SBMLsqueezer statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SBMLsqueezer
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Protocols

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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Versioning


No version available

Maintainer


  • person_outline Andreas Drager

Additional information


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

Publications for SBMLsqueezer

SBMLsqueezer citations

 (8)
call_split

Modeling of the jasmonate signaling pathway in Arabidopsis thaliana with respect to pathophysiology of Alternaria blight in Brassica

2017
Sci Rep
PMCID: 5711873
PMID: 29196636
DOI: 10.1038/s41598-017-16884-3
call_split See protocol

[…] SBMLsqueezer_v2.1 was applied to generate kinetic rate equations for each reaction of the constructed model through CellDesigner. This approach assists the modeling steps via programmed generation of […]

library_books

SABIO RK: an updated resource for manually curated biochemical reaction kinetics

2017
Nucleic Acids Res
PMCID: 5753344
PMID: 29092055
DOI: 10.1093/nar/gkx1065

[…] access the database automatically which is also used for retrieval of kinetics data by third-party software tools and data workflows. These tools include CellDesigner (), VirtualCell (), Sycamore (), SBMLsqueezer (), cy3sabiork (http://apps.cytoscape.org/apps/cy3sabiork), Path2Models (), LigDig (), FAIRDOMHub (). Currently SABIO-RK is accessed mostly (ca. 90%) via web services, which underlines th […]

library_books

Improving Collaboration by Standardization Efforts in Systems Biology

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

[…] ut 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 and easily […]

library_books

Modeling of the MAPK machinery activation in response to various abiotic and biotic stresses in plants by a system biology approach

2013
Bioinformation
PMCID: 3705613
PMID: 23847397
DOI: 10.6026/97320630009443

[…] 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 automat […]

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

[…] guage (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 [-]. The dr […]

library_books

Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)

2011
Stand Genomic Sci
PMCID: 3235518
PMID: 22180826
DOI: 10.4056/sigs.2034671

[…] nted 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). […]


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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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