Parsing And Visualization Of GenBank

From Protein Prediction 2 Winter Semester 2014
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Requirements

GUI mockups

User experience:

  • Quoting the Mentor (Dr.El Mazouari)*

“Practical use case: a team is developing a web app that implements in-house algorithms for annotated in-house proprietary sequences. The web app screens the company sequence database for specific set of features. Sequence hits are then annotated and a Genbank output is generated for annotated sequences. At this time, wet-lab users download the annotated sequence in Genbank format and then open it in VectorNTi or MacVector in order to view the annotation map and features. These extra steps are time consuming… If they can view the sequence directly in their browser from the web, they will be more productive and “happy scientists;)” Something that will help them to view the annotated sequence, select the features they want and export them will be very welcome”

Functionality

  • Select features from annotated input sequences
  • Parse and Visualize the input sequence in the genbank format
  • Export selected features which should be able to work with later*

Features

  • Easy to use for the end users
  • Highlight and export features in a user friendly
  • Should easily be able to integrated into other web applications.

MockUps

MockUps done before contacting the client:

GenBank input Prior to Mentor's directive:

  • GenBank input Prior to Mentor's directive

GenBank output Prior to Mentor's directive:

  • GenBank output Prior to Mentor's directive

Refactored MockUps resulting from Mentors updates:

GenBank input After to Mentor's directive:

  • GenBank input After to Mentor's directive

GenBank output After to Mentor's directive: 

  • GenBank output After to Mentor's directive


Application design

Expected technical difficulties

  • Implementing the parser
  • Selecting and exporting features dynamically
  • Highlighting multiple features

Fancy libraries you plan to use

  • Jquery
  • D3 (if necessary)
  • BioJava
  • BioJS(?)

Your data

Remarks about your input format

  • The input is going to be annotated sequence and it should be in the Genbank Format

Roadmap

Before Meeting the Mentor

  • 1. Understand the application domain and the logic that we are supposed to implement
  • 2. Understand the input we need to work ( how to convert sequence in genbank format to genbank file )
  • 3. Parse the genbank file and extract the features dynamically into Javascript objects.
  • 4. Visualize the results in a user friendly in the browser
  • 5. Make the features exportable!

After Meeting the Mentor

  • 1 meeting (email):
  • 2 meeting (Facetime videochat):