H-mito is a mitochondrial DNA haplogroup prediction tool based on the phylogenetic tree http://www.phylotree.org/. Ancillary scripts: mitoP.py to extract mutation lists and clustal-2-fasta.zip to join, align through clustalw and convert data.
Integration of results from multiple homology searches
The Hungarian Pediatric Cancer Registry contains data about leukemia and solid tumor patients younger than 18 year-old from 1970 and 1975, respectively. This project makes the stucture of the database (excluding patient data) and scripts helping to mainta
math lib for .NET. n-dim arrays, complex numbers, linear algebra, FFT, sorting, cells- and logical arrays as well as 3D plotting classes help developing algorithms on every platform supporting .NET. Sources from SVN, binaries: http://ilnumerics.net
IMPACT is an integrated multi-read peak calling tool for ChIP-Seq data. IMPACT utilizes multi-reads in calling peaks and provides users with high-confidence peaks. In addition, IMPACT provides a completely integrated pipeline which produces downstream analysis results such as motif discovery and peak-to-gene annotation.
Ida is a data analysis application framework that features user interface integration, database support, and bridges to popular statistical analysis packages. Application development is currently focused on the bio-informatic analysis of microarrays.
Platform for parallel computation in the Amazon cloud, including machine learning ensembles written in R for computational biology and other areas of scientific research. Home to MR-Tandem, a hadoop-enabled fork of X!Tandem peptide search engine.
jrgp is a strong-typed Genetic Programming system, which features a graphical interface (gool) to setup and run GP-problems and a tool (fs-d) that greatly simplifies the definition of a GP-problem.
Jylab is a java library for plotting graphs in Jython, using Matlab-like syntax. It is a wrapper for JFreeChart, and is similar to matplotlib for Python.
KAPPA (Key Aminoacid Pattern-based Protein Analyzer) is a sequence search program dedicated to the discovery and clustering of proteins defined by a key aminoacid pattern.
Lateral Gene Transfer utility
LGTmate is a simple and powerful bioinformatic software tool to identify lateral gene transfer events and contaminants in Eukaryotic proteomes. It is available as a GUI or command-line application, with no dependencies and no installation required.
LIMPortSys is a python cgi project providing web-based laboratory notes collecting, searching and analysis services. Based on a flexible template and XML as record format, this project could be considered as a way to integrate lab information.
Code repository for the Laboratory for Genome Bioinformatics at Texas A&M. The LGB project was initiated primarily to support biologists at Texas A&M needing help with bioinformatics in order to use new genomic technologies.
This project houses software to analyze data acquired from electrophysiology experiments. Currently, we have an Octave/MATLAB program to analyze electroneurogram traces of coupled oscillators, and a Perl library for the analysis of voltage trace data
A GUI-based search tool that allows the exploration of the relationships between Metabolites.
MAXIMUS is a genome assembly pipeline which takes the best out of multiple reference assemblies and de novo assembly. The benefits of this approach include better assembled repetitive regions, less gaps and higher accuracy for the resultant assembly.
MIVF - Medical Imaging and Visualization Factory, is a framework for medical applications. It supplies a platform, in which image processing and 3D visualization algorithms can be employed as reusable components (functional modules or plugins).
Artificial plants laboratory.
Variation analysis of metagenomic samples
The package enables detection of sequence variation between metagenomic samples.
Pipeline for creating core genome alignments for phylogenetic analysis
Maximum Common Genome Alignment (MCGA) Tool MCGA is a bioinformatics analysis tool written in Python for generating core genome alignment for bacterial whole genome sequences which can be used to construct phylogenetic trees.
Open Source Eye Tracking Solution
McGill Vision Research Eye Tracker is a complete solution to track oculomotor movements. We provide a list of equipment, we provide all the required software. We guide the user through the installation process until ready to track.
Clustering tool for publications from the MEDLINE database
MetabolODE derives, solves, and optimizes a set of differential equations describing the metabolic flux through any biochemical pathway.
Cis-element prediction tool from microarray data
We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this method. After optimization, MAMA accurately simulated more than 87% of gene expression. See Kakei Y, Ogo Y, Itai RN, et al. (2013) Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient. Rice 6(1): 22.
The Explorative Taxonomic Profiling Tool for Metagenomic Data
MicrobeGPS is a bioinformatics tool for the analysis of metagenomic sequencing data. The goal is to profile the composition of metagenomic communities as accurately as possible and present the results to the user in a convenient manner. One main focus is reliability: the tool calculates quality metrics for the estimated candidates and allows the user to identify false candidates easily.