SBML Layout statistics

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SBML Layout specifications

Information


Unique identifier OMICS_21499
Name SBML Layout
Software type Framework/Library
Interface Graphical user interface, Web user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C#
License BSD 3-clause “New” or “Revised” License
Computer skills Basic
Stability Stable
Maintained Yes

Download


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Maintainer


  • person_outline Frank Bergmann

Additional information


http://sysbioapps.dyndns.org/Layout

SBML Layout citations

 (6)
library_books

Improving Collaboration by Standardization Efforts in Systems Biology

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

[…] resentation standards. While, this format does not include rendering information, it has been proposed to incorporate a rendering extension, similar as can be done with SBML files. In contrast to the SBML layout extension, this format is focused on the concepts of SBGN only and can be validated against the SBGN specifications. The API library libSBGN facilitates the import and export of SBGN-ML fi […]

library_books

CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data

2014
BMC Syst Biol
PMCID: 4263207
PMID: 25466481
DOI: 10.1186/s12918-014-0123-1

[…] mpatible with standards –compatibility with the Systems Biology Markup Language (SBML) [], the Mathematical Markup Language (MathML) [] and several layout standards for visualization (SBGN-ML, XGMML, SBML Layout) rendering interoperability with other tools easier.In its current version, CBFA accommodates several tools and algorithms that have been developed for the manipulation of metabolic models […]

library_books

Conversion of KEGG metabolic pathways to SBGN maps including automatic layout

2013
BMC Bioinformatics
PMCID: 3765910
PMID: 23953132
DOI: 10.1186/1471-2105-14-250

[…] the closest work to ours is research on converting from SBML [] or BioPAX [] formats into graphical formats like SBGN. Some examples for SBML are Arcadia [], which uses GraphViz [] for layout and the SBML Layout Extension []. BioPAX to SBGN conversion is done, for example, by Paxtools [] and BioUML []. However, these approaches can’t translate the widely used KEGG maps into SBGN, and they mostly c […]

library_books

Representing physiological processes and their participants with PhysioMaps

2013
J Biomed Semantics
PMCID: 3632997
PMID: 23735231
DOI: 10.1186/2041-1480-4-S1-S2

[…] cal content of datasets, models, and research domains. Examples of PhysioMaps are the reaction pathway diagrams as generated by KEGG[], Reactome[], and the BioModels[] resources. See for example, the SBML layout package, sbmllayout.sourceforge.net, for visualizations of SBML models. Similarly, for Reactome, the BioPAX formalism[] provides the basis for a node-and-arc representation of processes. I […]

library_books

An efficient biological pathway layout algorithm combining grid layout and spring embedder for complicated cellular location information

2010
BMC Bioinformatics
PMCID: 2904761
PMID: 20565884
DOI: 10.1186/1471-2105-11-335

[…] mple positional constraints has been proposed for more general metabolic pathways [,]. In GOlorize [], an additional attractive force is applied to nodes belonging to the same Gene Ontology class. An SBML layout extension, SBWAutoLayout [], employs the spring embedder approach as its layout algorithm. Schreiber et al. [] proposed to a generic layout algorithm where the spring force cost is optimiz […]

library_books

BioPP: a tool for web publication of biological networks

2007
BMC Bioinformatics
PMCID: 1885811
PMID: 17519033
DOI: 10.1186/1471-2105-8-168

[…] l networks []. We have found that limitations in the symbolic representation of nodes, in drawing and layout tools and in visual representation using the current releases of Systems Biology Workbench SBML layout extension or Cytoscape make it difficult to construct an easily understood diagram for high granularity cell-specific signaling maps. For detailed networks, we find that CellDesigner [] pr […]

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