ArticleiScience2019
PyBioNetFit and the Biological Property Specification Language.
Article in iScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Using PyBioNetFit to leverage qualitative and quantitative data in biological model parameterization and uncertainty quantification.Frontiers in immunology · 2026Article
- A Roadmap for the Future of Systems Biology in Cancer Research.Cancer research · 2025Review
- CrossLabFit: A novel framework for integrating qualitative and quantitative data across multiple labs for model calibration.PLoS computational biology · 2025Article
- SIMPROV: Provenance capturing for simulation studies.PloS one · 2025Article
- The Constrained Disorder Principle Overcomes the Challenges of Methods for Assessing Uncertainty in Biological Systems.Journal of personalized medicine · 2024Review
- Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells.PLoS computational biology · 2024Article
- BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells.NPJ systems biology and applications · 2023Article
- Verifiable biology.Journal of the Royal Society, Interface · 2023Review
- Epigenetic targeting of autophagy for cancer: DNA and RNA methylation.Frontiers in oncology · 2023Review
- Article
- Control of cell state transitions.Nature · 2022Article
- Article
- Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit.Bioinformatics (Oxford, England) · 2022Article
- Bayesian Inference of State-Level COVID-19 Basic Reproduction Numbers across the United States.Viruses · 2022Article
- Programmatic modeling for biological systems.Current opinion in systems biology · 2021Article
- Relating simulation studies by provenance-Developing a family of Wnt signaling models.PLoS computational biology · 2021Article
- Modeling the Nonlinear Dynamics of Intracellular Signaling Networks.Bio-protocol · 2021Article
- Publishing reproducible dynamic kinetic models.Briefings in bioinformatics · 2021Article
- Atlas: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages.Bioinformatics (Oxford, England) · 2021Article
- Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry.Molecular biology of the cell · 2021Article
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Authors and funding
8 authors.
Funding
Abstract
In systems biology modeling, important steps include model parameterization, uncertainty quantification, and evaluation of agreement with experimental observations. To help modelers perform these steps, we developed the software PyBioNetFit, which in addition supports checking models against known system properties and solving design problems. PyBioNetFit introduces Biological Property Specification Language (BPSL) for the formal declaration of system properties. BPSL allows qualitative data to be used alone or in combination with quantitative data. PyBioNetFit performs parameterization with parallelized metaheuristic optimization algorithms that work directly with existing model definition standards: BioNetGen Language (BNGL) and Systems Biology Markup Language (SBML). We demonstrate PyBioNetFit's capabilities by solving various example problems, including the challenging problem of parameterizing a 153-parameter model of cell cycle control in yeast based on both quantitative and qualitative data. We demonstrate the model checking and design applications of PyBioNetFit and BPSL by analyzing a model of targeted drug interventions in autophagy signaling.
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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.