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  AgED

  AgED - Analysis given Experimental Data

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  Avian Freeware Suite

  Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)

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  Bayesian Network Tools in Java (BNJ)

  Java/XML toolkit for research using Bayesian networks and other graphical models of probability (exact and approximate inference, structure learning, etc.)

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  Bayesian Network tools in Java (BNJ)

  Bayesian Network tools in Java (BNJ) is an open-source suite of software tools for research and development using graphical models of probability. It is published by the Kansas State University Laboratory for Knowledge Discovery in Databases (KDD).

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  Biological Annotation Tool

  Biological Annotation Tool is a general-purpose high speed environment for manipulating biological sequence annotations in multiple input and output formats. A plugin-style API permits much extensibility.

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  CCB: Bioinformatics Tutorials & Training

  A bioinformatics project to create tutorials, including programming code examples, to help in bioinformatics training. Will primarily create examples with Perl, PostgreSQL, R, Bioperl, Emboss. Part of Comparative and Collaborative Bioinformatics Project.

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  Clearcut

  Clearcut is an open source implementation of the Relaxed Neighbor Joining (RNJ) algorithm, an efficient distance-based phylogenetic reconstruction method.

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  Comparative Toxicogenomics Database

  The Comparative Toxicogenomics Database (under development) will be a publicly-available, web-based database of genes and proteins of human toxicological significance. It is being developed using an Oracle 9i database, Tomcat, and Python.

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  Component Framework / GINY Graph Library

  CSBI is a component based framework that allows for inter-component data sharing and access. GINY is an Open Source Graph Library.

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  Coulson Plot Generator

  Graphics generator for pie diagram matrix from spreadsheets

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  EMBOSS Suite

  EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)

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  Entrainer

  Entrainer is a Java program (JRE 1.7.0_07+ required, available from http://java.sun.com/javase/downloads/index.jsp) which creates binaural beat frequencies with sound, light and animations for the purpose of entraining one's brain waves.

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  EuroPhenome

  EuroPhenome - a database for Mouse phenotype data

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  FlowLIMS

  The Flow Cytometry Laboratory Information Management System (FlowLIMS) is a web-based software system that gives users the ability to create and manage experiment protocols for the DiVa and FACScan flow cytometers

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  GeneX Gene Expression Database

  GeneX is an gene expression database system with an integrated toolset that enables researchers to store, analyze, and communicate their data.

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  GenomeDiff

  Compare virus genomes visually by dotplot! Java program. Download manually from pubmed! Use alignment view! Compare, for example, Hiv-1 & Visna. Locate p24 within Hiv-1! Compare natural language texts! Export diagram as PDF!

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  IGBM

  IGBM (Identification of gene blocks in microorganisms) implements a BLAST-like method to infer conserved gene clusters among closely related prokaryotes, and provides a graphical user interface to navigate the identified clusters and their annotated info

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  Indiana University Bioinfo Batch Scripts

  IU Batch Scripts are shell scripts that simplify the process of submitting batch jobs on Unix machines that use the PBS queueing system and on AIX machines that use LoadLeveler.

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  JChemPaint Applet and Swing Application

  The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and source code repository can be found on http://jchempaint.github.com

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  LRA-OSF

  Latronix Regnum Arts - Open Source Faction is an open source and freeware developer for all sorts of goodies. Be it games or applications. This is the home for the Drug Turfs Game (A Drug Wars like game) and the Drug Turfs Library.

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  Lucy

  Lucy is a program for DNA sequence quality trimming and vector removal. Its purpose is to process DNA sequence data acquired from DNA sequencers to prepare the data for downstream processing applications such as genome assembly.

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  Lush

  Lush is a Lisp dialect with extensions for object-oriented and array-oriented programming. Lush is intended for prototyping numerically intensive applications and is designed for easy integration of existing C/C++/Fortran codes.

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  LutefiskXP

  LutefiskXP is ANSI C compliant software used to perform de novo peptide sequencing from tandem mass spectra.

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  MAGPIE

  The Multi-purpose Automated Genome Project Investigation Environment (MAGPIE, http://magpie.ucalgary.ca/), is a software package for the automated curation and presentation of DNA and protein sequences. Freely available under terms of Apache license v2.0

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  MPSLiC

  Mutli-processor single linkage clustering

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