Team:TU Delft/Software/im-tutorial

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(New page: == Interaction Mapping Application == The interaction mapping application directs the user through a number of steps: Unfortunately a lot of steps are still required, because the data com...)
 
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== Interaction Mapping Application ==
== Interaction Mapping Application ==
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The interaction mapping application directs the user through a number of steps:
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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.
Unfortunately a lot of steps are still required, because the data comes from many sources. Look below for requirements of the application.
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=== Requirements ===
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* Access to running STRING database with the items, network and homology schema's.
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* For Cytoscape export, you will need to install the plugin jars from the Interaction Mapping binary package to the Cytoscape plugin directory.
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=== Steps and screenshots ===
Step 1: Enter parts or custom sequences
Step 1: Enter parts or custom sequences
<html><img src="http://dl.dropbox.com/u/602630/scr/step1-scr.PNG"></html>
<html><img src="http://dl.dropbox.com/u/602630/scr/step1-scr.PNG"></html>
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A binary version will be uploaded here:
A binary version will be uploaded here:
http://jcnossen.github.com/InteractionHomologMapping/
http://jcnossen.github.com/InteractionHomologMapping/
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=== Requirements ===
 

Latest revision as of 23:25, 27 October 2010

Contents

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/