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Jackson Fletcher: Systems Biology Visual Analytics







About Me:

I am an undergraduate at Mississippi State University. I’m studying Computer Engineering there and will be a third-year senior this fall. I have a passion for sports of any kind but I also enjoy optimizing daily life to be more efficient.

About My Project:

My research mentors, Dr. Alex Feltus and Dr. Melissa Smith, have teamed up to research genetics using GPU-optimized algorithms. My role in the project is to create an interface between an actively-developed program, BioDep-Vis, and its users, geneticists. BioDep-Vis is a gene clustering program that clusters genes that are exhibited at similar times. It can display the gene networks of organisms at the same time to see development from a common ancestor. We explored the use of various interaction methods to to control the BioDep-Vis interface such as a Microsoft Kinect and a Mobile Touch Interface.

Week 1

Week 1 was pretty chill despite getting off to a quick start. The first couple days consisted of a general briefing on the program, a meeting with our project mentors, and an orientation-esque tour of the campus. A normal day consists of either a planned educational session or a tour of some facility in the morning and then a meeting/work with mentor(s) after lunch. This week’s morning sessions included a session on writing a research paper (hint: LaTeX), a “Screen Capture and Video Editing” session (namely, Adobe Premier Pro and Camtasia), and a tour of the Watts Family Innovation Center on campus.

On the project side of things, I became somewhat familiar with the current infrastructure. However, I have been set back by an inability to build and run BioDep-Vis due to access restrictions on the Palmetto cluster and the cluster’s untimely maintenance. I spent most of Thursday downloading programs and compilers (along with trying to obtain cluster access). On Friday, the Kinect adapter finally arrived so I had an opportunity to play around with that while the cluster was down. Its a really cool piece of hardware but I don’t really have any idea how to program with it yet. That’ll have to wait for next week.

Week 2 – 8

Current Issues
1. What is the protocol to connect to a computer?
* For now, I’m experimenting with Unified Remote, the most popular remote desktop control app. Unified Remote uses either Wifi or Bluetooth to control the computer. Various controllers are available for specific applications and the mouse and keyboard control seems to be very good. I’m not sure if it is possible to add a visual that can be dragged around or not as discussed in the meeting.
2. How to best design the controller to manipulate the 3D space?
* 3D box model
* actual graph

Potential Improvements
Eventually, the controller application could interact directly with the remote server without needed to interface with the intermediate display computer. However, Palmetto does not support the opening of ports needed for this protocol.

Final Report

Hunter College
City University of New York
695 Park Ave
New York, NY 10065

Telephone: +1 (212) 396-6837
Email: oo700 at hunter dot cuny dot edu

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