Installation and setup guide

Installation and setup guide

• System requirements
• Installation procedure
  • Installation in Cytoscape
  • Setting up COMFI
    • Build your own index
    • Prepacked .zip file

---

System requirements

• Internet connection
• Java 1.5+
• Cytoscape 2.8
• ~2 G of free disk space
  (This only required during the set up if you build your index. If you download our prepacked .zip file or finished building the index, ~70 M will suffice)

Installation procedure

In general the installation procedure comprises 2 simple, quick steps:
1. Download and install COMFI in Cytoscape
2. Set up COMFI through the “(Re)build index/download dependencies” submenu

Installation in Cytoscape

There are three easy, different ways to install COMFI in Cytoscape:
1. Search for the COMFI plugin under the Cytoscape menu “plugins” “manage plugins” and click on install.
2. Download the COMFI.jar file from the project page and click on “Plugins” “Install plugin from file” and select the downloaded .jar file.
3. Download the COMFI.jar file from the project page and place it in the “plugins” folder in your Cytoscape installation directory.

If the plugin is correctly installed you should now be able to see a new “COMFI” entry in the “plugins menu”. If that is not the case try restarting Cytoscape.

Setting up COMFI

In order to work properly COMFI needs to build an index and to download several files from different databases. Under Windows it may be required that you need to run Cytoscape as administrator to make the downloader work! Otherwise Cytoscape could crash.

The files required for the index are:

• UniProt mapping file
• HomoloGene file
• YeastGenome mapping file

The files that contain the protein complex information are:

• CORUM
• Cyc2008

These files can either be manually downloaded und placed in a folder with the name "filesCOMFI" in the Cytoscape plugin folder (the CORUM file needs to be unzipped and renamed into corum_psimi.xml) or you can use the “(Re)build index/download dependencies” submenu in the “COMFI” entry.

When you select the "(Re)build index/download dependencies” submenu a dialogue like below should pop up. You then have basically two options:

1. You can build your own index
2. You can download a prepacked .zip file

Build your own index

Just click on the folder menus and consecutively download the files from box 1 & 2.
When the download is completed you will be notified of a successful download and the status icon will switch from the red cross to a green tick.
Downloading the UniProt mapping file can take quite long (~110 min) as it is quite large and the UniProt server bandwidth limited.
When you have finished downloading the files from box 1, build the index. Then proceed with downloading the files from box 2.

Prepacked .zip file

If this seems to time consuming or complex you can also download a prepacked .zip file of all the dependencies here or via the download menu. You simply need to unzip the file into your Cytoscape plugins folder. However this prepacked file will probably not be as up to date when it comes to homology mapping as if you build your own index.

In the end the menu should look like the lower panel in the following picture, which means COMFI is ready to use!

---