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Cytoscape linux10/5/2023 The installation section above explains how to install the JAR and once the JAR is installed and the plugin is loaded the data component will be downloaded by it. Data component containing protein-protein interaction data.īoth these components are required for the functioning of the plugin.The java executable file (JAR) which is the software component dealing with all the functionalities.(If you cannot see the iRefIndex panel, click on the title "iRefIndex", near the "Network" tab of Cytoscape.) If the installation was successful, you will see a list of indices in the Results text box in green text and if the installation fails you will see errors in red text.The installation process should now complete itself.If we are informed of demonstrations we could give you advice on how to perform the installation smoothly. If you are planing to use the plugin in a laboratory demonstration where more than 15 people would try to perform the installation simultaneously, we recommend that everyone is not using the same wireless resource and do this in subgroups (e.g. However we have experienced delays up to 15 to 30 minutes when the installation was done using wireless network with below average signal strength. The downloading and installation of indices usually takes less than 5 minutes if you have a internet connection of 10Mb/sec or more.If this message appears on second or subsequent attempts, this would mean there might be a problem accessing this directory and please make sure that you have write access and a minimum available free space of 1Gb. If the default directory is selected and it is not accessible the user would be prompted to restart Cytoscape.We encourage the users to use this default directory. The data and indices require a minimum disk space of 1 Gb at this location. The recommended place would be the plugin home directory which would appear as the recommended (default). First time you activate the plugin (In the main Cytoscape window, select "Plugins" -> "iRefIndex_0.6x"), you will be prompted to select an installation directory for the data and indices.
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