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SBMLDiagrams: a python package to process and visualize SBML layout and render.

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Název: SBMLDiagrams: a python package to process and visualize SBML layout and render.
Autoři: Xu, Jin, Jiang, Jessie, Sauro, Herbert M
Zdroj: Bioinformatics; Jan2023, Vol. 39 Issue 1, p1-2, 2p
Témata: PYTHON programming language, BIOCHEMICAL models, PDF (Computer file format), SYSTEMS biology, SOURCE code
Abstrakt: Summary The systems biology markup language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical model as a pathway diagram. However, up to now, there has been little support to help users easily add and retrieve such information from SBML. In this application note, we describe a new Python package called SBMLDiagrams. This package allows a user to add a layout and render information or retrieve it using a straightforward Python API. The package uses skia-python to support the rendering of the diagrams, allowing export to commons formats such as PNG or PDF. Availability and implementation SBMLDiagrams is publicly available and licensed under the liberal MIT open-source license. The package is available for all major platforms. The source code has been deposited at GitHub (github.com/sys-bio/SBMLDiagrams). Users can install the package using the standard pip installation mechanism: pip install SBMLDiagrams. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]
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Databáze: Complementary Index
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Abstrakt:Summary The systems biology markup language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical model as a pathway diagram. However, up to now, there has been little support to help users easily add and retrieve such information from SBML. In this application note, we describe a new Python package called SBMLDiagrams. This package allows a user to add a layout and render information or retrieve it using a straightforward Python API. The package uses skia-python to support the rendering of the diagrams, allowing export to commons formats such as PNG or PDF. Availability and implementation SBMLDiagrams is publicly available and licensed under the liberal MIT open-source license. The package is available for all major platforms. The source code has been deposited at GitHub (github.com/sys-bio/SBMLDiagrams). Users can install the package using the standard pip installation mechanism: pip install SBMLDiagrams. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]
ISSN:13674803
DOI:10.1093/bioinformatics/btac730