Genomica

Project Website: http://genomica.weizmann.ac.il/

Genomica is an analysis and visualization tool for genomic data that can integrate gene expression data, DNA sequence data, and gene and experiment annotation information.

Genomica is a Java-based application that downloads to your local machine when you launch it from GenomeSpace. Once it's downloaded to your machine (after a launch from GenomeSpace), you can start it locally (by opening the JNLP) or launch from GenomeSpace. If you launch Genomica from the Genomica website, at this time it will not be the version that is linked to GenomeSpace.

Logging In

When you launch Genomica from GenomeSpace, your login should be handled seamlessly.

If you start from your GenomeSpace-enabled JNLP of Genomica and want to log into GenomeSpace in order to access your cloud storage or other GenomeSpace tools, you need to select GenomeSpace>Login. You will be asked to log in with your GenomeSpace username and password.

Menus

Genomica has two menus containing GenomeSpace items.

GenomeSpace Menu

The GenomeSpace menu in Genomica allows you to interact with your GenomeSpace cloud storage in a number of ways.

Login GenomeSpace/Logout GenomeSpace	Signs into or out of GenomeSpace.
Open From GenomeSpace	Opens the GenomeSpace file browser to enable you to open a file from your GenomeSpace cloud storage into Genomica.
Save To GenomeSpace	Saves a file from Genomica to your GenomeSpace cloud storage.
Export Network To GenomeSpace	Export a network file from Genomica to your GenomeSpace cloud storage.
Launch GenomeSpace Tool	Allows you to launch another GenomeSpace-enabled tool from Genomica. If you click Launch with GS File, the GenomeSpace file browser opens to allow you to select a file to use in launching your selected tool.
Upload Local File To GenomeSpace	Uploads a file from your local machine to your GenomeSpace cloud storage.
Download GenomeSpace File to Local File	Downloads a file from your GenomeSpace cloud storage to your local machine.
Delete From GenomeSpace	Deletes a file from your GenomeSpace cloud storage.

Sets Menu

The Sets menu contains two GenomeSpace options.

With the Sets menu, you can load either Gene Sets or Experiment Sets from GenomeSpace.

In the User Interface

Select Algorithms>Create a Module Network... Under the Regulation tab is a GenomeSpace Load button that enables you to load a list of candidate regulator genes for the analysis.

Learn how to send data from Genomica to GenePattern using GenomeSpace.

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