LibSBML is an open-source software library that provides an application programming interface (API) for the SBML (Systems Biology Markup Language ) format. The libSBML library can be embedded in a software application or used in a web servlet (such as one that might be served by Apache Tomcat) as part of the application or servlet's implementation of support for reading, writing, and manipulating SBML documents and data streams. The core of libSBML is written in ISO standard C++; the library provides API for many programming languages via interfaces generated with the help of SWIG.
The libSBML library is free software released under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or any later version. LibSBML was developed thanks to funding from many agencies, particularly the National Institute of General Medical Sciences (NIGMS, USA) as well as the Defense Advanced Research Projects Agency (DARPA, USA) under the Bio-SPICE program.
Description
The Systems Biology Markup Language (SBML) is an XML-based format for encoding computational models of a sort common in systems biology. Although SBML is based upon XML, and thus software developers could support SBML using off-the-shelf XML parser libraries, libSBML offers numerous advantages that make it easier for developers to implement support for SBML in their software. The premise behind the development of libSBML is that it is more convenient and efficient for developers to start with a higher-level API tailored specifically to SBML and its distinctive features than it is to start with a plain XML parser library.
Significant features of libSBML
The following is a partial list of libSBML's features:
Supports all Levels and Versions of SBML with common API classes and methods, thus smoothing the differences between different flavors of SBML from the perspective of the application software. Provides facilities for manipulating mathematical formulas in both text-string format and MathML 2.0 format, as well as the ability to interconvert mathematical expressions between these forms. Internally, libSBML uses familiar Abstract Syntax Trees (ASTs) to represent formulas, and provides AST-oriented methods for calling applications. Performs validation of XML and SBML at the time of parsing files and data streams. This helps verify the correctness of models in a way that goes beyond simple syntactic validation. Offers support for dimensional analysis and unit checking. LibSBML implements a thorough system for dimensional analysis and checking units of quantities in a model. Provides facilities for the creation and manipulation of SBML annotations and notes. These have a specific format dictated by the SBML specifications. The formats and standards supported by libSBML include MIRIAM (Minimal Information Requested in the Annotation of a Model) and SBO (the Systems Biology Ontology). Supports transparently reading and writing compressed files in the ZIP, GZIP and BZIP formats. Provides interfaces for the C, C++, C#, Java, Python, Perl, MATLAB, Octave, and Ruby programming languages. The C and C++ interfaces are implemented natively; the C#, Java, Perl, Python, and Ruby interfaces are implemented using SWIG, the Simplified Wrapper Interface Generator; and the MATLAB and Octave interfaces are implemented through custom hand-written code. Provides many convenience methods, such as for obtaining a count of the number of boundary condition species, determining the modifier species of a reaction (assuming the reaction provides kinetics), constructing the stoichiometric matrix for all reactions in a model, and more.