Difference between revisions of "README Cytoscape plugin 3.0 Beta"
| Line 3: | Line 3: | ||
1. Before start : | 1. Before start : | ||
Make sure Cytoscape is not running. | Make sure Cytoscape is not running. | ||
| − | Remove any other | + | Remove any other installations of iRefIndex_beta# or directories created |
| − | Make sure | + | Make sure Cytoscape has at leas 128Mb memory (http://cytoscape.org/cgi-bin/moin.cgi/How%20to%20increase%20memory%20for%20Cytoscape) |
| − | 2. Copy both IRefIndex_beta3.jar and iRefDATA_MMDDYYYY.irfz file to the plugin directory of | + | 2. Copy both IRefIndex_beta3.jar and iRefDATA_MMDDYYYY.irfz file to the plugin directory of Cytoscape. |
| Line 19: | Line 19: | ||
3. Start Cytoscape and select IRefIndex_beta3 from plugin menu | 3. Start Cytoscape and select IRefIndex_beta3 from plugin menu | ||
| − | 4. First time | + | 4. First time installation may take up to 5 minutes (Creating Java index objects) |
| − | 5. If the | + | 5. If the installation was successful you will see a list of losed indexes in the Results text box in green |
| − | and if the | + | and if the installation fails you will get errors in red text. |
| Line 30: | Line 30: | ||
1. How do I search all the interactions involving the protein NP:477306 | 1. How do I search all the interactions involving the protein NP:477306 | ||
- Type NP_477306 on the search text box | - Type NP_477306 on the search text box | ||
| − | - Select ACCESSION from type | + | - Select ACCESSION from type drop down menu |
- (optional) restrict the search within a certain taxon identifier by selecting the id from Taxon | - (optional) restrict the search within a certain taxon identifier by selecting the id from Taxon | ||
- Click Search & load | - Click Search & load | ||
Revision as of 11:13, 21 November 2008
Date : 2008 Nov 21
1. Before start : Make sure Cytoscape is not running. Remove any other installations of iRefIndex_beta# or directories created Make sure Cytoscape has at leas 128Mb memory (http://cytoscape.org/cgi-bin/moin.cgi/How%20to%20increase%20memory%20for%20Cytoscape)
2. Copy both IRefIndex_beta3.jar and iRefDATA_MMDDYYYY.irfz file to the plugin directory of Cytoscape.
e.g :
Unix
/...../Cytoscape_v2.6.0/plugins/
Windows: \.....\Cytoscape_v2.6.0\plugins\
- you should have write privileges for this directory
3. Start Cytoscape and select IRefIndex_beta3 from plugin menu 4. First time installation may take up to 5 minutes (Creating Java index objects) 5. If the installation was successful you will see a list of losed indexes in the Results text box in green
and if the installation fails you will get errors in red text.
Q&A
1. How do I search all the interactions involving the protein NP:477306
- Type NP_477306 on the search text box - Select ACCESSION from type drop down menu - (optional) restrict the search within a certain taxon identifier by selecting the id from Taxon - Click Search & load
2. How do I load a list of identifiers form a file
- For this you need to create plain text file with the list of identifiers
- First line of the file should be the type of search and the taxonomy identifier
e.g. #accession:96065
- There is a sample file available in the following directory
Unix
/...../Cytoscape_v2.6.0/plugins/iRefIndex/Sample_batch.txt
Windows:
\.....\Cytoscape_v2.6.0\plugins\iRefIndex\Sample_batch.txt
