Affiliation: California Institute of Technology
- Path2Models: large-scale generation of computational models from biochemical pathway mapsFinja BÃ¼chel
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...
- SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and toolsClaudine 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...
- Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup LanguageDagmar 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...
- BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic modelsChen 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...
- Software that goes with the flow in systems biologyMichael 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...
- Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) projectM 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...
- The systems biology markup language (SBML): a medium for representation and exchange of biochemical network modelsM 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...
- MathSBML: a package for manipulating SBML-based biological modelsBruce 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...
- LibSBML: an API library for SBMLBenjamin 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...
- Escalating model sizes and complexities call for standardized forms of representationMichael Hucka
Mol Syst Biol 1:2005.0011. 2005
- SBMLToolbox: an SBML toolbox for MATLAB usersSarah 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...
- CellML2SBML: conversion of CellML into SBMLMaria 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%...
- 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....
- Next generation simulation tools: the Systems Biology Workbench and BioSPICE integrationHerbert M Sauro
Keck Graduate Institute, Claremont, California 91711, USA
OMICS 7:355-72. 2003....
- BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systemsNicolas 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...
- Rules for modeling signal-transduction systemsWilliam 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...