ArticleMolecular systems biology2013
Programming biological models in Python using PySB.
Article in Molecular systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 126 papers.
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Who cites it
126 citing papers in PubMed.
- Review
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- A Computational Model of Tumor Interactions with Bone-Resident Cells Predicts Tumor-Type-Specific Responses to Perturbations.bioRxiv : the preprint server for biology · 2026Article
- Mechanistic insights into photosynthetic linear electron transport flow: a mathematical modeling approach.Photosynthesis research · 2026Article
- Rules railroad: Syntax-inspired diagrams for visualizing and understanding rule-based model specifications.PLoS computational biology · 2026Article
- AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potential.NPJ digital medicine · 2025Review
- Design principles of gene circuits for longevity.Trends in cell biology · 2025Review
- MobsPy: A programming language for biochemical reaction networks.PLoS computational biology · 2025Article
- Visualizing mechanistic models by integrating site-specific molecular details into reaction networks.Frontiers in molecular biosciences · 2025Article
- G protein-coupled receptor digital twins for precision and personalized medicine.Computational and structural biotechnology journal · 2025Review
- Generating synthetic signaling networks for in silico modeling studies.Journal of theoretical biology · 2024Article
- Cell-specific models reveal conformation-specific RAF inhibitor combinations that synergistically inhibit ERK signaling in pancreatic cancer cells.Cell reports · 2024Article
- Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems.Bioinformatics (Oxford, England) · 2024Article
- Cell State Transition Models Stratify Breast Cancer Cell Phenotypes and Reveal New Therapeutic Targets.Cancers · 2024Article
66 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Mathematical equations are fundamental to modeling biological networks, but as networks get large and revisions frequent, it becomes difficult to manage equations directly or to combine previously developed models. Multiple simultaneous efforts to create graphical standards, rule-based languages, and integrated software workbenches aim to simplify biological modeling but none fully meets the need for transparent, extensible, and reusable models. In this paper we describe PySB, an approach in which models are not only created using programs, they are programs. PySB draws on programmatic modeling concepts from little b and ProMot, the rule-based languages BioNetGen and Kappa and the growing library of Python numerical tools. Central to PySB is a library of macros encoding familiar biochemical actions such as binding, catalysis, and polymerization, making it possible to use a high-level, action-oriented vocabulary to construct detailed models. As Python programs, PySB models leverage tools and practices from the open-source software community, substantially advancing our ability to distribute and manage the work of testing biochemical hypotheses. We illustrate these ideas using new and previously published models of apoptosis.
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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.