Gene

Jeep is a modular, abstract and distributed evolutionnary programming core written in Java, allowing to grow autonomous agents as well a gene pool (as in genetic algorithms). Platforms: Windows, Mac, Linux

Maple Tree is a Java based visualization tool used by researchers in the biological sciences to visualize and graphically browse the results of analyses of gene expression data collected from microarray experiments. Platforms: Windows, Mac, Linux

Manatee is a web-based gene evaluation and genome annotation tool. Manatee can store and view annotation for prokaryotic and eukaryotic genomes. Platforms: Windows, Mac, Linux

Microarray Gene Expression Database Group and OMG Gene Expression Standard (MAGE) Platforms: Windows, Mac, Linux

The Program to Assemble Spliced Alignments (PASA) is used to automatically incorporate ESTs and full-length cDNAs into gene structure annotations, in the process annotating UTRs, alternative splicing variations, and polyadenylation sites. Platforms: Mac, BSD, Linux

RmiR is an R package for the analysis of microRNA and gene expression microarrays.The package is designed to coupling microRNA and gene expression data, using different databases, like TargetScan, mirBase, picTar,TarBase and others... Platforms: Windows, Mac, Linux

RssGsc (Rank Sum Statistics for Gene Set Collections) is a bioinformatics tool used to find meaningful gene sets using a ranked list of genes (obtained form an experiment). Platforms: Windows, Mac, Linux

SysGenSIM is a bioinformatics toolbox to create artificial gene expression datasets by simulating Systems Genetics experiments. Platforms: *nix

In one type of gene expression analysis, fluorescently tagged messenger RNA from different cells are hybridized to a microscopic array of thousands of complimentary DNA spots that correspond to different genes. Illuminated spots emit different color light, indicating which genes are expressed... Platforms: Matlab

This user interface allows a user to load some Affymetrix data in an Excel file and perform some basic operations on it - log transform, log ratio, normalization, noise reduction, filtering, PCA and clustering, in addition to some visualizations like profile plots, boxplots and matrix... Platforms: Matlab

GETHGVBASE returns polymorphism data from the human genome variation db http://hgvbase.cgb.ki.seHGVDATA = gethgvbase(SNPID) reads in a %hgvbase web record fromEMBL and creates a structure DATA %containing fields correspondingto the hgvBase keywords.FIELDNAME DESCRIPTIONS: a complete %description... Platforms: Matlab

General implementation of matlab version of Viterbi algorithm specifically written for gene structure finding problem in mind. However, it can be modified to suit the goal of a user.Input:Transition Probability MatrixEmission Probability MatrixInitial Probability MatrixStates Matrix (ie.... Platforms: Matlab

Recent studies describe that the level of gene expression between species is positively correlated with the time that has passed since the species split from a common ancestor (Ranz et al., 2006). Moreover, Khaitovich et al. (2004) found a linear relationship between divergence time and... Platforms: Mac

ErmineJ performs analyses of gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists... Platforms: Mac

Gene Studio is a free tool for modelling of DNA manipulation. It will allow to work with vectors, to design primers, to clone molecules and provide user friendly intewrface. Platforms: Mac

NetAtlas is a Cytoscape plugin that uses tissue gene expression data to filter cellular signaling network. The plugin identifies of tissue-defined networks, tissue-specific network components, and components with correlated expression across tissues. Platforms: Mac

GSA-SNP is a gene set analysis software that can process SNP data as well as gene and haplotype data. Platforms: *nix

NetAtlas is a Cytoscape plugin that uses tissue gene expression data to filter cellular signaling network. The plugin identifies of tissue-defined networks, tissue-specific network components, and components with correlated expression across tissues. Platforms: *nix

Abuse is so good that some specialists consider it to be a 2D version of the legendary Doom. Full of powerful weapons, missiles, aliens and excellent illumination effects, the only difference is that Abuse plays in 3rd person, while Doom plays in 1st.The argument of the game is this: you are the... Platforms: Windows

The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities. This source kit has been built and tested on Windows NT/2000/XP, Mac OS X, and most major... Platforms: *nix