Bioinformatics

EMBOSS explorer is a web-based graphical user interface to the EMBOSS suite of bioinformatics tools. It is written in Perl and is exceedingly simple to install, configure, maintain and use. Platforms: Windows, Mac, Linux

Hawthorn provides a caching and lookup mechanism for bioinformatics ontology formats such as OBO and DAG. Platforms: Windows, Mac, Linux

HitKeeper is a database application for use in BioInformatics. It deals with 'hits' (predicted features) on biological sequences (protein, DNA), handles incremental updates effectively, supports taxonomy, and provides original query tools. Platforms: Windows, Mac, Linux

This project aims to develop a cross platform environment for utilisation of various open source and freely available molecular dynamics and bioinformatics tools. Some extra features are included such as protein hydrophobicity and hydrophilicity plots. Platforms: Windows, Mac, Linux

MatrixGen is a Bioinformatics application used to generate scoring matrices from analysis of aligned Amino Acid and DNA data sets. These matrices can then be used by Clustal to generate more accurate alignments. Based upon the Henikoff BLOSUM method. Platforms: Windows, Mac, BSD, Linux

Microarray Explorer (MAExplorer) is a Java microarray data-mining bioinformatics program. It includes data management, graphics, statistics, clustering, reports, gene data-filtering, user written MAEPlugins, documentation, tutorials, demo data. Platforms: Windows, Mac, Solaris, Linux

openSputnik is a robust distributed platform for massive scale precalculation of genetic and genomic data using contemporary bioinformatics methods. Annotated DNA, RNA and protein sequences are stored as binary objects in a variery of relational database Platforms: Windows, Mac, Linux

pygr is a bioinformatics toolkit for sequence analysis and comparative genomics. pygr is highly scalable (e.g. one can easily query multi-genome alignments) and easy to use. Please see our new project page and wiki at http://code.google.com/p/pygr. 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

The Swiss Protein Identification Toolbox (swissPIT) is a project at the Swiss Institute for Bioinformatics (SIB) in Geneva which aims at the development of an automated analysis system to identify proteins using MS and MS/MS based data. Platforms: Windows, Mac, Linux

TASSEL is a bioinformatics software package that can analyze diversity for sequences, SNPs, or SSRs. Genotype/phenotype associations can be carried out by GLM or a mixed model. Estimates distance and linkage disequilibrium statistics. Platforms: Windows, Mac, Linux

A collaborative workflow builder and enactor for e-Sciences, in particular bioinformatics. Platforms: Windows, Mac, Linux

Sight provides a friendly interface to create and connect agents for bioinformatics. The workflow supports multiple responses to a single request, structure transforms, filters and request history access.Can talk with ordinary http servers (get and post) Platforms: Windows, Mac, Linux

The BioPHP Project is a non-profit, open source software project that aims to extend the PHP scripting language so it can be used to develop bioinformatics applications. BioPHP is NOT a bioinformatics application. Rather, it is a collection of tools to help PHP developers write bioinformatics... Platforms: Windows, Mac, *nix, PHP, BSD Solaris

MGWT: Identification of protein coding regions using the ModifiedGabor-wavelet transform.Sequence of test:F56F11.4.fasta (included into the zip file)http://www.ncbi.nlm.nih.gov/entrez/viewer....de&val=AF099922http://www.vision.ime.usp.br/~jmena/projec...ome_results/F5/References:[1] J. P.... Platforms: Matlab

This function contains the well known greedy algorithm for solving Set Cover problem (ChvdodAtal, 1979), with two small modifications:* In case of more than one possible choice at a certain step, the biggest set is chosen;* Once the solution is found, we check the selected sets to find a better... Platforms: Matlab

It is application of solving ODE model pacemaker VI1 of cardiac cells with function ODE45 mat lab.It is first work objectifs for developing M-File-S-Function with Simulink-Mat lab for modele pacemaker VI1 of cardiac cells and Heart VI1 with Simulink Platform in Free SimCardiology in... Platforms: Matlab

PLOTPHYTREE(TREE) renders a phylogenetic tree object into a MATLAB figure as aphylogram with equal angle algorithm.plotphytree(...,'ROTATION',value) will orient the phylogenetic tree within the figure window. Positive angles cause counterclockwise rotation, otherwise clockwise... Platforms: Matlab

The CMVE toolbox estimates missing values by using correlation structure of the data. The software can be used to impute missing values in any correlated data especally microarray gene expression data. The imputation performance of the software has proven significant affect on gene regulatory... Platforms: Matlab

We attempt to reproduce and efficiently implement in MATLAB publicly available methods of Affymetrix MAS 5 and GCOS 1.2 software that perform single-array and comparison analysis for Affymetrix data given by CEL and CDF files and create corresponding CHP data structures:1. CHP data structure is... Platforms: Matlab