cy3sabiork: SABIO-RK for Cytoscape 3

cy3sabiork is a Cytoscape 3 app for accessing kinetic information from SABIO-RK via the RESTful web service.

Figure 1: Workflow overview.

App Store: http://apps.cytoscape.org/apps/cy3sabiork
Support & Forum: https://groups.google.com/forum/#!forum/cysbml-cyfluxviz
Issue Tracker: https://github.com/matthiaskoenig/cy3sabiork/issues
Tutorial: cy3sabiork Tutorial

License

• Source Code: GPLv3
• Documentation: CC BY-SA 4.0

Install

cy3sabiork is available via the Cytoscape App Store.

• install Cytoscape v3.5.1 or higher
• install cy3sbml and cy3sabiork via the app store
  Apps -> App Manager

For a manual install

• download latest versions of cy3sbml and cy3sabiork
  cy3sbml-vx.x.x.jar
cy3sabiork-vx.x.x.jar
  and move the downloaded jar files in the Cytoscape app folder CytoscapeConfiguration/3/apps/installed/

How to cite

König M. cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK [version 1; referees: awaiting peer review]. F1000Research 2016, 5:1736 (doi: 10.12688/f1000research.9211.1)

Screenshot

Figure 2: GUI overview.

Figure 3: Reaction kinetic networks based on SABIO-RK RESTful queries. cy3sbml provides access to annotation information.

Figure 4: Reaction kinetic network for Human galactose metabolism.

Build instructions

Clone the repository and build with maven

git clone https://github.com/matthiaskoenig/cy3sabiork.git
cd cy3sabiork
mvn clean install cy3sabiork

Development is done in develop branch, documentation in gh-pages

git checkout -b develop --track origin/develop
git checkout -b gh-pages --track origin/gh-pages

Acknowledgments

cy3sabiork was developed by Matthias König within the Virtual Liver Network (VLN) and the Systems Medicine of the Liver (LiSyM).
This work was supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM) [grant number 031L0054] and the Virtual Liver Network VLN [grant number 0315741].

                 

We thank the SABIO-RK team for their support. We thank the SBML and Cytoscape community for their support and help.

Change Log

v0.4.0 [?]

bug fixes

• #41 icon bug Cy36

v0.3.5 [2017-10-18]

• update of library dependencies
• bugfixes & cy3sbml update

v0.3.3 [2016-07-11]

• bug fixes & cy3sbml update
• release for zenodo DOI

v0.3.2 [2016-07-01]

• fixes SBML reading bug on Windows

v0.3.1 [2016-06-28]

• JavaFX based GUI
• autocomplete fields with suggestions
• WebView for Kinetic Information
• Query results window
• Full support of web services
• SBML information parsed in results table
• multiple bug fixes
• updated JSBML dependencies

v0.3.0 [2016-06-07]

• ported to Cytoscape 3
• updated documentation

v0.2.0 [2015-10-27]

• migration to github
• cy2sbml-v1.4.0

v0.17

• logger updated

v0.16

• update library dependecies -> jersey-1.17.1

v0.15

• first working version