1. Introduction

Interface overview



This is an overview of interface of the Genomic HyperBrowser. The HyperBrowser is built tightly connected to the Galaxy framework.
The Galaxy web application appears. Note the similarity between the two sites.
  • Go back one page in your web browser.
You are back at the HyperBrowser site. This overview will cover some of the basic interface elements that are common to both Galaxy and The Genomic HyperBrowser.

The interface is divided into four panels, one top panel and three panels dividing the area below vertically. The leftmost one, the tool panel, allows you to select tools and analyses.

The top section contains the Genomic HyperBrowser tools. The main tool is the "Perform analysis" tool under "The Genomic HyperBrowser". The "View regulomes" tool displays a set of regulomes, which are large heat maps of gene regulation by transcription factors and other regulating elements, created with the Genomic HyperBrowser. The "Help" tool displays this help page, which can also be accessed by clicking "HyperBrowser help" under the "Help" menu in the top right corner. The public HyperBrowser tools are used for extraction and manipulation of datasets. Restricted tools are not intended for regular users.

The bottom section contains the same tools that are available at the Galaxy site. There are tools for getting data, sending data, in addition to different kinds of tools for data manipulation and analysis.

The rightmost panel is the history panel, which is a backlog of all previous actions, including all intermediate data files and results. Histories can be saved so that you can continue on a task that you started at an earlier session. To be able to save histories you need to log in with a username. If you already have a user:
  • Log in  by clicking "Login" in the "User" menu. Type your e-mail address and your password. Click "Login".
If you need to register a new user:
  • Click "Register" in the "User" menu in the top right of the screen. Type your e-mail address and a password, and click "Create".
When you create a new user, you are automatically logged in with that user.

In order to more easily keep track of you histories, you should rename your history appropriately.
  • Click the pencil symbol next to the current history name ("Unnamed history") and type the new name, for instance "My first history" and hit the return key.
All output from tools will be stored in this history until you switch to a new one. Let's upload some data to this history from an external source.
  • In the tool panel, select "Get Data" under Galaxy Tools and select "UCSC Main table browser".
  • Select the "hg18" human genome, "Genes and Gene Prediction Tracks" and "UCSC Genes".
  • Select "BED - browser extensible data" in the "Output format" selection box, and make sure that "Send output to Galaxy" is checked.
  • Click "Get output". Click "Send query to Galaxy".
A new history element appears. The yellow color indicates that the data is being uploaded. When the upload is complete, the element turns green.
  • Click the name of the history element.
The history element is expanded, providing more information about the data set, e.g. the number of regions in the data set.
  • Click the eye symbol of the history element.
The middle panel, the action panel, now shows the contents of the dataset. The middle panel is also where you specify tool parameters and view analysis results.
  • Click the pencil symbol of the history element.
The action panel now changes to a form where you can edit the name and other information about the history element.
  • In order to delete a history element, click the X symbol.
Let's say that you want to change to a new task. You should then create a new history.
  • Click the "Options" menu in the top right corner of the history panel, and select "Create new".
A new history appears.
  • Click the pencil symbol next to the new history name ("Unnamed history"). Type "My second history" and hit the return key.
  • Select "Options" and "Stored by you".
A list of all your stored histories appear in the action panel.
  • Select the history named "My first history".
Notice that the history changes.
  • In order to share a history with another user, select "Share" in the "Options" menu. Type their HyperBrowser user e-mails and click "Submit".



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