MobsPy

MobsPy simplifies the modeling of biochemical reaction networks using meta-species constructed from base species through a bottom-up approach.

Key Features:

• Meta-species construction: Meta-species are built from base species representing elementary characteristics, with combined species inheriting reactions from their base species.
• Cartesian product characteristics: Combined meta-species possess characteristics that are the Cartesian product of the base species' characteristics.
• Query-based reaction targeting: Reactions can involve all states of a meta-species or only a subset selected via a query.
• State change reactions: Reactions of meta-species can express a state change of one of the reactants.
• Python package deployment: MobsPy is implemented and distributed as a Python package.

Scientific Applications:

• Biochemical reaction network modeling: MobsPy enables concise and manageable modeling of complex biochemical reaction networks from published literature.
• Biological process simulation: The language extends traditional chemical reaction network approaches to biological settings through generalized reaction kinetics.

Methodology:

MobsPy uses a bottom-up approach where base species representing elementary characteristics are combined to create meta-species; reactions involving base species are inherited by the combined meta-species, and new reactions can target all states or queried subsets of meta-species.