ArticlePLoS computational biology2025
MobsPy: A programming language for biochemical reaction networks.
Article in PLoS computational biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages.PLoS computational biology · 2026Article
- Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages.bioRxiv : the preprint server for biology · 2026Article
- A Quasi-Stationary Distribution Bound for Fault Analysis in Gene Regulatory Networks.bioRxiv : the preprint server for biology · 2025Article
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4 authors.
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Abstract
Biochemical Reaction Networks (BCRNs) model species and their interactions via reactions. They have been extensively used in chemistry and extended to biological settings by generalizing the reactions' kinetics. However, detailed models of biochemical processes tend to result in complex BCRN models. We present the Meta-species Oriented Biosystem Syntax (MobsPy), a language designed to simplify the modeling process using the concept of meta-species. Meta-species are constructed using a bottom-up approach from base species, which represent elementary, simple characteristics. These characteristics are then combined to create meta-species with all their complex behavior. The combined species have characteristics that are the Cartesian product of the base species' characteristics and feature inheritance of reactions involving the base species. New reactions can involve all the states of a meta-species or only a subset that is selected via a query. In particular, reactions of meta-species can express a state change of one of the reactants. MobsPy is deployed as a Python package. We showcase its modeling capabilities by building concise models for biochemical systems from the literature.
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