BioModels

BioModels
Name	BioModels
Type	Repository
Owner	European Bioinformatics Institute
Launch	2005
Country	United Kingdom

BioModels BioModels is a curated repository of computational models for systems biology, providing mathematical representations of biochemical networks for reuse and analysis. It supports reproducible research by offering models in standardized formats alongside metadata, annotations, and links to external resources for verification and integration. The resource is widely used by researchers working with signaling pathways, metabolic networks, and gene-regulatory circuits.

Overview

BioModels serves as a central archive integrating contributions from researchers, linking models to literature and databases such as European Bioinformatics Institute, Nature (journal), Science (journal), Cell (journal), Proceedings of the National Academy of Sciences, EMBL-EBI, Wellcome Trust, European Molecular Biology Laboratory, National Institutes of Health, National Center for Biotechnology Information, UniProt, Gene Ontology Consortium, KEGG, Reactome, BioGRID, STRING (database), PubMed, CrossRef, DOI system, Zenodo, Figshare, GitHub, European Research Council, Horizon 2020, Human Genome Project, ENCODE Project Consortium, 1000 Genomes Project, European Life Sciences Infrastructure for Biological Information to facilitate cross-referencing. It interoperates with modeling tools and platforms such as COPASI, CellDesigner, SBML (Systems Biology Markup Language), SBGN (Systems Biology Graphical Notation), Tellurium (software), PySB, MATLAB, R (programming language), Python (programming language), Jupyter Notebook, VCell, Mycoplasma laboratorium studies and large consortia outputs.

History and Development

The repository emerged in the context of early 21st century efforts from institutions including European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust and collaborations with journals like Nature Biotechnology and Bioinformatics (journal). Milestones include adoption of formats championed by initiatives such as SBML, coordination with standards bodies like COMBINE (COmputational Modeling in BIology NEtwork), and integration into infrastructures supported by Horizon 2020 funding and projects linked to Human Cell Atlas, International Human Epigenome Consortium, Systems Biology Markup Language Level 3 updates. Contributors and curators have included researchers affiliated with University of Oxford, University of Cambridge, Massachusetts Institute of Technology, Harvard University, Stanford University, European Molecular Biology Laboratory, Max Planck Society, Imperial College London, University College London, Karolinska Institute, and others.

Content and Scope

BioModels hosts kinetic, constraint-based, and hybrid models spanning pathways and organisms referenced in literature from journals such as Nature, Science, Cell Systems, PNAS, Journal of Biological Chemistry, Molecular Systems Biology, PLoS Computational Biology, BMC Systems Biology, Frontiers in Systems Biology, and databases like KEGG, Reactome, MetaCyc, BioCyc. Models cover systems studied by groups at Harvard Medical School, MIT, Caltech, ETH Zurich, University of Tokyo, RIKEN, CNRS, Helmholtz Association, Fred Hutchinson Cancer Research Center, Broad Institute, Scripps Research, and clinical collaborations with Johns Hopkins University, Mayo Clinic, Cleveland Clinic. The scope includes models for signaling pathways (e.g., those studied in Howard Hughes Medical Institute supported labs), metabolic reconstructions influenced by projects like Human Metabolome Database, and organismal models ranging from Escherichia coli to Homo sapiens datasets used in consortium studies.

Model Submission and Curation

Submission workflows mirror best practices advocated by organizations such as COMBINE, with curation standards influenced by recommendations from FAIR (principles), editorial policies of Nature Communications, PLOS, and community groups including ISBER and task forces from ELIXIR. Contributors from institutions like University of California, Berkeley, University of Washington, Duke University, University of Pennsylvania, Yale University submit models with supporting evidence linked to PubMed entries, CrossRef DOIs, and annotations to UniProt, ChEBI, Gene Ontology Consortium IDs. Curators verify models against laboratory data reported in works by researchers at Max Planck Institute for Molecular Genetics, Friedrich Miescher Institute, Salk Institute, and clinical trial reports indexed in ClinicalTrials.gov.

Access and Tools

Users access content via web interfaces maintained by European Bioinformatics Institute, programmatic APIs used by projects from ELIXIR, visualization through tools like Cytoscape, Gephi, and integration with computational environments such as Jupyter Notebook, MATLAB, RStudio, VS Code. Plugins and connectors tie BioModels to repositories and platforms including GitHub, Zenodo, Figshare, and workflow systems like Galaxy (platform), Nextflow, and Snakemake for reproducible pipelines used in labs at Broad Institute and European Molecular Biology Laboratory. Teaching and training resources align with courses at Cold Spring Harbor Laboratory, EMBL-EBI Training, Coursera, and summer schools hosted by National Institutes of Health.

Standards and Formats

The repository emphasizes machine-readable formats and ontologies established by groups like SBML, SED-ML, SBO (Systems Biology Ontology), SBGN, COMBINE, MIRIAM, Identifiers.org, and metadata conventions adopted by Dublin Core inspired initiatives. It interoperates with chemical and genomic resources such as ChEBI, UniProt, Ensembl, RefSeq, and utilizes persistent identifiers from ORCID, DOI system, and accession systems used by EMBL-EBI and NCBI.

Impact and Applications

BioModels has supported research cited in high-profile works from Harvard University, Stanford University, MIT, Max Planck Society, European Molecular Biology Laboratory, and translational projects at Pfizer, Roche, Novartis, GlaxoSmithKline, AstraZeneca, contributing to drug target identification, synthetic biology in labs at MIT Media Lab, metabolic engineering in industry collaborations, and educational case studies used at University of Oxford and University of Cambridge. Its curated models enable reproducibility initiatives connected to journals like Nature Methods and collaborative science networks such as ELIXIR, COMBINE, and the Human Cell Atlas.

Category:Biological databases