Team:TU Delft/Software/im-tutorial

From 2010.igem.org

Interaction Mapping Application

The interaction mapping application directs the user through a number of steps to eventually get putative interactions of proteins in a new host organism. Unfortunately a lot of steps are still required, because the data comes from many sources. Look below for requirements of the application.

Requirements

• Access to running STRING database with the items, network and homology schema's.
• For Cytoscape export, you will need to install the plugin jars from the Interaction Mapping binary package to the Cytoscape plugin directory.

Steps and screenshots

Step 1: Enter parts or custom sequences

Step 2: Use the string-db website to find STRING protein ID for each sequence.

Step 3: Map interactions to E. coli, or other organisms.

Step 4: Export to text or Cytoscape

Download

Source code is available in a [http://github.com/jcnossen/InteractionHomologMapping github repository], or by directly downloading the [http://github.com/jcnossen/InteractionHomologMapping/zipball/master code in zip format].

A binary version will be uploaded here: http://jcnossen.github.com/InteractionHomologMapping/