JSBML 1.0: providing a smorgasbord of options to encode systems biology models

Nicolas Rodriguez; Alex Thomas; Leandro Watanabe; Ibrahim Y. Vazirabad; Victor Kofia; Harold F. Gómez; Florian Mittag; Jakob Matthes; Jan Rudolph; Finja Wrzodek; Eugen Netz; Alexander Diamantikos; Johannes Eichner; Roland Keller; Clemens Wrzodek; Sebastian Fröhlich; Nathan Lewis; Chris J. Myers; Nicolas Le Novère; Bernhard Palsson; Michael Hucka; Andreas Dräger

doi:10.1093/bioinformatics/btv341

JSBML 1.0: providing a smorgasbord of options to encode systems biology models

Nicolas Rodriguez, Alex Thomas, Leandro Watanabe, Ibrahim Y. Vazirabad, Victor Kofia, Harold F. Gómez, Florian Mittag, Jakob Matthes, Jan Rudolph, Finja Wrzodek, Eugen Netz, Alexander Diamantikos, Johannes Eichner, Roland Keller, Clemens Wrzodek, Sebastian Fröhlich, Nathan Lewis, Chris J. Myers, Nicolas Le Novère, Bernhard PalssonMichael Hucka, Andreas Dräger

Novo Nordisk Foundation Center for Biosustainability

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Abstract

JSBML, the official pure Java programming library for the Systems Biology Markup Language (SBML) format, has evolved with the advent of different modeling formalisms in systems biology and their ability to be exchanged and represented via extensions of SBML. JSBML has matured into a major, active open-source project with contributions from a growing, international team of developers who not only maintain compatibility with SBML, but also drive steady improvements to the Java interface and promote ease-of-use with end users. Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML. More information about JSBML can be found in the user guide at http://sbml.org/Software/JSBML/docs/. [email protected] or [email protected] Supplementary data are available at Bioinformatics online.

Original language	English
Journal	Bioinformatics
Volume	31
Issue number	20
Pages (from-to)	3383-6
Number of pages	4
ISSN	1367-4803
DOIs	https://doi.org/10.1093/bioinformatics/btv341
Publication status	Published - 2015

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Rodriguez, N., Thomas, A., Watanabe, L., Vazirabad, I. Y., Kofia, V., Gómez, H. F., Mittag, F., Matthes, J., Rudolph, J., Wrzodek, F., Netz, E., Diamantikos, A., Eichner, J., Keller, R., Wrzodek, C., Fröhlich, S., Lewis, N., Myers, C. J., Le Novère, N., ... Dräger, A. (2015). JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics, 31(20), 3383-6. https://doi.org/10.1093/bioinformatics/btv341

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title = "JSBML 1.0: providing a smorgasbord of options to encode systems biology models",

abstract = "JSBML, the official pure Java programming library for the Systems Biology Markup Language (SBML) format, has evolved with the advent of different modeling formalisms in systems biology and their ability to be exchanged and represented via extensions of SBML. JSBML has matured into a major, active open-source project with contributions from a growing, international team of developers who not only maintain compatibility with SBML, but also drive steady improvements to the Java interface and promote ease-of-use with end users. Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML. More information about JSBML can be found in the user guide at http://sbml.org/Software/JSBML/docs/. [email protected] or [email protected] Supplementary data are available at Bioinformatics online.",

author = "Nicolas Rodriguez and Alex Thomas and Leandro Watanabe and Vazirabad, {Ibrahim Y.} and Victor Kofia and G{\'o}mez, {Harold F.} and Florian Mittag and Jakob Matthes and Jan Rudolph and Finja Wrzodek and Eugen Netz and Alexander Diamantikos and Johannes Eichner and Roland Keller and Clemens Wrzodek and Sebastian Fr{\"o}hlich and Nathan Lewis and Myers, {Chris J.} and {Le Nov{\`e}re}, Nicolas and Bernhard Palsson and Michael Hucka and Andreas Dr{\"a}ger",

year = "2015",

doi = "10.1093/bioinformatics/btv341",

language = "English",

volume = "31",

pages = "3383--6",

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Rodriguez, N, Thomas, A, Watanabe, L, Vazirabad, IY, Kofia, V, Gómez, HF, Mittag, F, Matthes, J, Rudolph, J, Wrzodek, F, Netz, E, Diamantikos, A, Eichner, J, Keller, R, Wrzodek, C, Fröhlich, S, Lewis, N, Myers, CJ, Le Novère, N, Palsson, B, Hucka, M & Dräger, A 2015, 'JSBML 1.0: providing a smorgasbord of options to encode systems biology models', Bioinformatics, vol. 31, no. 20, pp. 3383-6. https://doi.org/10.1093/bioinformatics/btv341

TY - JOUR

T1 - JSBML 1.0: providing a smorgasbord of options to encode systems biology models

AU - Rodriguez, Nicolas

AU - Thomas, Alex

AU - Watanabe, Leandro

AU - Vazirabad, Ibrahim Y.

AU - Kofia, Victor

AU - Gómez, Harold F.

AU - Mittag, Florian

AU - Matthes, Jakob

AU - Rudolph, Jan

AU - Wrzodek, Finja

AU - Netz, Eugen

AU - Diamantikos, Alexander

AU - Eichner, Johannes

AU - Keller, Roland

AU - Wrzodek, Clemens

AU - Fröhlich, Sebastian

AU - Lewis, Nathan

AU - Myers, Chris J.

AU - Le Novère, Nicolas

AU - Palsson, Bernhard

AU - Hucka, Michael

AU - Dräger, Andreas

PY - 2015

Y1 - 2015

N2 - JSBML, the official pure Java programming library for the Systems Biology Markup Language (SBML) format, has evolved with the advent of different modeling formalisms in systems biology and their ability to be exchanged and represented via extensions of SBML. JSBML has matured into a major, active open-source project with contributions from a growing, international team of developers who not only maintain compatibility with SBML, but also drive steady improvements to the Java interface and promote ease-of-use with end users. Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML. More information about JSBML can be found in the user guide at http://sbml.org/Software/JSBML/docs/. [email protected] or [email protected] Supplementary data are available at Bioinformatics online.

AB - JSBML, the official pure Java programming library for the Systems Biology Markup Language (SBML) format, has evolved with the advent of different modeling formalisms in systems biology and their ability to be exchanged and represented via extensions of SBML. JSBML has matured into a major, active open-source project with contributions from a growing, international team of developers who not only maintain compatibility with SBML, but also drive steady improvements to the Java interface and promote ease-of-use with end users. Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML. More information about JSBML can be found in the user guide at http://sbml.org/Software/JSBML/docs/. [email protected] or [email protected] Supplementary data are available at Bioinformatics online.

U2 - 10.1093/bioinformatics/btv341

DO - 10.1093/bioinformatics/btv341

M3 - Journal article

C2 - 26079347

SN - 1367-4803

VL - 31

SP - 3383

EP - 3386

JO - Bioinformatics

JF - Bioinformatics

IS - 20

ER -

JSBML 1.0: providing a smorgasbord of options to encode systems biology models

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