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PySCeS CBMPy is a new platform for constraint based modelling and analysis. It has been designed using principles developed in the PySCeS simulation software project: usability, flexibility and accessibility.
CBMPy supports the latest standards for encoding CBM models encoding, SBML L3 FBC, COBRA as well as MIRIAM compliant RDF and custom annotations.
Its architecture is both extensible and flexible using data structures that are intuitive to the biologist while transparently translating these into the underlying mathematical structures.
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CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as advanced methods developed for the ecosystem modelling.
CBMPy supports user interaction via:
- interactive console or as a library for advanced use
- GUI, visual representation of the model, analysis methods
- a SOAP based webAPI exposes high level functionality via web services
Features
- support for modelling standards: SBML, SED-ML, SBML3FBC, OMEX (Combine archive)
- supports MIRIAM compliant annotation as RDF as well as custom key-value data
- multiple user interfaces, GUI CLI, NOUI
- flexible, open architecture
Project Samples
