TieDIE_Cytoscape

For users interested in TieDIE app. for Cytoscape

Download tiedie app and tutorials from here tiedie

For developers interested in TieDIE app. for Cytoscape (How to set up Netbeans IDE)

1. Install Netbeans [from here] (https://netbeans.org/downloads/)
2. Once installed ,Go to File-> Open Project and this dialog appears [dialog like here] (http://s29.postimg.org/dqseabrhj/Capture.png)
3. You just have to select our TieDIE maven project which should be already downloaded(cloned) on your computer in advance from here clone this repo
4. Cytoscape javadocs are available here 3.0.0 3.0.1 3.2.0
5. More references for Cytoscape app. development Cytoscape app. developer
6. [Cytoscape App. cookbook] (http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/Cytoscape_3_App_Cookbook)
7. Once you are done with developing the project, you can clean and build the project and you'll find a jar file in the target folder of sourcecode. This jar file is used to install TieDIE app. through Cytoscape. You should download Cytoscape 3.x from here Download Cytoscape

More about TieDIE

1. "TieDIE" journal

2. Existing TieDIE software

3. Existing TieDIE repo (There is a cytoscape branch which has the code for tiedie app. hosted there as well)

About this project

======= [TieDIE algorithm] (http://bioinformatics.oxfordjournals.org/content/29/21/2757.short) finds "subnetworks" connecting genomic perturbations to transcriptional changes in large gene interaction networks. This algorithm is useful in optimizing cancer treatment by viewing cancer from a gene network perspective thus enhancing our understanding of disease initiation, progression and therapy. This project deploys TieDIE algorithm into cytoscape as an app.

This is a GSOC 2014 project developed by [Srikanth.B] (https://github.com/srikanthBezawada) under the supervision of Evan Paull