ArticleBMC systems biology2013
Path2Models: large-scale generation of computational models from biochemical pathway maps.
Article in BMC systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
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- From Single Organisms to Communities: Modeling Methanotrophs and Their Satellites.Microorganisms · 2025Review
- In vivo and in silico models of Drosophila for Parkinson's disease.The FEBS journal · 2025Review
- UnifiedGreatMod: a new holistic modelling paradigm for studying biological systems on a complete and harmonious scale.Bioinformatics (Oxford, England) · 2025Article
- Genome-scale models in human metabologenomics.Nature reviews. Genetics · 2025Review
- Mathematical basis and toolchain for hierarchical optimization of biochemical networks.PLoS computational biology · 2024Article
- Community metabolic modeling of host-microbiota interactions through multi-objective optimization.iScience · 2024Article
- BioNexusSentinel: a visual tool for bioregulatory network and cytohistological RNA-seq genetic expression profiling within the context of multicellular simulation research using ChatGPT-augmented software engineering.Bioinformatics advances · 2024Article
- Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism.Nature communications · 2023Article
- A new metabolic model ofLife science alliance · 2023Article
- Review
- Design considerations for representing systems biology information with the Systems Biology Graphical Notation.Journal of integrative bioinformatics · 2022Article
- Perseus plugin "Metis" for metabolic-pathway-centered quantitative multi-omics data analysis for static and time-series experimental designs.Cell reports methods · 2022Article
- Boolean modelling as a logic-based dynamic approach in systems medicine.Computational and structural biotechnology journal · 2022Review
- GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction.PLoS computational biology · 2021Article
- Model Balancing: A Search for In-Vivo Kinetic Constants and Consistent Metabolic States.Metabolites · 2021Article
- Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus.NPJ systems biology and applications · 2021Review
- A detailed map of coupled circadian clock and cell cycle with qualitative dynamics validation.BMC bioinformatics · 2021Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
26 authors.
Funding
Abstract
backgroundSystems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data.
resultsTo increase the efficiency of model creation, the Path2Models project has automatically generated mathematical models from pathway representations using a suite of freely available software. Data sources include KEGG, BioCarta, MetaCyc and SABIO-RK. Depending on the source data, three types of models are provided: kinetic, logical and constraint-based. Models from over 2 600 organisms are encoded consistently in SBML, and are made freely available through BioModels Database at http://www.ebi.ac.uk/biomodels-main/path2models. Each model contains the list of participants, their interactions, the relevant mathematical constructs, and initial parameter values. Most models are also available as easy-to-understand graphical SBGN maps.
conclusionsTo date, the project has resulted in more than 140 000 freely available models. Such a resource can tremendously accelerate the development of mathematical models by providing initial starting models for simulation and analysis, which can be subsequently curated and further parameterized.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.