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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 == | ||
| - | The interaction mapping application directs the user through a number of steps | + | |
| + | 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. | ||
| + | === 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 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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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 github repository, or by directly downloading the code in zip format.
A binary version will be uploaded here: http://jcnossen.github.com/InteractionHomologMapping/
