ArticleBioinformatics (Oxford, England)2020
BioModels Parameters: a treasure trove of parameter values from published systems biology models.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
7 citing papers in PubMed.
- Literature-derived, context-aware gene regulatory networks improve biological predictions and mathematical modeling.Bioinformatics (Oxford, England) · 2026Article
- A multiscale, Bayesian inference approach to augment mechanistic models of cell signaling with machine-learning predictions of binding affinity.PLoS computational biology · 2026Article
- Quantitative systems toxicology: modelling to mechanistically understand and predict drug safety.Nature reviews. Drug discovery · 2026Review
- A scoping review of mathematical modeling techniques for gingival keratinization: A framework for periodontal research.Journal of clinical and experimental dentistry · 2025Review
- Systems Biology in ELIXIR: modelling in the spotlight.F1000Research · 2022Article
- Validation Through Collaboration: Encouraging Team Efforts to Ensure Internal and External Validity of Computational Models of Biochemical Pathways.Neuroinformatics · 2022Review
- Generation of multicellular spatiotemporal models of population dynamics from ordinary differential equations, with applications in viral infection.BMC biology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
motivationOne of the major bottlenecks in building systems biology models is identification and estimation of model parameters for model calibration. Searching for model parameters from published literature and models is an essential, yet laborious task.
resultsWe have developed a new service, BioModels Parameters, to facilitate search and retrieval of parameter values from the Systems Biology Markup Language models stored in BioModels. Modellers can now directly search for a model entity (e.g. a protein or drug) to retrieve the rate equations describing it; the associated parameter values (e.g. degradation rate, production rate, Kcat, Michaelis-Menten constant, etc.) and the initial concentrations. Currently, BioModels Parameters contains entries from over 84,000 reactions and 60 different taxa with cross-references. The retrieved rate equations and parameters can be used for scanning parameter ranges, model fitting and model extension. Thus, BioModels Parameters will be a valuable service for systems biology modellers. AVAILABILITY AND IMPLEMENTATION: The data are accessible via web interface and API. BioModels Parameters is free to use and is publicly available at https://www.ebi.ac.uk/biomodels/parameterSearch. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
Identifiers
What OpenQuestion holds
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.