Oded and Liat's final project for the biological networks course. http://www.cs.tau.ac.il/~roded/courses/bnet09.html

Computes pairwise correlations between flowjo runs for different nodes, and outputs them in various human- and computer-readable formats.

Translate gene sequences into a wave, with one "sample" per codon or nucleotide. Multifractal analysis or other machine learning techniques can be applied to the output in the hopes of identifying interesting patterns within the original sequence. A variety of translation approaches will be includ...

This site keeps track of the open source projects that are being submitted to Google Summer of Code 2009. The Informatics Core at the Institute for Systems Biology is the mentoring organization.

*This project hosts source code related to the Pathway Commons project.* Pathway Commons is a collection of publicly available pathways from multiple organisms. It provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common l...

This is the project page for my class project in bioinformatics. I have selected the topic of implementing and comparing a number of fragment assembly algorithms using the open source toolkit BioJava. I am a graduate student at the University of Colorado at Colorado Springs taking CS 509, Bioinf...

I am working on creating programs to do synthetic biology using biopython. I will be teaching a class about this at the Tech Shop in Menlo Park. This is meant as a practice area and class exercise research and development area for that purpose. Hopefully the end result will be specific python cla...

Code for managing and analyzing large numbers of microarray platforms

A lot useful bioinformatics tools will be contained in this toolkit. Here is a list: KEGG KGML parser, NCBI GPL/SOFT parser, NCBI HomoloGene/GeneInfo/Gene2accession parser. More will be included. See Wiki for the usages.

This project implements four algorithms that maps short reads to one reference sequence or a set of reference sequences. The primary objective is to measure the performance of the algorithms. However, the code and result can be easily adopted and used in other projects.