Computational Framework for Biotechnological Research

Generic tools

Software Name Description
Bioclipse The Bioclipse is a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP).
BioRails BioRails combines traditional biology data management with an electronic laboratory notebook.
UGENE UGENE is a free cross-platform genome analysis suite.
GENtle GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more.
EMBOSS EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web.
AutoDock AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
BioPerl Bioperl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.
BioPHP BioPHP is a package of Open Source PHP code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other Bioinformatics tools.
Biopython Biopython is a set of modules and packages for biology, including sequence analysis, database access, etc. or parsers components.
Integrated Genome Browser The Integrated Genome Browser is an interactive, zoomable, scrollable software program you can use to visualize and explore genome-scale data sets, such as tiling array data, next-generation sequencing results, genome annotations, microarray designs, and the sequence itself.
Java TreeView Java TreeView is an open source, cross-platform Gene Expression Visualization Tool. It provides interactive display of Clustered Gene Expression Data.
LabKey Server LabKey Server is free, open source software available for scientists to integrate, analyze, and share biomedical research data. The platform provides a secure data repository that allows web-based querying, reporting, and collaborating across a range of data sources.
APBioKnoppix Knoppix based bioinformatics software
Protein Colourer Miscellaneous
ReadSeq Miscellaneous
FastPCR PCR Primer Design
MA Explorer Data Mining Gene Expression Patterns
Ondex Data Integration and Visualisation Platform
DARWIN Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences
DNATrapper Assembly editing and visualization tool
GMOD (Generic Model Organism Database) Project Collection of software for managing biological data
MIRA Sequence assembler for whole genome shotgun and EST sequencing data
SMSD (Small Molecule Subgraph Detector) Screening drug like compounds
Sockeye Analysis of Genomic data
STRAP Interactive Structure based Sequences Alignment Program
STRING Search for Tandem Repeats IN Genomes
Tandem Repeats Finder Search for Tandem Repeats IN Genomes
pDRAW32 DNA Software
Expression Profiler MicroArray Analysis