Software
ImmunoTar - Integrative prioritization of cell surface targets for cancer immunotherapy
ImmunoTar is a program written in R for identifying and systematically prioritizing immunotherapeutic targets.
- GitHub repository: https://github.com/sacanlab/immunotar
CellTrack: An Open-Source Software for Cell Tracking and Motility Analysis
Cell motility is a critical part of many important biological processes. Automated and sensitive cell tracking is essential to
cell motility studies where the tracking results can be used for diagnostic or curative decisions and where mathematical models can be developed to deepen the understanding mechanisms underlying the cell motility.
We propose a novel edge-based method for sensitive tracking of cells, and propose a scaffold of methods that achieves refined
tracking results even under large displacements or deformations of the cells. The proposed methods along with other general purpose image enhancement methods are implemented in CellTrack, a self-contained, extensible, and cross-platform software package.
If you use CellTrack for you own research, please cite the following paper:
Ahmet Sacan, Hakan Ferhatosmanoglu, and Huseyin Coskun. CellTrack: An Open-Source Software for Cell Tracking and Motility Analysis. Bioinformatics (2008, submitted)
LFM-Pro: A Tool for Detecting Significant Local Structural Sites in Proteins
The rapidly growing protein structure repositories have opened up new opportunities for discovery and analysis of functional and evolutionary relationships among proteins. Detecting conserved structural sites that are unique to a protein family is of great value in identification of functionally important atoms and residues. Currently available methods are computationally expensive and fail to detect biologically significant local features. We have developed LFM-Pro (Local Feature Mining in Proteins) as a framework for automatically discovering family specific local sites and the features associated with these sites. Our method uses the distance field to backbone atoms to detect geometrically significant structural centers of the protein. A feature vector is generated from the geometrical and bio-chemical environment around these centers. These features are then scored using a statistical measure, for their ability to distinguish a family of proteins from a background set of unrelated proteins, and successful features are combined into a representative set for the protein family. The utility and success of LFM-Pro are demonstrated on Trypsin-like Serine Proteases family of proteins. The results verify that our method is successful both in identifying the distinctive sites of a given family of proteins, and in classifying proteins using the extracted features.
Pattern Formation by Reaction Diffusion
- This software was developed with Sertan Girgin as a project for Ceng566 Image Processing course (back when I was doing my Phd at Middle East Technical University). It implements a simulator for Turing's Reaction and Diffusion.
- You can read the project report or the presentation for details of the methodology.
Mancala Game
I developed this software for an assignment in an AI course at CEng at Middle East Technical University to implement the Alpha-Beta Pruned Search Algorithm.
EPI - Educational Programming Interface
A simple Windows interface to Borland's free TurboC compiler. EPI is intended for use in Introduction to C Programming
courses. The idea is to have as simple and easy to use a compiler interface as possible. The installation is simple, and no complicated configuration or project creation is involved when you are writing your programs. All you have to do is to write your code, save your file, and hit Run.
mySet -- Visual Perception Card Game
Version | 2007-09-15 |
---|---|
Requirements | .NET Platform |
Development Language | C# |
Download | myset.exe |
- This is a single player version of the classic “Set the Family of Visual Perception” game.
Vocabuilder - Improve your Foreign Language Vocabulary
Vocabuilder is a program to help you practice new words you learn in a foreign language. You type in words
and their meanings (denoted as sense
) as you learn them. The program will score your performance, and try to test you on the new words, or on words that you score poorly.
RunAppWhenIdle -- Run an application when you are not using your computer
Version | 2007-11-08 |
---|---|
Requirements | MS Windows |
Development Language | C++, MFC |
Download | runappwhenidle.exe |
I wrote RunAppWhenIdle
to execute some of the cpu-intensive programs only when I was not using my computer. The cpu-intensive programs were some experiments I was performing as part of my bioinformatics research. I also managed to persuade some of my friends to execute these programs on their computer, and with RunAppWhenIdle
, I made sure that their computer usage was not disturbed.
With RunAppWhenIdle, you can either bind to an already running process on your system, or execute a new application. The application will be suspended (not killed!) while you are using your computer, and will resume when you are idle.
Pickle - A Simple and Easy PHP Online Picture Gallery
This software is likely outdated and may not be compatible with the newer versions of php.
Pickle is a software for publishing your pictures on your website. Publishing is as simple as saving your pictures in a folder. If you just want to show your pictures on your website, try Pickle. No database, or maintenance is needed.
MediaPlayer Controller - a Windows Media Player Plugin
This software is likely outdated and may not be compatible with the newer versions of Windows Media Player.
I have lots of songs of songs on my computer, and I don't really want to go through the songs to filter out the majority that I don't like. And it's annoying to bring the MediaPlayer to front, select the song, and delete it every time a song that I don't like is playing. So, I wrote the MediaPlayerController program that would delete the currently playing song, with minimal distraction to what I'm working on. Other features include play/pause, next/previous song, volume up/down, and fast forward operations, which are useful especially if you don't have media shortcut keys on your keyboard.
Retired Software and Services
The following software and services are no longer available.
- webiler: C/C++ compiler web service.