BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
Nucleic Acids ResearchPublished 28 December 2005Open access
Nicolas Le Novère
Citations783
SJR quartileQ1
SJR score7.78
SNIP4.71
Generate an AI Snapshot to get a quick, structured summary of this paper.
Study Snapshot
ObjectiveStudy objective
MethodsResearch methodology
PopulationPopulation studied
Sample sizeSample sizes
OutcomesStudy outcomes here
ResultsStudy results comes here
LimitationsResearch study limitations comes here
A concise AI-generated summary of the paper will appear here once you click Generate AI Snapshot.
TL;DR
TheBioModels Database (), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems.
Abstract
BioModels Database (http://www.ebi.ac.uk/biomodels/), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated to verify that it corresponds to the reference publication and gives the proper numerical results. Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources. 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.
Keywords
ChemistryBiochemistry, Genetics and Molecular Biology
BioinformaticsThe systems biology markup language (SBML): a medium forrepresentation and exchange of biochemical network models
3,150 Citations2003Michael Hucka, Andrew Finney +41 more
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.
Nature BiotechnologyMinimum information requested in the annotation of biochemical models (MIRIAM)
635 Citations2005Nicolas Le Novère, Andrew Finney +14 more
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.
Progress in Biophysics and Molecular BiologyCellML: its future, present and past
505 Citations2004Catherine M. Lloyd, Matt Halstead +1 more
The structure of CellML is summarized, its current applications (including biological pathway and electrophysiological models), and its future development--in particular, the development of toolsets and the integration of ontologies are summarized.
BioinformaticsWeb-based kinetic modelling using JWS Online
335 Citations2004Brett G. Olivier, Jacky L. Snoep
UNLABELLED JWS Online is a repository of kinetic models, describing biological systems, which can be interactively run and interrogated over the Internet, using a client-server strategy.
Biochemical Society TransactionsSystems biology markup language: Level 2 and beyond
193 Citations2003Andrew Finney, Michael Hucka
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.
BioinformaticsThe Database of Quantitative Cellular Signaling:management and analysis of chemical kinetic models of signalingnetworks
126 Citations2003Sudhir Sivakumaran, Sridhar Hariharaputran +2 more
The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways intended both to serve the growing field of chemical-reaction level simulation of signaling networks, and to anticipate issues in large-scale data management for signaling chemistry.
NeuroinformaticsModelDB: Making Models Publicly Accessible to Support Computational Neuroscience
115 Citations2003Michele Migliore, Thomas M. Morse +4 more
ModelDB provides a resource for the computational neuroscience community that enables investigators to increase their understanding of published models by enabling them to run the models as published and build on them for further research.
Science s STKEQuantitative Information Management for the Biochemical Computation of Cellular Networks
41 Citations2004Fabien Campagne, Susana R. Neves +5 more
This work has focused on the biochemical computation of cellular interactions and developed an IMS that stores both quantitative information on the cellular components and their interactions, and the basic reactions governing those interactions that can be used to construct pathways and eventually large-scale networks.
Molecular Systems BiologyInternational alliances for quantitative modeling in systems biology
39 Citations2005Hiroaki Kitano
The recent success of global alliance in biology is signified by the human genome project, but the emerging alliance requires quite a different approach, and alliances for quantitative modeling are exploratory in nature as what needs to be investigated as the project move on.
FigshareSchema representing the cascading search strategy
1 Citations2011Le Novère Nicolas, Bornstein Benjamin +10 more