Literature DB >> 18252737

LibSBML: an API library for SBML.

Benjamin J Bornstein1, Sarah M Keating, Akiya Jouraku, Michael Hucka.   

Abstract

UNLABELLED: LibSBML is an application programming interface library for reading, writing, manipulating and validating content expressed in the Systems Biology Markup Language (SBML) format. It is written in ISO C and C++, provides language bindings for Common Lisp, Java, Python, Perl, MATLAB and Octave, and includes many features that facilitate adoption and use of both SBML and the library. Developers can embed libSBML in their applications, saving themselves the work of implementing their own SBML parsing, manipulation and validation software. AVAILABILITY: LibSBML 3 was released in August 2007. Source code, binaries and documentation are freely available under LGPL open-source terms from http://sbml.org/software/libsbml.

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Year:  2008        PMID： 18252737      PMCID： PMC2517632          DOI： 10.1093/bioinformatics/btn051

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  3 in total

1.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Authors:  M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang
Journal:  Bioinformatics       Date:  2003-03-01       Impact factor: 6.937

2.  Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

Authors:  Michael Hucka; Frank T Bergmann; Andreas Dräger; Stefan Hoops; Sarah M Keating; Nicolas Le Novère; Chris J Myers; Brett G Olivier; Sven Sahle; James C Schaff; Lucian P Smith; Dagmar Waltemath; Darren J Wilkinson
Journal:  J Integr Bioinform       Date:  2015-09-04

3.  Minimum information requested in the annotation of biochemical models (MIRIAM).

Authors:  Nicolas Le Novère; Andrew Finney; Michael Hucka; Upinder S Bhalla; Fabien Campagne; Julio Collado-Vides; Edmund J Crampin; Matt Halstead; Edda Klipp; Pedro Mendes; Poul Nielsen; Herbert Sauro; Bruce Shapiro; Jacky L Snoep; Hugh D Spence; Barry L Wanner
Journal:  Nat Biotechnol       Date:  2005-12       Impact factor: 54.908
  3 in total
  136 in total

1.  Arcadia: a visualization tool for metabolic pathways.

Authors:  Alice C Villéger; Stephen R Pettifer; Douglas B Kell
Journal:  Bioinformatics       Date:  2010-05-07       Impact factor: 6.937

2.  von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.

Authors:  Ronan M T Fleming; Ines Thiele
Journal:  Bioinformatics       Date:  2010-11-28       Impact factor: 6.937

3.  Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.

Authors:  Peter D Karp; Mario Latendresse; Suzanne M Paley; Markus Krummenacker; Quang D Ong; Richard Billington; Anamika Kothari; Daniel Weaver; Thomas Lee; Pallavi Subhraveti; Aaron Spaulding; Carol Fulcher; Ingrid M Keseler; Ron Caspi
Journal:  Brief Bioinform       Date:  2015-10-10       Impact factor: 11.622

4.  BioSimulator.jl: Stochastic simulation in Julia.

Authors:  Alfonso Landeros; Timothy Stutz; Kevin L Keys; Alexander Alekseyenko; Janet S Sinsheimer; Kenneth Lange; Mary E Sehl
Journal:  Comput Methods Programs Biomed       Date:  2018-10-10       Impact factor: 5.428

Review 5.  Designing and encoding models for synthetic biology.

Authors:  Lukas Endler; Nicolas Rodriguez; Nick Juty; Vijayalakshmi Chelliah; Camille Laibe; Chen Li; Nicolas Le Novère
Journal:  J R Soc Interface       Date:  2009-04-01       Impact factor: 4.118

6.  Towards programming languages for genetic engineering of living cells.

Authors:  Michael Pedersen; Andrew Phillips
Journal:  J R Soc Interface       Date:  2009-04-15       Impact factor: 4.118

7.  A C library for retrieving specific reactions from the BioModels database.

Authors:  M L Neal; M Galdzicki; J T Gallimore; H M Sauro
Journal:  Bioinformatics       Date:  2013-09-29       Impact factor: 6.937

8.  SBML and CellML translation in antimony and JSim.

Authors:  Lucian P Smith; Erik Butterworth; James B Bassingthwaighte; Herbert M Sauro
Journal:  Bioinformatics       Date:  2013-11-08       Impact factor: 6.937

9.  A portable structural analysis library for reaction networks.

Authors:  Yosef Bedaso; Frank T Bergmann; Kiri Choi; Kyle Medley; Herbert M Sauro
Journal:  Biosystems       Date:  2018-05-30       Impact factor: 1.973

10.  Antimony: a modular model definition language.

Authors:  Lucian P Smith; Frank T Bergmann; Deepak Chandran; Herbert M Sauro
Journal:  Bioinformatics       Date:  2009-07-03       Impact factor: 6.937
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