UK
    BMC Syst Biol 4:92. 2010
    ..In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification...
  5. pmc Software that goes with the flow in systems biology
    Michael Hucka
    Control and Dynamical Systems, California Institute of Technology, Pasadena, CA 91125, USA
    BMC Biol 8:140. 2010
    ..Their work is a harbinger of the next generation of more powerful software for systems biologists...
  6. ncbi request reprint Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project
    M Hucka
    Control and Dynamical Systems, California Institute of Technology, Pasadena 91125, USA
    Syst Biol (Stevenage) 1:41-53. 2004
    ..We also provide a brief overview of the many SBML-compatible software tools available today...
  7. ncbi request reprint The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    M Hucka
    Control and Dynamical Systems, MC 107 81, California Institute of Technology, Pasadena, CA 91125, USA
    Bioinformatics 19:524-31. 2003
    ..Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively...
  8. pmc MathSBML: a package for manipulating SBML-based biological models
    Bruce E Shapiro
    Jet Propulsion Laboratory, California Institute of Technology, Mail Stop 126 347, 4800 Oak Grove Drive, Pasadena, CA 91109, USA
    Bioinformatics 20:2829-31. 2004
    ..By accessing the full breadth of Mathematica functionality, MathSBML is fully extensible to SBML models of any size or complexity...
  9. pmc LibSBML: an API library for SBML
    Benjamin J Bornstein
    NASA Jet Propulsion Laboratory, Biological Network Modeling Center, California Institute of Technology, Pasadena, CA, USA
    Bioinformatics 24:880-1. 2008
    ..Developers can embed libSBML in their applications, saving themselves the work of implementing their own SBML parsing, manipulation and validation software...
  10. pmc Escalating model sizes and complexities call for standardized forms of representation
    Michael Hucka
    Mol Syst Biol 1:2005.0011. 2005
  11. ncbi request reprint SBMLToolbox: an SBML toolbox for MATLAB users
    Sarah M Keating
    Science and Technology Research Institute, University of Hertfordshire Hatfield, UK
    Bioinformatics 22:1275-7. 2006
    ..SBMLToolbox supports all levels and versions of SBML...
  12. ncbi request reprint CellML2SBML: conversion of CellML into SBML
    Maria J Schilstra
    Biological and Neural Computation Group, STRI, University of Hertfordshire, Hatfield AL10 9AB, UK
    Bioinformatics 22:1018-20. 2006
    ..Of all 306 models in the CellML repository in April 2005, CellML2SBML converted 91% automatically into SBML. Minor manual changes to the unit definitions in the originals raised the percentage of successful conversions to 96%...
  13. ncbi request reprint Minimum information requested in the annotation of biochemical models (MIRIAM)
    Nicolas Le Novère
    European Bioinformatics Institute, Hinxton, CB10 1SD, UK
    Nat Biotechnol 23:1509-15. 2005
    ....
  14. ncbi request reprint Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration
    Herbert M Sauro
    Keck Graduate Institute, Claremont, California 91711, USA
    OMICS 7:355-72. 2003
    ....
  15. pmc BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
    Nicolas Le Novère
    European Bioinformatics Institute EMBL, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
    Nucleic Acids Res 34:D689-91. 2006
    ..This allows the users to search accurately for the models they need. The models can currently be retrieved in the SBML format, and import/export facilities are being developed to extend the spectrum of formats supported by the resource...
  16. ncbi request reprint Rules for modeling signal-transduction systems
    William S Hlavacek
    Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Sci STKE 2006:re6. 2006
    ..We also discuss rule visualization and exchange and the software available for rule-based modeling...