Science Biology Bioinformatics Software Software Development

30 sites in Software Development

Bioperl.org Save
The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research. The Bioperl server provides an online resource for modules, scripts, and web links.
http://www.bioperl.org

AceDB Save
A hierarchical database system for displaying genomic data (originally C. elegans), suitable also for displaying other scientific data.
http://www.acedb.org/

AcePerl Save
OO Interface to AceDB
http://stein.cshl.org/AcePerl/

BSML Save
Bioinformation Sequence Markup Language. Extensible language specification and container for bioinformatic data.
http://www.bsml.org/

Bielefeld University Bioinformatics Server Save
BiBiServ supports Internet-based collaborative research, software development and distance education in bioinformatics.
http://bibiserv.techfak.uni-bielefeld...

BioJava.org Save
The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
http://biojava.org/

BioLisp.org Save
BioLisp.org is a public resource supporting scientists who use Lisp to develop intelligent applications in the biological sciences. We collect and disseminate Lisp biocomputing code, and gather pointers to Lisp and other Intelligent BioComputing methods.
http://nostoc.stanford.edu/Docs/

BioPHP Save
An open source project to develop PHP code and scripts for biocomputing. A wiki-like service allows collaboration between developers.
http://www.biophp.org

BioPython Save
The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
http://biopython.org/

BioQuery Save
Tools that searches multiple biomedical databases from your desktop.
http://www.bioquery.org/

BioRuby Save
BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language.
http://bioruby.org

BioWarehouse Database Integration System Save
Integrates multiple public bioinformatics databases into a single relational database system within a common bioinformatics schema.
http://biowarehouse.ai.sri.com/

Biochemical Algorithms Library Save
C++ framework for rapid software prototyping in molecular modeling.
http://www.bioinf.uni-sb.de/OK/BALL/

Bionconductor Save
The Bioconductor project produces an open source software framework that will assist biologists and statisticians working in bioinformatics, with primary emphasis on inference using DNA microarrays, built mostly using R.
http://www.bioconductor.org/

Boulder.pm Save
Simple but powerful data exchange language, suitable for serializing biological data objects.
http://www.broad.mit.edu/genome_softw...

CLEML: Carbon Labeling Experiment Markup Language Save
CLEML open format for representing and exchanging 13C metabolic flux analysis models.
http://sg.ustc.edu.cn/MFA/cleml/

Dynamite Save
Code generator for writing dynamic programming programs.
http://www.ebi.ac.uk/Dynamite/

EST2uni Save
A tool to analyze a set of ESTs. Cleans, clusters and annotates the sequences and prepares a web site to browse the results in a complete automatic way.
http://www.melogen.upv.es/genomica/we...

High Throughput Screening Tools Save
Analytical tools and SQL scripts that solve common problems in drug discovery.
http://www.htstools.com/

InterMine Save
InterMine is an general-purpose object-oriented data warehouse system developed as part of the FlyMine project and made available as stand-alone open-source software.
http://www.intermine.org

JCell Save
A Java based framework to reconstruct genetic interactions from microarray data.
http://www-ra.informatik.uni-tuebinge...

MolTalk Save
Software development for structural bioinformatics. Runs on Unix, Windows and MacOSX.
http://www.moltalk.org/

NCICB Core Infrastructure Save
The National Cancer Institute's Center for Bioinformatics produces the caCORE infrastructure, an open-source enterprise architecture for cancer informatics.
http://ncicb.nci.nih.gov/NCICB/infras...

NeoBio Save
An open source library of Java bioinformatics algorithms. The current version consists mainly of sequence alignment algorithms such as Needleman- Wunsch and Smith-Waterman.
http://neobio.sourceforge.net

PISE Save
Given an abstract definition of a program's parameters, PISE can generate whatever style of interface from the configuration module.
http://www.pasteur.fr/recherche/unite...

Phylogenetic Analysis Library Save
PAL library is a Java toolkit for determining evolutionary trends.
http://www.cebl.auckland.ac.nz/pal-pr...

Sight Save
Extendable parallel system for automatic genome analysis. Software for analysing all potential genes in a defined genome region. Given two marker names, can output reports of genomic features between them. Features for converting between naming systems, sequence retrieval, E-PCR, gene prediction, similarity search, protein pattern search, and report formatting. Written in Java.
http://bioinformatics.org/jSight/

The Darwin Manual Save
Guide to running this programming language. Library contains programs to compute pairwise alignments, phylogenetic trees, multiple sequence alignments, and to make secondary structure predictions.
http://www.inf.ethz.ch/personal/gonne...

The Scriptome Save
A set of software tools that filter, format, and merge data in tabular or common biological formats. Organized as a classified collection of Perl one-liners.
http://sysbio.harvard.edu/csb/resourc...

The XEMBL Project Save
XEMBL provides access to the EMBL/GenBank/DDBJ Nucleotide Sequence Database, providing output in various XML standards.
http://www.ebi.ac.uk/xembl/