1. Genome Navigator Patrick Mar and Jennifer Maurer

2. 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.

3. 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

4. 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

5. 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

6. 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

7. Feasibility • All previously mentioned architectures are achievable, some more so than others • Risks include: time, team’s 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

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