SBML2APM

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Conversion from SBML to APM

Introduction

About SBML
SBML is a machine-readable format for representing models. It's oriented towards describing systems where biological entities are involved in, and modified by, processes that occur over time. An example of this is a network of biochemical reactions. SBML's framework is suitable for representing models commonly found in research on a number of topics, including cell signaling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others. If you want to know more, you can read the Basic Introduction on SBML
About APM
APM (APMonitor Modeling Language) is an optimization software for mixed-integer and differential algebraic equations. It is coupled with large-scale solvers for linear, quadratic, nonlinear, and mixed integer programming (LP, QP, NLP, MILP, MINLP). Modes of operation include data reconciliation, real-time optimization, dynamic simulation, and nonlinear predictive control. It is freely available through MATLAB, Python, or from a web browser interface. To know more, you can read the What is it? page.


Documentation

The converter is based on jsbml, so support all the levels and versions of SBML until SBML level 3 version 1 core.


Download

Currently we do not have a specific package for sbml2apm, but you can find this converter inside the main sbfc package: sbfc-1.3.7.zip.

End users

To run SBML2APM you need java 1.6 or higher.

After unpacking the zipped file, move to the folder that have been created and run:

    # Convert SBML (any *.xml files if you put a folder) to APM
    # The output file(s) will be in the same folder as the SBML file(s) with an extension .apm
    ./sbml2apm.sh [file.xml | folder]

Developers

To compile SBML2APM from source, you also need Apache Ant 1.6.5 or higher.

After editing the source code you can build the jar file by just typing in the SBML2APM folder:

    # Generate the jar file
    ant jar

    # Generate the java documentation
    ant javadoc


Getting Help and Support

In case you discover a bug within SBFC or request new features, please let us know. There are two dedicated trackers:

For general discussions about SBFC, please use the forum:

sbfc-forum [at] googlegroups.com.

If you need further support or you wish to develop new modules in SBFC you can contact the team using the following e-mail address:

sbfc-devel [at] googlegroups.com.