ArticleBMC systems biology2013
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
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.
- Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages.PLoS computational biology · 2026Article
- From prior knowledge to data-informed models: a review of Boolean network inference.Briefings in bioinformatics · 2026Review
- Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages.bioRxiv : the preprint server for biology · 2026Article
- From FAIR to CURE: guidelines for computational models of biological systems.NPJ systems biology and applications · 2026Review
- Path-based quantification of activation and repression in Boolean models using BooLEVARD.NPJ systems biology and applications · 2025Article
- Reproducible Boolean model analyses and simulations with the CoLoMoTo software suite: a tutorial.Interface focus · 2025Article
- LM-Merger: a workflow for merging logical models with an application to gene regulatory network models.BMC bioinformatics · 2025Article
- Augusta: From RNA-Seq to gene regulatory networks and Boolean models.Computational and structural biotechnology journal · 2024Article
- Comprehensive molecular interaction map of TGFβ induced epithelial to mesenchymal transition in breast cancer.NPJ systems biology and applications · 2024Article
- Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems.BMC bioinformatics · 2024Article
- Kinetic modelling of the cellular metabolic responses underpinning in vitro glycolysis assays.FEBS open bio · 2024Article
- Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis.NPJ systems biology and applications · 2024Article
- GatekeepR: an R Shiny application for the identification of nodes with high dynamic impact in Boolean networks.Bioinformatics (Oxford, England) · 2024Article
- A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint.NPJ systems biology and applications · 2023Article
- Trap spaces of multi-valued networks: definition, computation, and applications.Bioinformatics (Oxford, England) · 2023Article
- Reducing Boolean networks with backward equivalence.BMC bioinformatics · 2023Article
- Applications of Boolean modeling to study the dynamics of a complex disease and therapeutics responses.Frontiers in bioinformatics · 2023Article
- Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts.Computational and structural biotechnology journal · 2023Article
- A multiscale mechanistic model of human dendritic cells forFrontiers in immunology · 2023Article
- Metabolic reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: A hybrid modeling approach.PLoS computational biology · 2022Article
23 more citing papers are in PubMed but not listed here.
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24 authors.
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Abstract
backgroundQualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing.
resultsWe present the Systems Biology Markup Language (SBML) Qualitative Models Package ("qual"), an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks. We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools. Furthermore, the collective effort to define the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyse qualitative models.
conclusionsSBML qual allows the exchange of qualitative models among a number of complementary software tools. SBML qual has the potential to promote collaborative work on the development of novel computational approaches, as well as on the specification and the analysis of comprehensive qualitative models of regulatory and signalling networks.
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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.