SBML
SBML (the Systems Biology Markup Language) is an XML-based format for communicating and storing representations of biological processes. Its aim is to be a lingua franca for representing models in biology. SBML is suitable for models commonly found in research on a number of topics, including cell signaling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others.
Here are 20 public repositories matching this topic...
A graphical editor for systems biology models.
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May 9, 2018 - Java
Translation between CellDesigner-flavoured SBML and SBGN-ML
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Nov 17, 2018 - Java
JSBML is a community-driven project to create a free, open-source, pure Java™ library for reading, writing, and manipulating SBML files (the Systems Biology Markup Language) and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.
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Aug 19, 2019 - Java
A convenient library that greatly simplifies application development with Java™
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Aug 28, 2019 - Java
An efficient Java™ solver implementation for SBML
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Jun 2, 2020 - Java
Easily usable JavaFx-based inSilico module for dynamic Systems Biology Markup Language (SBML) model simulation visualization. Provides an intuitive Graphical User Interface for dynamic processing based on SBSCL.
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Jul 11, 2020 - Java
JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim's primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains.
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Feb 5, 2021 - Java
Translation between CellDesigner-flavoured SBML and SBGN-ML
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Feb 26, 2021 - Java
SBMLreporter provides a way to read the contents of XML-based SBML files. This is helpful and important for, e.g., error detection, proofreading and model communication. SBMLreporter is a new implementation of SBML2LaTeX.
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Aug 17, 2021 - Java
the SBML module of BiVeS
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Dec 10, 2021 - Java
Cross platform highly-extensible JavaFx based application which provides functions for reading, writing, manipulating, and validating SBML files.
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Jan 11, 2022 - Java
cy3sbml: SBML for Cytoscape 3
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Nov 16, 2022 - Java
Encoding ME models in SBML
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Dec 21, 2022 - Java
ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
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May 27, 2024 - Java
JSBML is a community-driven project to create a free, open-source, pure Java™ library for reading, writing, and manipulating SBML files (the Systems Biology Markup Language) and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.
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Jan 3, 2023 - Java
A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.
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Feb 2, 2023 - Java
A Java-based software for visualizing and translating the KEGG PATHWAY database. Conversion of KGML files into BioPAX, SBML, GraphML, GML, and various other formats.
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Jun 26, 2023 - Java