SBMLsqueezer specifications

Information


Unique identifier OMICS_17469
Name SBMLsqueezer
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Andreas Drager <>

Additional information


https://webservices.cs.uni-tuebingen.de/

Information


Unique identifier OMICS_17469
Name SBMLsqueezer
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 2.1
Stability Stable
Source code URL http://www.ra.cs.uni-tuebingen.de/software/SBMLsqueezer/downloads/SBMLsqueezer_v2.1.zip
Maintained Yes

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Maintainer


  • person_outline Andreas Drager <>

Additional information


https://webservices.cs.uni-tuebingen.de/

Publications for SBMLsqueezer

SBMLsqueezer in publications

 (6)
PMCID: 5711873
PMID: 29196636
DOI: 10.1038/s41598-017-16884-3

[…] study explains the outcome of integrated systems based approach that explored the intricate nature of jasmonate signalling pathway during pathogenesis at molecular level. the rate laws produced by sbmlsqueezer were utilized to predict the dynamic behavior of the pathway (table  ). this could be useful for understanding the pathophysiology of alternaria blight in brassica for developing […]

PMCID: 4259112
PMID: 25538939
DOI: 10.3389/fbioe.2014.00061

[…] the next gadget or receive input from other gadgets. a powerful workflow would be to create a model with keggtranslator (wrzodek et al., , ), which can forward its result to the rate law generator sbmlsqueezer (dräger et al., , ), which in turn launches sbmlsimulator (keller et al., )in order to run a simulation and parameter calibration on the resulting model. garuda provides a nice […]

PMCID: 3705613
PMID: 23847397
DOI: 10.6026/97320630009443

[…] the data of molecular interaction are stored in system biology markup language (sbml; http://www.sbml.org/). sbml is a standard machine readable model representation format []., the software sbmlsqueezer was used to generate kinetic rate equations for our model. in which the kinetic equations have to be associated with each reaction. this approach facilitates the modeling step via […]

PMCID: 3623889
PMID: 23433509
DOI: 10.1186/1752-0509-7-15

[…] (sbml) [] and biological pathway exchange (biopax) []. these formats can be used with graphical modeling applications (e.g., celldesigner [] or cytoscape []), complemented with rate laws (e.g., sbmlsqueezer []), used for flux balance analysis (e.g., fasimu []), and many more applications. therefore, converters exist that perform mostly basic conversions from kgml to those formats [-]. […]

PMCID: 3235518
PMID: 22180826
DOI: 10.4056/sigs.2034671

[…] an update on jsbml, a native java sbml api library [,]. they were followed by presentations on two end-user tools supporting sbml: ibiosim [-], by chris myers of the university of utah (usa) and sbmlsqueezer [,], a plug-in for celldesigner, by andreas dräger of the bioinformatics center of tübingen (germany)., the combine meeting proper was followed on the last day by a symposium […]


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SBMLsqueezer institution(s)
Systems Biology Research Group, University of California, San Diego, La Jolla, CA, USA; Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany; Novo Nordisk Foundation Center for Biosustainability, Horsholm, Denmark
SBMLsqueezer funding source(s)
This work was supported by Federal Ministry of Education and Research (BMBF, Germany) for funding the Virtual Liver Network (grant number 0315756) and to the 7th EU Framework Program for Research and Technological Development for AD’s Marie Curie International Outgoing Fellowship (project AMBiCon, 332020) as well as a National Institute of Health grant for the continued development of essential SBML software support (NIH, United States, award number GM070923).

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