Genome Navigator

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Genome Navigator

• Patrick Mar and Jennifer Maurer

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Overview

• For the geneticist who wishes to visualize DNA
  before conducting an experiment, the Genome
  Navigator is a desktop application that allows
  the 3D viewing and manipulation of genetic
  sequences and subsequences. Our software will
  replace current 2D viewers and will be usable
  across a wider variety of genomes.

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Operational Concept

• Main concept a graphical 3D viewer that permits
  the user freedom of motion around an input
  genetic sequence as well as the ability to modify
  the sequence
• Evolutionary concept design will plan for
  adaptability within a larger future framework
  possibly as a tool for a larger desktop
  application

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System Requirements

• Desktop application w/ 3D capabilities
• Later releases will have database support for
  download of genetic sequences will require
  network/internet connection
• A Viewer with flexibility of up, down, left,
  right motion as well as variation of viewing
  angles
• Users will be able to select, highlight, add,
  delete subsequences

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Architecture

• Option 1 Completely contained desktop
  application most feasible, least useful in
  terms of genomic sequence availability
• Option 2 Desktop application with database
  support most risky, very useful. Client-server
  architecture only involved in obtaining genomic
  sequences
• Option 3 Web server interface with backend
  database support medium risk, very useful but
  requires more maintenance work on our part, also
  graphics will suffer

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Life Cycle Plan

• Users/Clients research educational
  institutions
• Developers/Maintenance CSE 403 team
• Life Cycle Model combination of spiral and
  design-to-schedule models
• We will handle risks in the following order
  sequence input/download, 3D viewing, moving,
  manipulation, database support
• Business Plan focus is on research, not profit,
  CSE 403 students to provide cheap labor ?
• Research and Educational potential large, likely
  to grow

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Feasibility

• All previously mentioned architectures are
  achievable, some more so than others
• Risks include time, teams lack of biological
  background, programming inexperience, any
  database designed within allotted time cannot
  possibly be comprehensive
• Success of project may depend in large part to
  success in designing good graphical
  representations

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Qualifications

• Both of us have research experience in
  computational biology
• Jennifer has experience with 3D Graphics
• Patrick has experience with web interfaces and
  databases