Bioinformatics Institute

BioQuery is a bioinformatics tool that acts as a query builder for genetic, protein, publication, and other biomedical databases. BioQuery is also an update service that periodically resubmits saved searches and sends you new data as it is found.

The aim of the BioWeka project is to add bioinformatics functionalities such as e.g. alignments to the popular machine learning framework Weka.

Current Comparative Table is a bioinformatics tool for running searches (like BLAST) with large sets of genes.It creates a table that allows you to view many results in many databases and downloads databases daily to ensure the most up-to-date results.


Platforms: Mac, BSD, Linux

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV


Platforms: Windows, Mac, Linux

DimReduction project provide an open-source multiplatform (Java) graphical environment for bioinformatics problems that supports many feature selection algorithms, pattern recognition techniques, criterion functions and graphic visualization tools.


Platforms: Windows, Mac, Linux

Disease Gene Profiler (DGP) comprises of a set of (bioinformatics) tools that can be used to identify the genes underlying susceptibility to common multifactorial diseases (such as diabetes, asthma and cancer) using freely available datasources.


Platforms: Windows, Mac, Linux

DNAGalaxy is an attempt to produce an open-source bioinformatics software alternative to the expensive DNAStar Lasergene software. Its features currently include Blast and Entrez searching, a frontend to clustal and a sequence editor. It requires java1.5


Platforms: Windows, Mac, Linux

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

A multiplayer tank game developed in Java as a first-year project for Computer Science at the Royal Institute of Technology, Stockholm.


Platforms: Windows, Mac, Linux

This is the high throughput PCR primer design software that is used at the J. Craig Venter Institute. See: Li K, et al. 'Novel computational methods for increasing PCR primer design effectiveness in directed sequencing'. BMC Bioinformatics 2008, 9:191.


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

A course timetable application for students at the Royal Institute of Technology (KTH) in Sweden. Imports the timetable from TimeEdit and Daisy and shows it graphically. Also exports vCalendar data and HTML.


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

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