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  AAARF Genomic Repeat Investigation

  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.

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  ASGARD

  ASGARD is software for metabolic pathway reconstruction, but it can also generate other types of biological sequence annotation (EC and GO numbers, BLAST reports). This program is intended to be run in UNIX-like systems, and supports SGE or PBS.

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  ASpipe

  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.

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  Agar

  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.

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  AquaTerm (Mac OS X graphics terminal)

  AquaTerm is a Mac OS X grahics renderer. It allows command line applications written in ObjC, C, FORTRAN, Lisp, Perl or Python to display vector graphics, text and images using a simple API. Adapters for gnuplot, PGPLOT, and PLplot exists as well.

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  BASIS

  Build system And Software Implementation Standard

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  Bio::NEXUS

  If you manage phylogenetic data, Bio::NEXUS can make your life easier with a library and ready-made tools to manipulate and visualize NEXUS files (see http://www.molevol.org/nexplorer and http://search.cpan.org/dist/Bio-NEXUS/doc/Tutorial.pod).

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  BisSNP

  Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller

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  CUBioS

  A web-based system for upoading, managing, sharing, and analyzing bioinformatic data. The system is primarily written in python, and runs on both linux and MacOs.

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  CapsimTMK

  Capsim(r) C Text Mode Kernel(TMK),DSP and communication blocks, topologies, libraries and tools for the development of high performance block diagram digital signal processing and communications systems,built in interpreter for scripting.SystemC support.

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  CorneliOS web OS & application framework

  The CorneliOS WebOS is an easy-to-use and cross-browser "Web Desktop Environment", "Web Operating System" or "Web Office". It's also a powerful web application framework that can be used to build community platforms.

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  Current Comparative Table

  Current Comparative Table is a bioinformatics tool for running searches (like BLAST) with large sets of genes. It creates a table that allows you to view many results in many databases and downloads databases daily to ensure the most up-to-date results.

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  DIASER

  Cloud storage class, open source software.

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  FSA

  FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.

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  GMDR

  A Generalized Combinatorial Approach for Detecting Gene-by-Gene and Gene-by-Environment Interactions

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  GNU EPrints

  GNU EPrints is a system for creating large archives of documents, with a searchable database of metadata. It's main target is for scholarly material. The primary site for EPrints is; http://software.eprints.org/

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  Ham Radio Control Libraries

  Library to control radio transceivers and receivers

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  IFEFFIT: Interactive XAFS Analysis

  IFEFFIT is a library and set of interactive programs for the analysis of x-ray absorption fine-structure (XAFS) data. IFEFFIT combines state-of-the-art analysis algorithms with graphical display of XAFS data, and general data manipulation. It can be

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  IsoFind

  Project to create a set of algorithms which will identify and isolate mRNA isoforms through primer design for RT-PCR techniques.

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  LoCI Software Suite

  Software from LoCI Laboratory is devoted to information logistics, the study of the flexible coscheduling of the physical resources that underpin computer systems: storage, computation, and data transmission. We use IBP, L-Bone, exNode and LoRS.

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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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  MAVEN

  Elastic network models (ENMs) have been shown to generate the dominant functional equilibrium motions of biomolecules quickly and efficiently. MAVEN simplifies ENM generation, allows for diverse models to be used, and facilitates useful analyses.

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  Magic Number

  Tracking New Horizons Spacecraft on Mac OS X Dashboard.

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  Maximal Clique Motif Reduction

  Maximal Clique Motif Reduction (MCMR) is a software program for running and then combining the output of multiple motif finder programs, such as MEME, AlignACE and Weeder, into a set of consensus predictions with associated confidence rankings.

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  MicroGP

  A multi-purpose extensible self-adaptive evolutionary algorithm

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