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Cross platform highly-extensible JavaFx based application which provides functions for reading, writing, manipulating, and validating SBML files.

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SBTabEditor

Version License (MIT) Build Status

Free, open-source application to help you read, write, manipulate and validate SBML files

The available information about biological systems increased strongly in the last decade and will increase further as more advanced methods are developed.
To store and distribute computer models of biological systems, it was necessary
to develop consistent data formats to store this information about an organism and the corresponding biochemical networks. One widely used format for this task is Systems Biology Markup Language (SBML). However, this data format is not suitable for editing large amounts of data. For this reason the table based data
format SBtab was developed, up until now there is no proper editor designed explicitly for SBtab, the aim of this project solves this problem by developing an extensible editor which can read, write and save SBtab and SBML data and display them in table form.

Authors

Franziska Daumueller, Granit Guri, Melina Maier, Anton Rabe, Julian Wanner, Mykola Zakharchuk

Supervisor: Dr. Andreas Draeger

How to start

In order to run JavaFX application, a valid JRE 8+ needed.

Packaging into an executable Jar file:

To create executable jar, call mvn jfx:jar. Target jar-file will be placed at: target/jfx/app.

To run: java -jar sbmltab-x.x.x-jfx.jar

Assembling into platform-specific bundle:

To create os-specific launcher/installer, call mvn jfx:native. Target folder: target/jfx/native

Running process is platform specific. Example ./sbmltab-x.x.x (running on Unix-like system)

Documentation

All relevant information you can find on GitHub Wiki.

Third-party libraries, which we are using

JSBML: Pure Java library for reading, writing, and manipulating SBML files and data streams.

JUnit: Test framework which uses annotations to identify methods that specify a test.

Log4j: Java-based logging utility.

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Cross platform highly-extensible JavaFx based application which provides functions for reading, writing, manipulating, and validating SBML files.

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