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This is an extension to the standard 2D HF package (A Numerical Hartree-Fock Program for Diatomic Molecules by Jacek Kobus, Leif Laaksonen and Dage Sundholm) that adds some extra functionality.
ANATEMA is a natural way of information input since it is resembles a plain old email, but can be translated to any "modern" markup language such as LaTeX, HTML, DocBook, etc. Using ANATEMA, although, the original remains Human Readable.
ASSD is a simple biological sample database focused on the storage of proteomics data. It tracks every processing step incl. results throughout a sample's lifetime. Next to proteomics data it can also store other results like FACS or Western Blots.
AAARF, written in PERL and with numerous adjustable parameters, identifies sequence overlaps in small shotgun sequence datasets and walks them out to create long pseudomolecules representing the most abundant repeats in a genome.
Part-of-speech tagging is the task of assigning symbols from a particular set to words in a natural language text. ACOPOST implements and extends well-known machine learning techniques and provides a uniform environment for testing.
A framework of drivers on which generic astronomical applications can be built.
ALEXA-Seq is a method for using massively parallel paired-end transcriptome sequencing for 'alternative expression analysis'.
AMOS is a collection of tools for genome assembly69 weekly downloads
ANDES. This is a library and a set of applications that can be used to analyze the results of deep sequencing results. (See Li et al.: ANDES: Statistical tools for the ANalyses of DEep Sequencing. BMC Research Notes 2010 3:199.)1 weekly downloads
APEX Tools is a collection of utilities used in conjunction with the processing of airborne hyperspectral data developed for the ESA-Prodex supported Airborne Prism EXperiment (APEX).
APoDIx is a Portable Bio-Database Index system. It retrieves biological database information from the website of Oxford Journals, save them in a local position, and provides a viewer for display and search the information.
Alternative splicing event analysis tool
Metabolic reconstruction from DNA or protein sequences.
ASKGene (Automated Sequence Knowledge GENErator) - a customizeable integration platform for sequence-processing bioinformatics tools.
ASpipe is a pipeline to process GeneSeqer/GMAP alignments and identify alternative splicing (AS) events from the alignments. It requires unix bash, perl 5.0+ with DBI module and MySQL5.0+ to run properly.
Novel Solexa (Illumina 1G) Base-Caller.
Visual GUI programmer for Attiny26 microcontroller for outputting assembly, assembling into hexedecimal and uploading to hardware with an intuitive interface (Tekbots-OSU).
This is an another open-source search engine, which can be use for educational fields.
ActionFolders are content-aware folders that allow you to orchestrate tasks based on file events. Whether you need automation, notification, workflow, or something more, ActionFolders are as flexible as your imagination.
Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the wiki: http://sourceforge.net/p/adamajava/wiki/Home/16 weekly downloads
AdmIRC is a webmin module for irc server administration. It provides a config interface and advanced security and linking automatism support. Currently UnrealIRCD 3.2 and the services Anope and Epona are supported. Subprojects: irc newsbot and java tools3 weekly downloads
Genetic analysis programs for affected sibling pair data and discrete traits, including multipoint exclusion mapping, map distance estimation, transmission disequilibrium testing, and relationship validation
A fast, unobtrusive and modern cross-platform GUI toolkit. Agar fully exploits hardware acceleration where available, but also supports simple frame-buffer interfaces. Agar is stand-alone and easily portable to new platforms and graphics systems.1 weekly downloads
Job Accounting and User and Project managment for Clustered Computing using Perl, Apache, and MySQL. Designed to be extensible, it processes logs from currently PBS, OpenPBS and Maui2. It also contains a web frontend for User and Project Managment
Algorithm::MatchingModel is a perl library for running match simulations and statistics for two-sided matching problems. It includes classes for a preference factory, algorithm plug-ins, and gathering statistics between rounds.