M. Hucka

Publications157
h-index44
Citations14,235
Highly Influential Citations833
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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
TLDR
This work summarizes the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks, a software-independent language for describing models common to research in many areas of computational biology.
A community-driven global reconstruction of human metabolism
TLDR
Recon 2, a community-driven, consensus 'metabolic reconstruction', is described, which is the most comprehensive representation of human metabolism that is applicable to computational modeling and has improved topological and functional features.
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
TLDR
BioModels Database has become a recognised reference resource for systems biology and is being used by the community in a variety of ways; for example, it is used to benchmark different simulation systems, and to study the clustering of models based upon their annotations.
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
BioModels Database (), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is…
Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.
TLDR
The current and upcoming versions of SBML are summarized and efforts at developing software infrastructure for supporting and broadening its use are outlined.
The Systems Biology Graphical Notation
TLDR
The Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists, believes that it will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge.
Systems biology markup language: Level 2 and beyond.
  • A. Finney, M. Hucka
  • Computer Science, Medicine
    Biochemical Society transactions
  • 1 December 2003
TLDR
The SBML (systems biology markup language) is a standard exchange format for computational models of biochemical networks and features under development include model composition, multistate chemical species and diagrams.
Minimum information requested in the annotation of biochemical models (MIRIAM)
TLDR
These rules define procedures for encoding and annotating models represented in machine-readable form to enable users to have confidence that curated models are an accurate reflection of their associated reference descriptions and to facilitate model reuse and composition into large subcellular models.
BioPAX – A community standard for pathway data sharing
TLDR
Thousands of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases, and this large amount of pathway data in a computable form will support visualization, analysis and biological discovery.
Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.
TLDR
The SBW architecture, a selection of current modules, including Jarnac, JDesigner, and SBWMeta-tool, and the close integration of SBW into BioSPICE, which enables both frameworks to share tools and compliment and strengthen each others capabilities are described.
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