Cytoscape Wiki|
← Revision 1 as of 2008-03-07 15:41:11 →
Size: 1899
Comment:
|
Size: 1690
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 3: | Line 3: |
| Cytoscape includes the ability to import networks and pathways directly from external databases. | Cytoscape users can import networks and pathways directly from external databases. |
| Line 5: | Line 5: |
|
To get started, select: File → Import → Network from web services... [PICTURE GOES HERE] By default, Cytoscape provides direct access to the following external resources: |
By default, direct access to the following external resources is provided: |
| Line 14: | Line 10: |
| === Basic Usage === | === Getting Started === |
| Line 16: | Line 12: |
| Cytoscape includes four !CytoPanels: '''''Control Panel''''' on the left, '''''Tool Panel''''' on the bottom of ''Control Panel'', '''''Data Panel''''' on the bottom, and '''''Result Panel''''' on the right. By default, ''Control Panel'' and ''Data Panel'' will appear. ''Result Panel'' may appear, depending on the mix of Cytoscape plugins that you currently have installed. ''Tool Panel'' will appear when you select the following commands under the ''Layout'' menu: ''Rotate'', ''Scale'', and ''Align and Distribute''. | To get started, select: File → Import → Network from web services... |
| Line 18: | Line 14: |
| All panels can be shown or hidden using the View → Show/Hide functions. | attachment:file_import.png |
| Line 20: | Line 16: |
| attachment:cytopanel-menu-items_25.png | === Example #1: Retrieving Data from IntAct === |
| Line 22: | Line 18: |
| In addition, !CytoPanels can be floated or docked by selecting the icon at the top right corner of each !CytoPanel. The icon and tooltip will change based on the !CytoPanel state. If the !CytoPanel is docked, clicking on the icon will float the !CytoPanel, as indicated by the “Float Window” tooltip. Alternatively, if the !CytoPanel is floating, clicking on the icon will dock the !CytoPanel, as indicated by the “Dock Window” tooltip. |
* Select: File → Import → Network from web services... * From the pull-down menu, select the Int``Act Web Service Client. * Enter a search term, such as BRCA1 * Click the Search button. |
| Line 24: | Line 23: |
| attachment:cytopanel-float-dock-icon.png |
attachment:intact_import.png After confirming the download of interaction data, the network of BRCA1 will be imported and visualized. === Example #2: Retrieving Data from Pathway Commons === * Select: File → Import → Network from web services... * From the pull-down menu, select the Pathway Commons Service Client. Then, follow the three-step process outlined below: * Step 1: Enter your search term; for example: BRCA1 * Step 2: Select the protein or small molecule of interest. Full details regarding each molecule is shown in the bottom left panel. * Step 3: Download a specific pathway or interaction network. attachment:3_steps.png |
Importing Networks from External Databases
Cytoscape users can import networks and pathways directly from external databases.
By default, direct access to the following external resources is provided:
[http://www.ebi.ac.uk/intact/site/index.jsf IntAct]: an open source database of protein interaction data, hosted at EMBL-EBI.
[http://www.pathwaycommons.org Pathway Commons]: an open source portal, providing access to multiple integrated data sets, including: Reactome, IntAct, HPRD, HumanCyc, MINT, the MSKCC Cancer Cell Map, and the NCI/Nature Pathway Interaction database.
Getting Started
To get started, select: File → Import → Network from web services...
attachment:file_import.png
Example #1: Retrieving Data from IntAct
Select: File → Import → Network from web services...
From the pull-down menu, select the IntAct Web Service Client.
- Enter a search term, such as BRCA1
- Click the Search button.
attachment:intact_import.png
After confirming the download of interaction data, the network of BRCA1 will be imported and visualized.
Example #2: Retrieving Data from Pathway Commons
Select: File → Import → Network from web services...
- From the pull-down menu, select the Pathway Commons Service Client.
Then, follow the three-step process outlined below:
- Step 1: Enter your search term; for example: BRCA1
- Step 2: Select the protein or small molecule of interest. Full details regarding each molecule is shown in the bottom left panel.
- Step 3: Download a specific pathway or interaction network.
attachment:3_steps.png