Diff for "Cytoscape_User_Manual/Launching_Cytoscape"

Differences between revisions 11 and 12

Cytoscape is a Java application that runs on Linux, Windows, and Mac OS X.

System requirements: The system requirements for Cytoscape depend on the size of the networks the user wants to load, view and manipulate. We recommend a recent computer (1GHz CPU or higher) with a high-end graphics card and at least 512MB of free physical RAM. Cytoscape expects a minimum screen resolution of 1024x768.

(1) If necessary, install Java

If not already installed on your computer, download and install Java SE 5 or 6. Cytoscape 2.4 will no longer run with Java version 1.4.x or lower. You must install Java SE 5 or 6!!!

These can be found at:

[http://java.sun.com/javase/downloads/index_jdk5.jsp Java SE 5]

[http://java.sun.com/javase/downloads/index.jsp Java SE 6]

(2) Install Cytoscape

There are a number of options for downloading and installing Cytoscape. All options can be downloaded from the [http://cytoscape.org] website.

Automatic installation packages exist for Windows, Mac OS X, and Linux platforms.
You can install cytoscape from a compressed archive distribution.
You can build cytoscape from source.
You can check out the latest and greatest software from our [http://chianti.ucsd.edu/svn Subversion repository].

Cytoscape installations (regardless of platform) containing the following files and directories:

File	Description
cytoscape.jar	Main Cytoscape application (Java archive)
cytoscape.sh	Script to run Cytoscape from command line (Linux, Mac OS X)
cytoscape.bat	Script to run Cytoscape (Windows)
LICENSE.txt/html	Cytoscape GNU LGPL License
lib/	library jar files needed to run Cytoscape.
docs/	Manuals in different formats. What you are reading now.
licenses/	Licence files for the various libraries distributed with Cytoscape.
plugins/	Directory containing cytoscape PlugIns, in .jar format.
sampleData/
	galFiltered.gml -- Sample molecular interaction network file *
	galFiltered.sif -- Identical network in Simple Interaction Format *
	galExpData.pvals -- Sample gene expression matrix file *
	galFiltered.nodeAttrTable.xls -- Sample node attribute file in Microsoft Excel format
	galFiltered.cys -- Sample session file created from datasets above plus GO Annotations *
	BINDyeast.sif -- Network of all yeast protein-protein interactions in the BIND database as of Dec, 2006 **
	BINDhuman.sif -- Network of all human protein-protein interactions in the BIND database as of Dec, 2006 **
	yeastHighQuality.sif -- Sample molecular interaction network file ***
	interactome_merged.networkTable.gz -- Human interactome network file in tab-delimited format ****

* From Ideker et al., Science 292:929 (2001)

** Obtained from data hosted at http://www.blueprint.org/bind/bind_downloads.html

** From von Mering et al., Nature, 417:399 (2002) and Lee et al, Science 298:799 (2002)

**** Created from Cytoscape tutorial web page. Original data sets are available at: http://www.cytoscape.org/cgi-bin/moin.cgi/Data_Sets/ A merged human interactome by Andrew Garrow, Yeyejide Adeleye and Guy Warner Unilever, Safety and Environmental Assurance Center

(3) Launch the application

Double-click on the icon created by the installer or by running cytoscape.sh from the command line (Linux or Mac OS X) or double-clicking cytoscape.bat (Windows). Alternatively, you can pass the .jar file to Java directly using the command java -Xmx512M -jar cytoscape.jar -p plugins. The -Xmx512M flag tells java to allocate more memory for Cytoscape and the -p plugins option tells cytoscape to load all of the plugins in the plugins directory. Loading the plugins is important because many key features like layouts, filters and the attribute browser are included with Cytoscape as plugins in the plugins directory. See the Command Line chapter for more detail. In Windows, it is also possible to directly double-click the .jar file to launch it. However, this does not allow specification of command-line arguments (such as the location of the plugin directory).

Cytoscape Window When you succeed in launching Cytoscape, a window will appear that looks like this (captured on Linux):

attachment:cytoscape_startup.png

Note on Memory Consumption

For users interested in loading large networks, the amount of memory needed by Cytoscape will increase. Memory usage depends on both number of network objects (nodes+edges) and the number of attributes. Here are some rough suggestions for memory allocation:

Suggested Memory Size

Number of Objects (nodes + edges)	Create View	Suggested Memory Size
~70,000	No	512M (default)
70,000-150,000	No	800M
~70,000	Yes	800M
70,000-150,000	Yes	1G

Note on Directory Location

For the application to work properly, all files should be left in the directory in which they were unpacked. The core Cytoscape application assumes this directory structure when looking for the various libraries needed to run the application. If you are adventurous, you can get creative with the $CLASSPATH and/or the cytoscape.jar manifest file and run Cytoscape from any location you want.

Cytoscape_User_Manual/Launching_Cytoscape (last edited 2010-10-07 18:01:55 by malbec)

-  ← Revision 11 as of 2007-01-09 00:29:15 →
  Size: 5499
  Editor: KeiichiroOno
  Comment:
+  ← Revision 12 as of 2007-01-09 23:21:00 →
  Size: 5380
  Editor: nebbiolo
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 5:
-There are a number of options for downloading and installing Cytoscape:
+=== (1) If necessary, install Java ===
 Line 7:
- * For Windows and Linux platforms, one-step installation is available via ''!InstallAnywhere''. For one-step installation, go to http://www.cytoscape.org, click Download Cytoscape, and follow the on-screen instructions.

 * For Mac OS X, we provide an alternative installation, available as a .dmg.zip file. When installed via this method, Cytoscape functions as a regular Mac application, and can be accessed via your Applications folder.

 * Finally, you can download and install a compressed archive distribution. Instructions for this option are provided below.

''' (1)''' '''Download and unpack the distribution.''' Cytoscape is distributed as a compressed archive (tar.gz or zip) containing the following files and directories:
+If not already installed on your computer, download and install Java SE 5 or 6.  '''''Cytoscape 2.4 will no longer run with Java version 1.4.x or lower.  You must install Java SE 5 or 6!!!'''''
-Line 12:
+Line 9:
-{{{

cytoscape.jar		Main Cytoscape application (Java archive)
+These can be found at:
-Line 15:
+Line 11:
-cytoscape.props		User-configurable properties and preferences

vizmap.props		User-configurable visual mapping preferences
+[http://java.sun.com/javase/downloads/index_jdk5.jsp Java SE 5]
-Line 18:
+Line 13:
-cytoscape.sh		Script to run Cytoscape from command line (Linux, Mac OS X)

cytoscape.bat		Script to run Cytoscape (Windows)
+[http://java.sun.com/javase/downloads/index.jsp Java SE 6]
-Line 21:
+Line 15:
-LICENSE.txt		Cytoscape GNU LGPL License

Cytoscape2_4Manual.pdf	Cytoscape 2.4 Manual (the document you are reading now)
-Line 24:
+Line 16:
-sampleData/

  galFiltered.gml	Sample molecular interaction network file *

  galFiltered.sif	Identical network in Simple Interaction Format *

  galExpData.pvals	Sample gene expression matrix file *

  galFiltered.nodeAttrTable.xls	Sample node attribute file in Microsoft Excel format

  galFiltered.cys	Sample session file created from datasets above plus GO Annotations *

  BINDyeast.sif		Network of all yeast protein-protein interactions in the 

   BIND database as of Dec, 2006 **

  BINDhuman.sif		Network of all human protein-protein interactions in the 

   BIND database as of Dec, 2006 **

  yeastHighQuality.sif	Sample molecular interaction network file ***

  interactome_merged.networkTable.gz	Human interactome network file in tab-delimited format ****
+=== (2) Install Cytoscape ===
-Line 37:
+Line 18:
-plugins/		Directory containing cytoscape PlugIns, in .jar format.
+There are a number of options for downloading and installing Cytoscape.  All options can be downloaded from the [http://cytoscape.org] website.



 * Automatic installation packages exist for Windows, Mac OS X, and Linux platforms.  

 * You can install cytoscape from a compressed archive distribution.

 * You can build cytoscape from source.

 * You can check out the latest and greatest software from our [http://chianti.ucsd.edu/svn Subversion repository].



Cytoscape installations (regardless of platform) containing the following files and directories:



||'''File'''||'''Description'''||

||cytoscape.jar||Main Cytoscape application (Java archive)||

||cytoscape.sh||Script to run Cytoscape from command line (Linux, Mac OS X)||

||cytoscape.bat	||Script to run Cytoscape (Windows)||

||LICENSE.txt/html||Cytoscape GNU LGPL License||

||lib/||library jar files needed to run Cytoscape.||

||docs/||Manuals in different formats.  What you are reading now.||

||licenses/||Licence files for the various libraries distributed with Cytoscape.||

||plugins/||Directory containing cytoscape PlugIns, in .jar format.||

||sampleData/||||

|| ||galFiltered.gml -- Sample molecular interaction network file *||

|| ||galFiltered.sif -- Identical network in Simple Interaction Format *||

|| ||galExpData.pvals -- Sample gene expression matrix file *||

|| ||galFiltered.nodeAttrTable.xls -- Sample node attribute file in Microsoft Excel format||

|| ||galFiltered.cys -- Sample session file created from datasets above plus GO Annotations *||

|| ||BINDyeast.sif -- Network of all yeast protein-protein interactions in the BIND database as of Dec, 2006 **||

|| ||BINDhuman.sif -- Network of all human protein-protein interactions in the BIND database as of Dec, 2006 **||

|| ||yeastHighQuality.sif -- Sample molecular interaction network file ***||

|| ||interactome_merged.networkTable.gz -- Human interactome network file in tab-delimited format ****||
-Line 40:
+Line 49:
-** Obtained from data hosted at 

     http://www.blueprint.org/bind/bind_downloads.html

** From von Mering et al., Nature, 417:399 (2002) and Lee et al, 

     Science 298:799 (2002)

**** Created from Cytoscape tutorial web page.  Original data sets are available at:

    http://www.cytoscape.org/cgi-bin/moin.cgi/Data_Sets/

    ''A merged human interactome by Andrew Garrow, Yeyejide Adeleye and Guy Warner

      Unilever, Safety and Environmental Assurance Center 

}}}

'''(2) If necessary, install Java.''' If not already installed on your computer, download and install the Java SE 5 or 6. It can be found at:
-Line 51:
+Line 50:
-http://java.sun.com/javase/downloads/index_jdk5.jsp (Java SE 5)
+** Obtained from data hosted at http://www.blueprint.org/bind/bind_downloads.html
-Line 53:
+Line 52:
-http://java.sun.com/javase/downloads/index.jsp (Java SE 6)
+** From von Mering et al., Nature, 417:399 (2002) and Lee et al, Science 298:799 (2002)
-Line 55:
+Line 54:
-'''Cytoscape 2.4 does not support Java 1.4.x series.  You must install Java SE 5 or 6.'''
+**** Created from Cytoscape tutorial web page.  Original data sets are available at: http://www.cytoscape.org/cgi-bin/moin.cgi/Data_Sets/  ''A merged human interactome by Andrew Garrow, Yeyejide Adeleye and Guy Warner Unilever, Safety and Environmental Assurance Center ''
-Line 57:
+Line 56:
-'''(3) Launch the application '''by running "cytoscape.sh" from the command line (Linux or Mac OS X) or double-clicking "cytoscape.bat" (Windows). Alternatively, you can pass the .jar file to Java directly using the command "java -Xmx512M -jar cytoscape.jar -p plugins". The ''-Xmx512M'' flag tells java to allocate more memory for Cytoscape and the ''-p plugins'' option tells cytoscape to load all of the plugins in the plugins directory.  Loading the plugins is important because many key features like layouts, filters and the attribute browser are included with Cytoscape as plugins in the ''plugins'' directory. See the Command Line chapter for more detail. In Windows, it is also possible to directly double-click the .jar file to launch it. However, this does not allow specification of command-line arguments (such as the location of the plugin directory). On '''Mac OS X''', users who downloaded the Mac OS X version of Cytoscape, can double-click on the Cytoscape icon to start Cytoscape. Either double-clicking or dragging onto the Cytoscape application icon any .sif or .gml file will load that file into Cytoscape.
+=== (3) Launch the application ===



Double-click on the icon created by the installer or by running {{{cytoscape.sh}}} from the command line (Linux or Mac OS X) or double-clicking {{{cytoscape.bat}}} (Windows). Alternatively, you can pass the .jar file to Java directly using the command {{{java -Xmx512M -jar cytoscape.jar -p plugins}}}. The {{{-Xmx512M}}} flag tells java to allocate more memory for Cytoscape and the {{{-p plugins}}} option tells cytoscape to load all of the plugins in the plugins directory.  Loading the plugins is important because many key features like layouts, filters and the attribute browser are included with Cytoscape as plugins in the {{{plugins}}} directory. See the Command Line chapter for more detail. In Windows, it is also possible to directly double-click the .jar file to launch it. However, this does not allow specification of command-line arguments (such as the location of the plugin directory). 



'''Cytoscape Window''' When you succeed in launching Cytoscape, a window will appear that looks like this (captured on Linux):



attachment:cytoscape_startup.png





==== Note on Memory Consumption ====

For users interested in loading large networks, the amount of memory needed by Cytoscape will increase. Memory usage depends on both number of network objects (nodes+edges) and the number of attributes. Here are some ''rough'' suggestions for memory allocation:
-Line 66:
+Line 77:
-Memory usage depends on both number of objects (nodes+edges) and number of attributes.  If the data includes a lot of  attributes, more memory may be required.
-Line 68:
+Line 78:
-||'''Important Note:'''For the application to work properly, all files should be left in the directory in which they were unpacked. The core Cytoscape application assumes this directory structure when looking for the various libraries needed to run the application.  If you are adventurous, you can get creative with the $CLASSPATH and/or the cytoscape.jar manifest file and run Cytoscape from any location you want.||



'''Cytoscape Window''' When you succeed in launching Cytoscape, a window will appear that looks like this (captured on Linux):



attachment:cytoscape_startup.png
+==== Note on Directory Location ====

For the application to work properly, all files should be left in the directory in which they were unpacked. The core Cytoscape application assumes this directory structure when looking for the various libraries needed to run the application.  If you are adventurous, you can get creative with the $CLASSPATH and/or the cytoscape.jar manifest file and run Cytoscape from any location you want.