Difference between revisions of "README Cytoscape plugin 3.0 Beta"

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Date : 2008 Nov 21
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Date : Nov 21st, 2008
  
1. Before start :
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The iRefIndex plugin for Cytoscape has not been officially released. If you are looking at this page, you have probably been directed here from the Cytoscape plugin directory at ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin . This plugin is for testing purposes only. Join the Google groups e-mail list at http://groups.google.com/group/irefindex?hl=en to be informed of the official release and updates.
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.
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==Installation==
  
 +
# Obtain Cytoscape from http://cytoscape.org/ and follow the installation instructions for that software.
 +
# Before starting:
 +
#* Make sure that Cytoscape is not running.
 +
#* Remove any other installations of iRefIndex beta or directories created by iRefIndex.
 +
#* Make sure Cytoscape has at least 128MB memory (http://cytoscape.org/cgi-bin/moin.cgi/How%20to%20increase%20memory%20for%20Cytoscape)
 +
# Copy both the <tt>IRefIndex_beta3.jar</tt> and <tt>iRefDATA_MMDDYYYY.irfz</tt> files to the <tt>plugins</tt> directory of Cytoscape. For example:
 +
#* On Unix: <tt>/...../Cytoscape_v2.6.0/plugins/</tt>
 +
#* On Windows: <tt>\.....\Cytoscape_v2.6.0\plugins\</tt>
 +
#* (You should have write privileges for this directory.)
 +
# Start Cytoscape and select IRefIndex_beta3 from plugin menu.
 +
# First time installation may take up to 5 minutes (while the plugin creates Java index objects).
 +
# If the installation is successful, you will see a list of indices in the Results text box in green and if the installation fails you will see errors in red text. (If you cannot see the iRefIndex panel please click on the title iRefIndex, near the Network tab.)
  
e.g :
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; Windows Vista users : Cytoscape installation inside "Program files" directory is '''not''' recommended. Use <tt>C:\Cytoscape_v2.6.1\</tt> instead. The iRefIndex plugin requires unrestricted hard disk drive access in its installation folder for low level operations.
Unix
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; MacOS users : The plugin will not work unless Java 1.6X is installed (and there is no official release of this version available from Sun yet). But the following approach was tested and can be recommended.
/...../Cytoscape_v2.6.0/plugins/  
+
If you are running MACOSX 10.4, a Java environment
 +
that works (in the absence of version 6 for that OS version) is this one:
 +
http://landonf.bikemonkey.org/static/soylatte/
  
Windows:
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1)Downloading the binary here:
\.....\Cytoscape_v2.6.0\plugins\
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http://hg.bikemonkey.org/archive/javasrc_1_6_jrl_darwin/soylatte16-i386-1.0.3.tar.bz
  
**you should have write privileges for this directory
+
2)Making sure that you override the default 1.5 Java of the MacOSX by modifying the PATH statement in /etc/profile
  
3. Start Cytoscape and select  IRefIndex_beta3 from plugin menu.
+
3)Increasing a bit the Xmx (512m) and Xms (512m) settings in the startup cytoscape 2.6.1 shell file (cytoscape.sh)
  
4. First time installation may take up to 5 minutes (Creating Java index objects).
+
should produce a workable irefindex Cytoscape plugin on a 10.4.11 (8.11.1) system.
  
5. If the installation was successful you will see a list of losed indexes in the Results text box in green
+
==Q&A==
and if the installation fails you will get errors in red text.
 
  
 
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# How do I search all the interactions involving the protein NP:477306?
-----------------------------------------
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#* Type <tt>NP_477306</tt> on the search text box.
 
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#* Select <tt>ACCESSION</tt> from type drop down menu.
Q&A
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#* (Optional) Restrict the search within a certain taxon identifier by selecting the id from Taxon.
 
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#* Click Search & load.
1. How do I search all the interactions involving the protein NP:477306
+
# How do I load a list of identifiers from a file?
  - Type NP_477306 on the search text box
+
#* For this you need to create plain text file with the list of identifiers.
  - Select ACCESSION from type drop down menu
+
#* First line of the file should be the type of search and the taxonomy identifier. For example:<br><tt>#accession:9606</tt>
  - (optional) restrict the search within a certain taxon identifier by selecting the id from Taxon
+
#* There is a sample file available in the following directory:
  - Click Search & load
+
#** On Unix: <tt>/...../Cytoscape_v2.6.0/plugins/iRefIndex/Sample_batch.txt</tt>
 
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#** On Windows: <tt>\.....\Cytoscape_v2.6.0\plugins\iRefIndex\Sample_batch.txt</tt>
2. How do I load a list of identifiers form a file
+
# What is the result showing?
  - For this you need to create plain text file with the list of identifiers
+
#* The blue nodes are the query nodes, while the green nodes are the first interactors of the query nodes.
  - First line of the file should be the type of search and the taxonomy identifier
+
#* Hexagons represent pseudo-nodes (indication that proteins linked to it belong to the same complex) and not interactors.
    e.g. #accession:96065
+
#* Multiple edges between two nodes are due to several sources containing the same interaction.
  - 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
 

Latest revision as of 13:17, 25 February 2009

Date : Nov 21st, 2008

The iRefIndex plugin for Cytoscape has not been officially released. If you are looking at this page, you have probably been directed here from the Cytoscape plugin directory at ftp://ftp.no.embnet.org/irefindex/Cytoscape/plugin . This plugin is for testing purposes only. Join the Google groups e-mail list at http://groups.google.com/group/irefindex?hl=en to be informed of the official release and updates.

Installation

  1. Obtain Cytoscape from http://cytoscape.org/ and follow the installation instructions for that software.
  2. Before starting:
  3. Copy both the IRefIndex_beta3.jar and iRefDATA_MMDDYYYY.irfz files to the plugins directory of Cytoscape. For example:
    • On Unix: /...../Cytoscape_v2.6.0/plugins/
    • On Windows: \.....\Cytoscape_v2.6.0\plugins\
    • (You should have write privileges for this directory.)
  4. Start Cytoscape and select IRefIndex_beta3 from plugin menu.
  5. First time installation may take up to 5 minutes (while the plugin creates Java index objects).
  6. If the installation is successful, you will see a list of indices in the Results text box in green and if the installation fails you will see errors in red text. (If you cannot see the iRefIndex panel please click on the title iRefIndex, near the Network tab.)
Windows Vista users 
Cytoscape installation inside "Program files" directory is not recommended. Use C:\Cytoscape_v2.6.1\ instead. The iRefIndex plugin requires unrestricted hard disk drive access in its installation folder for low level operations.
MacOS users 
The plugin will not work unless Java 1.6X is installed (and there is no official release of this version available from Sun yet). But the following approach was tested and can be recommended.

If you are running MACOSX 10.4, a Java environment that works (in the absence of version 6 for that OS version) is this one: http://landonf.bikemonkey.org/static/soylatte/

1)Downloading the binary here: http://hg.bikemonkey.org/archive/javasrc_1_6_jrl_darwin/soylatte16-i386-1.0.3.tar.bz

2)Making sure that you override the default 1.5 Java of the MacOSX by modifying the PATH statement in /etc/profile

3)Increasing a bit the Xmx (512m) and Xms (512m) settings in the startup cytoscape 2.6.1 shell file (cytoscape.sh)

should produce a workable irefindex Cytoscape plugin on a 10.4.11 (8.11.1) system.

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 from 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. For example:
      #accession:9606
    • There is a sample file available in the following directory:
      • On Unix: /...../Cytoscape_v2.6.0/plugins/iRefIndex/Sample_batch.txt
      • On Windows: \.....\Cytoscape_v2.6.0\plugins\iRefIndex\Sample_batch.txt
  3. What is the result showing?
    • The blue nodes are the query nodes, while the green nodes are the first interactors of the query nodes.
    • Hexagons represent pseudo-nodes (indication that proteins linked to it belong to the same complex) and not interactors.
    • Multiple edges between two nodes are due to several sources containing the same interaction.