Overview:
The Red Team is comprised of Computer Science students at Old Dominion University who are passionate about professional end-to-end software development. We are creating a Graphical User Interface to be used with genome sequencers. Domain information and presentations on the tool can be found on the resources and deliverables pages. This tool will present the placement of the repeat elements using several lines of evidence such as: 1) presence of incomplete repeat element fragments on the ends of unjoined contigs, 2) mate-pair evidence, and 3) synteny (similarity in gene organization) with reference genomes. The easy to use GUI will show any joins made and present to the user the evidence used to make the joins. Therefore, users can independently assess their confidence in the joins made by the tool. This software is needed so that we can demystify the computational process of genome assembly. Appropriate references, and a glossary of terms can be found on the resource page.
Team Members:
John is 24 years old and an undergraduate senior studying computer science at Old Dominion University. John has lived in Virginia the majority of his life and currently calls Suffolk his home. In his free time he is the co-president of the ODU Heavy Metal club and enjoys learning more about software development and machine learning.
Role: Algorithms and Data Structures, Java Specialist
Tasks assigned: 3,8
James is an undergraduate senior studying computer science at Old Dominion University. As a former Biology major at Virginia Tech, he hopes to integrate his previous education experience with new programming knowledge in a professional capacity after graduation. He is also an avid guitar player, car enthusiast, and skier.
Role: UX Designer, Interfaces
Tasks assigned: 2,6
Tim is a senior studying Computer Science at Old Dominion University. His areas of interest are web and mobile development. Currently, he is the Peer Advisor for the ODU CS department. In his spare time he enjoys riding road bikes, playing guitar, and drinking coffee.
Role: UX Designer, Interfaces
Tasks assigned: 7,9
James is a senior at Old Dominion University and is pursuing a bachelors degree in computer science. He is currently an intern at ZZ servers located in Chesapeake, VA. Outside of academia James is the proud owner of a Labrador Retriever and enjoys bouldering, surfing, and cooking.
Role: Core Application Implementer
Tasks assigned: 1,4
Joe is a Java Enterprise Edition developer for Multivision, Inc. and a senior at Old Dominion University pursuing a bachelor's degree in Computer Science. Currently in his free time, Joe is working on an electronics project that will utilize radio frequency communications between microcontrollers and an application server in order to provide software development students a physical interface with which to log their progress/request help on daily assigned tasks without having to break immersion in their work by using a software based interface or verbal requests.
Role: Algorithms and Data Structures, Java Professional
Tasks assigned: 10,5
A Ph.D student at Old Dominion University who has developed ISQuest and CARP. He is the mentor of the Fall 2015 Red Team.
Task List:
1: Left Pane
- Select a feature as a join
- Populate table on selected join
- List of other features
- Select other features to draw
2: Top Pane
- Display features
- Display joins
- Contents zoom
3: Zoom
- Effects top pane
- Effects center pane
- Levels of zoom
- Shortcut buttons
- Selectable from menu bar
4: Center Pane
- Draw full genome sequence
- Draw joins on outside of circle
- Draw selected features
5: High Resolution Screen Capture
- Capture contents of center pane
- Captured image minimum fidelity of 600dpi
- Produce image formats: tiff, gif, png, jpg
6: UI Responsiveness
- Move file io off main thread
7: Color Options
- Individual sequence parts
- Joins
- Selected Features
- Full sequence
8: Redraw Functionality
- Effects only UI element requiring redraw
- Improved speed
9: UI control groups
- Buttons
- Control groups interact with other panes
10: Feature Classess
- Abstraction BioJava features
- Drawable
- Colorable