Planned Releases

This page describes the planned releases of Genotet, and their feature summaries.

Release Feb 15, 2016

Summary

Refactors the previous code base and provides a cleaner, easier-to-use interface to the user, along with custom data upload functionality.

Details

• Data Upload

  • Accept uploaded binding dat; Store serialized data structures for binding queries.
  • Accept uploaded bed tracks; Store serialized data structures for bed queries.
  • Accept uploaded networks & expression matrices; Store networks in text file.
  • Accept uploaded gene-binding mapping file. The user interface supports the selection of uploaded data.

• Network

  • Visualize the network
    • Encode user selected edge attribute by color.
    • Distinguish TF genes from non-TF genes.
    • Show gene info on subtiwiki.
    • Zooming and panning navigation.
  • Edit the network
    • Query node list by gene names (text or regex). User may choose to add/remove genes. (To do: Jiaming)
    • Query edge list by incident edges of selected gene. User may choose to add/remove edges. (To do: Jiaming)

• Expression Matrix

  • Visualize the expression matrix
    • Show expression matrix as heatmap.
    • Box zoom in, and zoom out.
  • Visualize the gene profiles
    • Show selected gene profiles line charts (with or without TFA).
  • Edit the expression matrix
    • Query row list by gene names (text or regex). User may choose to add/remove rows.
    • Query condition list by condition names (text or regex). User may choose to add/remove columns.
    • User may choose to add/remove genes to be profiled.

• Genome Browser (Binding)

  • Visualize the binding data
    • Show overview tracks at top of the view.
    • Show binding tracks below the overview.
    • Show bed tracks below the binding tracks.
    • Show exons track below the bed tracks.
  • Edit the binding data
    • User may choose binding tracks to add/remove.
    • User may choose bed tracks to add/remove. (To do: Liana)

• Linked Queries: The linked queries are only supported for preset layouts, e.g. 1 network + 1 expression + 1 genome browser.

  • Clicking a network node loads the binding track for the clicked gene, in the 1st binding track.
  • Clicking a network node loads the gene profile for the clicked gene.
  • Clicking a network edge (s, t) loads the binding track for gene s, in the 1st binding track. All binding tracks are then centered at the locus of t.
  • Clicking a network edge (s, t) loads the gene profiles for gene s and t.
  • The linked queries shall be built with a code architecture that is extensible to user-configurable linked query settings.
  • User is able to upload a link mapping file, e.g. mapping each gene name in the network to a binding track name.

• User Interface

  • Side panel for view control options.
  • View creation with data selection.
  • Data upload interface.

Development related items

• Build Infrastructure: Employ package management system (gulp)
• Test Infrastructure
  • Support unit test for computational modules and functions.
  • Support unit test for user interface and visualization related elements. Handle async tests. (QUnit)
  • Support unit test for http requests to the server. (jasmine-node)