ArticleBriefings in bioinformatics2022
A protocol for dynamic model calibration.
Article in Briefings in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed.
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- Mathematical Modelling of the Mitochondrial Dicarboxylate Carrier (SLC25A10).Bulletin of mathematical biology · 2026Article
- Decoding cellular population dynamics through mechanistic modelling and statistical data analysis.NPJ systems biology and applications · 2026Review
- Prediction of short‑term drought variation in tea plantations using a LASSO-COX-NOMOGRAM approach.Scientific reports · 2026Article
- Leveraging mathematical models to predict and control T-cell activation.PLoS computational biology · 2026Article
- From FAIR to CURE: guidelines for computational models of biological systems.NPJ systems biology and applications · 2026Review
- PEtab-GUI: a graphical user interface to create, edit, and inspect PEtab parameter estimation problems.Bioinformatics (Oxford, England) · 2026Article
- In silico modeling of anterior foregut endoderm differentiation towards lung epithelial progenitors.NPJ systems biology and applications · 2026Article
- Identification of dynamic models of microbial communities: A workflow addressing identifiability and modeling pitfalls.PLoS computational biology · 2025Article
- Cost-effectiveness of eHealth-based HIV pre-exposure intervention for recreational drugs using among men who have sex with men in China: a modelling study.BMC public health · 2025Article
- Analysing the Structural Identifiability and Observability of Mechanistic Models of Tumour Growth.Bioengineering (Basel, Switzerland) · 2025Article
- In silico modeling of directed differentiation of induced pluripotent stem cells to definitive endoderm.PLoS computational biology · 2025Article
- Modeling Chemical Reaction Networks Using Neural Ordinary Differential Equations.Journal of chemical information and modeling · 2025Article
- Conformal prediction for uncertainty quantification in dynamic biological systems.PLoS computational biology · 2025Article
- Employing Observability Rank Conditions for Taking into Account Experimental Information a priori.Bulletin of mathematical biology · 2025Article
- Building blocks needed for mechanistic modeling of bioprocesses: A critical review based on protein production by CHO cells.Metabolic engineering communications · 2024Review
- Integrative modeling uncovers p21-driven drug resistance and prioritizes therapies for PIK3CA-mutant breast cancer.NPJ precision oncology · 2024Article
- Benchmarking methods for computing local sensitivities in ordinary differential equation models at dynamic and steady states.PloS one · 2024Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Ordinary differential equation models are nowadays widely used for the mechanistic description of biological processes and their temporal evolution. These models typically have many unknown and nonmeasurable parameters, which have to be determined by fitting the model to experimental data. In order to perform this task, known as parameter estimation or model calibration, the modeller faces challenges such as poor parameter identifiability, lack of sufficiently informative experimental data and the existence of local minima in the objective function landscape. These issues tend to worsen with larger model sizes, increasing the computational complexity and the number of unknown parameters. An incorrectly calibrated model is problematic because it may result in inaccurate predictions and misleading conclusions. For nonexpert users, there are a large number of potential pitfalls. Here, we provide a protocol that guides the user through all the steps involved in the calibration of dynamic models. We illustrate the methodology with two models and provide all the code required to reproduce the results and perform the same analysis on new models. Our protocol provides practitioners and researchers in biological modelling with a one-stop guide that is at the same time compact and sufficiently comprehensive to cover all aspects of the problem.
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