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. Its architecture is both
extensible and flexible using data structures that are intuitive to the biologist (metabolites, reactions, compartments)
while transparently translating these into the underlying mathematical structures used in advanced analysis (LP's, MILP's).
PySCeS CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis
and model editing as well as advanced methods developed
the ecosystem modelling: minimal distance
methods, flux minimization and input selection.
To cater for a diverse range of modelling needs PySCeS CBMPy supports user interaction via:
interactive console, scripting for advanced use or as a library for software development
GUI, for quick access to a visual representation of the model, analysis methods and annotation tools
SOAP based web services: using the Mariner framework much high level functionality is exposed for integration into web tools
CBMPy fully supports a number of open community standards, SBML Level 3 Core, FBC, Groups as well as OMEX and the creation of COMBINE archives.
Models can be read/written in SBML FBC versions 1 and 2 as well as older SBML leve 2 dialects.
CBMPy 0.7.4 has been released. This version adds SBML Groups support and many new utility functions, bugfixes and a "nose" based unit test suite called using cbmpy.test() (2016-04-15)
CBMPy can be downloaded from SourceForge (see below) or installed from PyPI using pip or easy_install e.g. on windows try: easy_install cbmpy or on Linux try pip install cbmpy (2015-09-15)
CBMPy 0.7.3 has been released. This version adds FBC Version 2 support, introduces a new module name: cbmpy that should be used from now on e.g. "import cbmpy". It also includes new network analysis tools and documentation. (2015-09-14)
CBMPy Reference Documentation and Installation guide updated (0.7.2) and available as: html, pdf or epub (2015-08-13)
CBMPy (0.7.2) now fully supports the SBML Level 3 Flux Balance Constraints (FBC) Package Version 2 in addition to FBC Version 1, SBML Level 2 FBA annotation, SBML Level 2 COBRA dialect and models encoded as CSV, Excel and Python. CBMPy also supports the COMBINE archive or OMEX standards(2015-07-27)
CBMPy 0.7.0 has been released. Many new features, bugfixes and updated documentation. This release includes complete support for the SBML Level 3 FBC format, importing/exporting COBRA format, exporting human and machine readable version of models as OMEX/COMBINE archives, reading/writing Excel workbooks and MIRIAM annotations using Identifiers.org urls. CPLEX/GLPK solver API's have been enhanced and,amongst other things,FVA functionality has been optimized (2014-12-02)
PySCeS CBMPy Reference Documentation and Installation guide (0.7.0) htmlpdf (2014-12-02)
CBMPy 0.7.0 Release Candidate 2 (final) now available, many new features and bugfixes.(2014-09-03)
CBMPy 0.7.0 Release candidate 1 now available and now supports Thomas W. Finley's pyGLPK for LP optimization. For Linux build friendly source and Windows binaries try Daniel's build - mirror (2012-12-17)
Information on reading, writing and optimising constraint based models on the wiki.
For more information on the open standards supported by PySCeS-CBM see the following documentation:
CBMPy supports the reading, writing and creation of MIRIAM compliant annotations for model components.
The CBMPy developers are actively involved in community standards development for the description and
annotation of constraint based models:
SBML Level 3 Package: Flux Balance Constraints (FBC), a draft specification is available for preview: 0.2
SBML Level 2 with FBA annotation (FBA), the working annotation used in the proposal to the FBA community and as
a development platform for the Level 3 specification.
A generic KeyValueDataPair annotation for encoding annotations that can not be encoded as MIRIAM has been
developed to provided a more formal annotation mechanism than is currently used in genome scale reconstructions.
The latest human metabolic reconstruction Recon2 (MODEL1109130000) has been translated into SBML Level 3 with FBC extension and is available below. Also available is a CBMPy (0.6.7) generated spreadsheet containing model information, FBA and FVA results. Note that in the translation the objective function has been set as "R_biomass_reaction". Details on the model translation and analysis in CBMPy are available here.
Using CBMPy (0.6.7), FBA is virtually instantaneous and FVA takes about an hour using using 2 threads in multicore mode with CPLEX on an Intel quad core laptop. Please note that other than basic syntax checks no in depth checking has been done to validate the correctness of the translations or results presented here.
PySCeS CBMPy is developed by
PySCeS CBMPy is developed under the GNU GPL version 3 as Open Source software.
Disclaimer: this software is under active development
and is provided as is.
Please read the licence the disclaimer
provided with the source code for details.