LibSBML 3'0:

1
LibSBML 3.0 An API library for SBML
Download from http//sbml.org
Sarah M. Keating Benjamin J. Bornstein Akiya
Jouraku Michael Hucka
STRI, University of Hertfordshire, Hertfordshire,
UK NASA Jet Propulsion Laboratory, Pasadena, CA,
USA Keio University, Japan California Institute
of Technology, Pasadena, CA, USA
libSBML is a high-level, SBML-specific interface
library that provides features for parsing and
manipulating SBML objects directly. New features
in libSBML 3.0 include

• XML Parser abstraction layer

• Full support for ALL levels/versions of SBML

• Use either
• Expat
• Xerces
• libxml2

• read/write
• validate
• convert

• Support for MIRIAM compliant annotation

• Octave binding

ltdccreator rdfparseType"Resource"gt
ltrdfBaggt ltrdfli
rdfparseType"Resource"gt ltvCardN
rdfparseType"Resource"gt
ltvCardFamilygtLe Noverelt/vCardFamilygt
ltvCardGivengtNicolaslt/vCardGivengt
lt/vCardNgt ltvCardEMAILgtlenov_at_ebi.ac.uklt/
vCardEMAILgt ltvCardORGgt
ltvCardOrgnamegtEMBL-EBIlt/vCardOrgnamegt
lt/vCardORGgt lt/rdfligt
lt/rdfBaggt lt/dccreatorgt

• interact with Objects

Emulates the MATLAB binding
CVTerm

• Annotations notes as strings or XMLNodes

ltbqbiolisgt\n ltrdfBaggt\n ltrdfli
rdfresource\foo\/gt\n lt/rdfBaggt\n
lt/bqbiolisgt\n

• get MIRIAM compliant annotations

• Consistency checking and model validation

• can control required validation

Get or set as strings or XMLNodes
Category
setConsistencyChecks(SBMLConsistency, true)
SBMLConsistency SBOConsistency IdConsistency Unit
sConsistency MathMLConsistency Overdetermined L1Co
mpatability L2v1Compatability L2v2Compatability L2
v3Compatability ModelingPractice
Select only the required category
Act on only the required severity

• Documentation upgraded

Extensive documentation of C / C / Java /
Python APIs
if (getNumFailsWithSeverity(Error) gt 0)
LibSBML 3.0 is written in ISO C and C and
provides language bindings for C, C, Java,
Python, Perl, Lisp, MATLAB, and Octave on Linux,
Windows and MacOS X. The package is distributed
in both source-code form and as precompiled
dynamic libraries for the Microsoft Windows.
LibSBML is distributed under the terms of the
LGPL open-source license.
This and other projects of the SBML Team have
been supported by the following organizations
the National Institutes of Health (USA) under
grants R01 GM070923 and R01 GM077671 the
International Joint Research Program of NEDO
(Japan) the JST ERATO-SORST Program (Japan) the
Japanese Ministry of Agriculture the Japanese
Ministry of Education, Culture, Sports, Science
and Technology the BBSRC e-Science Initiative
(UK) the DARPA IPTO Bio-Computation Program
(USA) the Army Research Office's Institute for
Collaborative Biotechnologies (USA) the Air
Force Office of Scientific Research (USA) the
California Institute of Technology (USA) the
University of Hertfordshire (UK) the Molecular
Sciences Institute (USA) the Systems Biology
Institute (Japan) and Keio University (Japan).