A. Finney

Publications44
h-index20
Citations6,506
Highly Influential Citations478
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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.
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.
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.
Erratum: Profiling PARP inhibitors
TLDR
Thousands of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available, and large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery.
Controlled vocabularies and semantics in systems biology
TLDR
Three ontologies created specifically to address the needs of the systems biology community are described, including the Systems Biology Ontology, which provides semantic information about the model components, and the Kinetic Simulation Algorithm Ontology and the Terminology for the Description of Dynamics, which categorizes dynamical features of the simulation results and general systems behavior.
SBMLToolbox: an SBML toolbox for MATLAB users
TLDR
SBMLToolbox provides functionality that enables an experienced user of either SBML or MATLAB to combine the computing power of MATLAB with the portability and exchangeability of an SBML model.
Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
TLDR
This is Release 1 of the specification for SBML Level 2 Version 4, describing the structures of the language and the rules used to build a valid model.
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