iRefScape plugin menu

==Search tools== .

Retrieve interactions for the selected nodes

To load all protein-protein interactions and complexes involving one or more selected nodes. This action is same as performing a iteration=1 search using iRefScape for the selected nodes.

Expand one level

To load all protein-protein interactions and complexes involving at least one of the nodes in the current network. The behaviour is same as performing iteration=1 search using iRefScape for all the nodes.

Load interactions between neighbours

To complete the interactions between the currently loaded nodes. When a search & load operation is performed in iRefScape the network retuned contains all the proteins interacting with the query and the corresponding interactions. This does not return interactions between the neighbours of the query. This operation is same as performing a iteration=0 search using iRefScape for all the nodes. This action has no effect for networks for which this operation has already been performed using the option presented at the end of the search.

Clear load history (Reload everything next time)

This will clear the iRefScape cache memory containing currently loaded nodes and edges. IRefScape keep track of what is loaded to avoid reloading and thus increase efficiency. Therefore, if a search is performed twice without requesting to make a new view or selecting this menu option the network will not be re-loaded. If the user wishes to reload the network then this option has to be used. When using other methods of expanding network like “Expand one level” iRefScape handles the cache clearing automatically.

Reset node degree

This option resets the i.alive_degree of nodes. i.alive_degree provides how many nodes with a certain attribute type is connected to each node (set using filters).

Load user variables

Users can load there own variables for proteins which are mapped to a ROGID. The file should follow the format given below;

1. Should be a plain text file with exactly two columns and each line ending with a new line character (pressing enter).
2. First column should contain the ROGID
3. Second column should contain the user attribute/variable.
4. The file name should have the format _rog_#USER_VARIABLE_NAME.iruv (The text between # and the .iruv will be variable name)

e.g
#rog	USER_VARIABLE
j4H4IZH/ecTvEDjCel+eLTCmFyE9606	1
j4H4IZH/ecTvEDjCel+eLTCmFyE9606	1
q6/pRFyay7gQ6bb2rzvKYgfkeaE9606	2
8sODZSppCsuEgRmhSHp3UjwOf2M9606	3
obze7v7i2yTIIcJjd7laIriNFg89606	4
Ty0OLkmhoUPjUuLQQv5ykN057oM9606	5
4bhW4sEt1YhYwHnHCyDNV3vvThs9606	6
Al8M+JdB4H+QnwITh8KcicdI2x49606	6
rkL/SGL1Enj6KoFkPbbcoJ5vKJE9606	6