• Affymetrix - Affymetrix Power Tools
  "The Affymetrix Power Tools (APT) contains C++ source code for analyzing Affymetrix data and a set of command line tools built on this source code."
  in Public bookmarks with microarray opensource sdk software
• BioMart Project
  "BioMart is a query-oriented data management system developed jointly by the European Bioinformatics Institute (EBI) and Cold Spring Harbor Laboratory (CSHL)."
  1.5 annotation biomart das data database generic genes management open protein searches server source warehouse
  in Public bookmarks with bioinformatics database ensembl opensource
• CaArray - Molecular WIKI
  "caArray is an open-source, web and programmatically accessible array data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG™)."
  in Public bookmarks with database microarray opensource
• CGL Home Page
  Comparative Genomics Library
  in Public bookmarks with bioinformatics genomics opensource perl
• DarwinPorts - UNIX & Open Source
  in Public bookmarks with darwin mac opensource unix
• encfs
  "EncFS provides an encrypted filesystem in user-space. It runs without any special permissions and uses the FUSE library and Linux kernel module to provide the filesystem interface."
  in Public bookmarks with encryption linux opensource security software sysadmin
• GeneMania/Blog - Bader Lab @ The University of Toronto
  in Public bookmarks with bioinformatics genomics opensource
• GMOD | Generic Software Components for Model Organism Databases
  "The Generic Model Organism Database (GMOD) Project is a largely open source project to develop a complete set of software for creating and administering a model organism database."
  in Public bookmarks with bioinformatics database genomics opensource
• Home | www.broadinstitute.org/software/scripture
  "Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio."
  in Public bookmarks with opensource rnaseq
• HSQLDB
  HSQLDB is a sql relational database written in Java.
  hsqldb: Full-featured 100% Java ORDBMS
  database hsqldb hypersonicsql java jdbc ordbms rdbms sql
  in Public bookmarks with database java opensource by 3 users
• Jakarta ORO
  "The Jakarta-ORO Java classes are a set of text-processing Java classes that provide Perl5 compatible regular expressions, AWK-like regular expressions, glob expressions, and utility classes for performing substitutions, splits, filtering filenames, etc."
  in Public bookmarks with java opensource programming regexp
• Javolution
  
  Java library for real-Time, embedded and high-performance applications.
  cldc critical embedded fast free j2me java library open-source parser real-time safety sax2 xml
  in Public bookmarks with java opensource performance programming by 4 users
• JScience
  
  The most comprehensive Java library for the scientific community.
  java library module open-source plugin science sciences scientific
  in Public bookmarks with algorithms java opensource programming science by 2 users
• O'Reilly CodeZoo
  in Public bookmarks with opensource software by 5 users
• openbiomind - Google Code
  "OpenBiomind is a toolkit for analysis of gene expression, SNP and other biological datasets using advanced machine learning and pattern mining techniques, and includes traditional clustering, hybrid clustering, and other techniques."
  in Public bookmarks with bioinformatics microarray opensource
• R, the Software, Finds Fans in Data Analysts - NYTimes.com
  in Public bookmarks with analysis data education news opensource programming r software statistics
• SGT Graphics Package
  "The Scientific Graphics Toolkit (SGT) facilitates easy development of platform independent, Java applications to produce highly interactive, flexible, publication quality, object oriented graphics of scientific data."
  in Public bookmarks with graphics interactivescientificplotting java opensource plotting visualization by 2 users
• The Rgenetics Project Website — Rgenetics Project
  "R Genetics Project is an open-source project, which solicits contributions in a community-supported, collaborative effort to provide the data structures and analytic tools needed for the management, visualization, exchange and analysis of genetic data."
  in Public bookmarks with bioinformatics genetics opensource programming r statistics
• The Yahoo! User Interface Library (YUI)
  "The Yahoo! User Interface (YUI) Library is a set of utilities and controls, written in JavaScript, for building richly interactive web applications using techniques such as DOM scripting, DHTML and AJAX. "
  in Public bookmarks with ajax dom opensource webdev by 40 users
• UnoSeq - Expression profiling with next generation sequencing without a ...
  "UnoSeq is a Java library to analyze next generation sequencing data (e.g. data generated by Illumina's mRNAseq method) and especially perform expression profiling in organisms where no well-annotated reference genome exists. The library can help you to extend your mRNAseq sequencing and transcription profiling approaches to any species you like."
  in Public bookmarks with bioinformatics geneexpression genomics opensource sequenceanalysis sequenceassembly

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