Cytoscape Wiki|
← Revision 3 as of 2008-10-09 22:37:03
Size: 2088
Comment:
|
← Revision 4 as of 2009-02-12 01:03:00
Size: 2099
Comment: converted to 1.6 markup
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 5: | Line 5: |
| This set of web pages contains a set of tutorials for advanced operation of Cytoscape, especially using selected plugins. Before starting these tutorials, we recommend that you first run through the [:Presentations/Basic:introductory tutorials]. While all of the introductory tutorials can be executed using Java Web Start, the advanced tutorials cannot, due to the redistribution terms of many of the plugin user agreements. Note that all plugins covered in these tutorials are freely available, as is Cytoscape. | This set of web pages contains a set of tutorials for advanced operation of Cytoscape, especially using selected plugins. Before starting these tutorials, we recommend that you first run through the [[Presentations/Basic|introductory tutorials]]. While all of the introductory tutorials can be executed using Java Web Start, the advanced tutorials cannot, due to the redistribution terms of many of the plugin user agreements. Note that all plugins covered in these tutorials are freely available, as is Cytoscape. |
| Line 7: | Line 7: |
| To execute the advanced tutorials, you will first need to install Cytoscape (and any required plugins) on your local system. The [:Cytoscape_User_Manual:Cytoscape manual] includes instructions for installing Cytoscape. All plugins described are available through the Cytoscape [http://cytoscape.org/plugnis2.php plugins page]. Most plugins can be installed by downloading the plugin JAR files and copying them to the plugins subdirectory of your Cytoscape directory. For some plugins, special download links are provided, detailing specific installation steps. Each tutorial lists the required plugins, and outlines the installation procedure in detail. | To execute the advanced tutorials, you will first need to install Cytoscape (and any required plugins) on your local system. The [[Cytoscape_User_Manual|Cytoscape manual]] includes instructions for installing Cytoscape. All plugins described are available through the Cytoscape [[http://cytoscape.org/plugnis2.php|plugins page]]. Most plugins can be installed by downloading the plugin JAR files and copying them to the plugins subdirectory of your Cytoscape directory. For some plugins, special download links are provided, detailing specific installation steps. Each tutorial lists the required plugins, and outlines the installation procedure in detail. |
| Line 9: | Line 9: |
| Note that for those interested in developing plugins, there is a [:Cytoscape_Plugin_Tutorial:tutorial] on writing Cytoscape plugins. | Note that for those interested in developing plugins, there is a [[Cytoscape_Plugin_Tutorial|tutorial]] on writing Cytoscape plugins. |
| Line 16: | Line 16: |
| For comments and suggestions, please post to the [http://www.cytoscape.org/community.php cytoscape-discuss] mailing list. | For comments and suggestions, please post to the [[http://www.cytoscape.org/community.php|cytoscape-discuss]] mailing list. |
| Line 21: | Line 21: |
| Tutorial 5: [:Presentations/05_Literature:Literature Searching] | Tutorial 5: [[Presentations/05_Literature|Literature Searching]] |
| Line 23: | Line 23: |
| Tutorial 6: [:Presentations/06_GO:Gene Ontology] | Tutorial 6: [[Presentations/06_GO|Gene Ontology]] |
| Line 25: | Line 25: |
| Tutorial 7: [:Presentations/07_Complexes:Modules and Complexes] | Tutorial 7: [[Presentations/07_Complexes|Modules and Complexes]] |
| Line 27: | Line 27: |
| Tutorial 8: [:Presentations/08_Web_Services:Public Web Services] | Tutorial 8: [[Presentations/08_Web_Services|Public Web Services]] |
Cytoscape Advanced Tutorials
Some of the most interesting functionality available with Cytoscape comes from external plugins, which can be developed by anyone with a certain degree of Java programming skill.
This set of web pages contains a set of tutorials for advanced operation of Cytoscape, especially using selected plugins. Before starting these tutorials, we recommend that you first run through the introductory tutorials. While all of the introductory tutorials can be executed using Java Web Start, the advanced tutorials cannot, due to the redistribution terms of many of the plugin user agreements. Note that all plugins covered in these tutorials are freely available, as is Cytoscape.
To execute the advanced tutorials, you will first need to install Cytoscape (and any required plugins) on your local system. The Cytoscape manual includes instructions for installing Cytoscape. All plugins described are available through the Cytoscape plugins page. Most plugins can be installed by downloading the plugin JAR files and copying them to the plugins subdirectory of your Cytoscape directory. For some plugins, special download links are provided, detailing specific installation steps. Each tutorial lists the required plugins, and outlines the installation procedure in detail.
Note that for those interested in developing plugins, there is a tutorial on writing Cytoscape plugins.
The following web browsers are supported for these tutorials:
- Netscape 5.0 or later
- Internet Explorer 5.0 or later
- Mozilla 6.0 or later
For comments and suggestions, please post to the cytoscape-discuss mailing list.
Advanced Tutorials
Tutorial 5: Literature Searching
Tutorial 6: Gene Ontology
Tutorial 7: Modules and Complexes
Tutorial 8: Public Web Services