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Protocols

JSBML specifications

Information


Unique identifier OMICS_17478
Name JSBML
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU Lesser General Public License version 2.1
Computer skills Advanced
Version 1.2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Andreas Drager

Publication for JSBML

JSBML citations

 (8)
library_books

Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis

2016
Nucleic Acids Res
PMCID: 4937331
PMID: 27216817
DOI: 10.1093/nar/gkw462

[…] m a curated liver GEM, iHepatocyte2322 () (the second step in Supplementary Figure S1). Enzymes with their corresponding lipid metabolic pathways were obtained from iHepatocyte2322 by a Java library, JSBML (). Focusing on only lipid metabolism, we reconstructed a new lipid-specific ‘Pool reactions’ pathway, by selecting enzymes of reactions pooling FFAs: a list of FFAs was obtained from fatty acid […]

call_split

The systems biology format converter

2016
BMC Bioinformatics
PMCID: 4820913
PMID: 27044654
DOI: 10.1186/s12859-016-1000-2
call_split See protocol

[…] ools to read and write models. All classes should return the same value for the getURI() method. For instance, the implementation of a converter for the Systems Biology Markup Language [] may rely on JSBML [], libSBML [], or a DOM document structure []. This design can be advantageous when 1) a given library does not read a version of a format properly; 2) a converter was written with an old or ne […]

library_books

Combining computational models, semantic annotations and simulation experiments in a graph database

2015
PMCID: 4352687
PMID: 25754863
DOI: 10.1093/database/bau130

[…] Models and Simulation Descriptions are added to the database using format-dependent importers. Each supported format has its specification. Consequently, importers were implemented for SBML [based on jSBML ()], for CellML and for SED-ML [based on jlibsedml ()]. All importers share a common interface which maps the model and simulation files onto a graph structure. The import keeps the models’ sema […]

library_books

Improving Collaboration by Standardization Efforts in Systems Biology

2014
Front Bioeng Biotechnol
PMCID: 4259112
PMID: 25538939
DOI: 10.3389/fbioe.2014.00061

[…] ale behind this design decision is that the same model can be interpreted in terms of a different modeling framework, such as stochastic simulation, etc.The libraries libSBML (Bornstein et al., ) and JSBML (Dräger et al., ) facilitate the implementation of import and export functions of SBML models in customized software solutions. While libSBML provides bindings to a large variety of programing l […]

library_books

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

2013
BMC Syst Biol
PMCID: 3892043
PMID: 24321545
DOI: 10.1186/1752-0509-7-135

[…] e identification, model reduction) that are common to many scientific efforts relying upon a discrete modelling approach. The library further provides import and export filters for SBML qual (through JSBML; see Methods section), as well as an interface enabling the integration of logical models and SBML qual with additional formats and a number of existing software tools. The development of this l […]

library_books

Precise generation of systems biology models from KEGG pathways

2013
BMC Syst Biol
PMCID: 3623889
PMID: 23433509
DOI: 10.1186/1752-0509-7-15

[…] with BioPAX that facilitates building and writing the internal BioPAX data structure (http://www.biopax.org/paxtools.php). To establish the SBML data structure, KEGGtranslator uses the Java™ library JSBML [] and supports SBML Level 2 Version 4 [] and SBML Level 3 Version 1 [].KEGGtranslator is implemented in Java™, provides an interactive, user-friendly and easy-to-use graphical user interface (G […]


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JSBML institution(s)
European Bioinformatics Institute (EBI), Hinxton, UK; Babraham Institute, Babraham Research Campus, Cambridge, UK; University of California, San Diego, La Jolla, CA, USA; Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, CA, USA; The University of Utah, Salt Lake City, UT, USA; Marquette University, Milwaukee, WI, USA; The University of Toronto, Toronto, ON, Canada; Boston University, Boston, MA, USA; Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tubingen, Germany; Tel Aviv University, Tel Aviv, Israel; Roche Pharmaceutical Research and Early Development, pRED Informatics, Roche Innovation Center, Penzberg, Germany; Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany; Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany; The California Institute of Technology, Pasadena, CA, USA
JSBML funding source(s)
This work was supported by a National Institute of Health grant for the continued development of essential SBML software support (NIH, United States, award number GM070923), European Union projects SynSys (FP7 242167) and BBSRC Signalling Institute Strategic Programme (BBS/E/B/000C0419), a National Science Foundation grant (CCF-1218095), a Marie Curie International Outgoing Fellowship within the EU 7th Framework Programme for Research and Technological Development (project AMBiCon, 332020), Google Inc. (Summer of Code 2014), the Federal Ministry of Education and Research (BMBF, Germany) as part of the Virtual Liver Network (grant number 0315756), the Novo Nordisk Foundation and the NIH HHSN272201000053C.

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