Cytoscape Version 2.2 Pathway Builder
| About Pathway Builder |
Pathway Builder uses Cytoscape's network editor to let you create pathway or network diagrams. Cytoscape is an open source program for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other data.
Java Webstart 1.5.0 is required. The
first time you run Cytoscape, Java Webstart automatically downloads and
installs the program on your computer. On subsequent runs, Java Webstart
makes sure your copy of
Cytoscape
is up-to-date and will download and install a new version if necessary.
Cytoscape
is a large program and you should expect a lengthy download the first time you
run it.
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Operating Instructions:
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To operate the program. click the "Start Cytoscape"
link. Cytoscape will launch with an empty canvas. To create a new
network, choose File->SetEditor->T1DBaseEditor. Then
click and drag a node from the panel on the left to the canvas on the right.
In the Node Attribute Browser at the bottom, Select Attribute "commonName".
Click on your node then in the space at the bottom for "commonName" type in a
name. If you wish to search for that name on the T1DBase website right click
on the node after naming it, a box will pop up and you can mouse over "Search
T1DBase" and click on the popup to search. Choose one result from the box and
your node will be renamed.
To load a pathway from T1DBase, choose
File->T1DBase->Load network from T1DBase. At present, the only
public T1DBase pathway that can be loaded is L-Arginine Uptake and Metabolism.
You can also load pathways stored on your own computer using Cytoscape's
Load->File (sif, gml, sbml) options.
Please note that after loading a network you
will need to choose the editor you were working in for your shapes and colors
to show up correctly.
It is not possible at present to save pathways to
T1DBase. However, this is how it is supposed to work: (1) Sign in
to T1DBase through File->T1DBase->Login to T1DBase using your My T1DBase
username and password. (2) You can then
load and save pathways to My T1DBase.
You can save pathways to your local computer using
Cytoscape's Save command.
Cytoscape is an open source program for visualizing molecular
interaction networks and integrating these interactions with gene expression
profiles and other data. The Cytoscape project is an ongoing collaboration among the Institute for Systems Biology, the
University of California at San Diego, the
Memorial Sloan-Kettering Cancer Center and the
Institut Pasteur. Further information about Cytoscape is available at www.cytoscape.org. We suggest that you read the Cytoscape tutorial or User Manual.
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Open help in separate window
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| Create Pathway |
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Start Cytoscape
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