Library to control radio transceivers and receivers
The Hamlib project's purpose is to develop flexible and portable shared libraries that offer a standardized API to control any radio oriented equipment through a computer interface.
Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl. Developers/testers/documenters needed.
A project to increase free Arabic fonts on Unix/Linux
Arabeyes is a Meta project that is aimed at fully supporting the Arabic language in the Unix/Linux environment. It is designed to be a central location to standardize the Arabization process. Arabeyes relies on voluntary contributions.
The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
AMOS is a collection of tools for genome assembly
AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation.
LatexInWord provides macros for Microsoft Word that allow the use of LaTeX input to create equations images in both inline and display modes. Similar macros for other word processors will hopefully be added in the future. We are currently in the process of migrating this project to GitHub: Client: https://github.com/EngineeroLabs/latex_in_word Server: https://github.com/EngineeroLabs/Process_LaTeX
MARF is a general cross-platform framework with a collection of algorithms for audio (voice, speech, and sound) and natural language text analysis and recognition along with sample applications (identification, NLP, etc.) of its use, implemented in Java.
gputils is a collection of tools for Microchip PIC microcontrollers. Its goal is to be fully compatible with Microchip's tools, MPASM, MPLINK, and MPLIB.
Genetic variants discovery tool
Bioinformatics pipeline for discovery of genetic variants from NGS reads.
miRDeep-P,miRDP for short, is a computational tool for analyzing the microRNA (miRNA) transcriptome in plants.
Maq is a set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.
HaploPainter - a pedigree and haplotypes drawing tool written in Perl/Tk. The software processes pedigree information in standard linkage formats combining haplotype information outputs from Simwalk, Genehunter, Allegro and Merlin.
BreakDancer-0.0.1 is a Perl package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.
A set of very optimized tools for indexing/querying huge genomes/files. Provided so far: a very fast exact mapper, and an unconstrained split-mapper
A neural network package for Octave! Goal is to be as compatible as possible to the one of MATLAB(TM).
We describe a simple XML format to share text documents and annotation
A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We are interested in reuse, and we focus on common NLP tasks that are broadly useful for textmining.
A collection of software made by Milos Rancic.
GGI stands for "General Graphics Interface", and it is a project that aims to develop a reliable, stable and fast graphics system that works everywhere. We want to allow any program using GGI to run on any platform requiring at most a recompile.
The Trinity RNA-Seq Assembly project provides software solutions targeted to the reconstruction of full-length transcripts and alternatively spliced isoforms from Illumina RNA-Seq data.
Meta Assembler for de novo assembly results. GARM (Genome Assembly Reconciliation and Merging) is a pipeline to merge results from different assemblers or results from different DNA sequencing technologies.
http://genetik.charite.de/hoffmann/easyLINKAGE/index.html for most recent versions! easyLINKAGE is a GUI for automated setup/performance of linkage analyses/simulation programs (FastLink, SuperLink, SPLink, GeneHunter-/PLUS, Allegro, PedCheck, SimWalk).
DAWGPAWS is a suite of command line programs written in Perl that accelerates annotation of genes and transposable elements in plant genomes by automating the process of running annotation programs and facilitating combined evidence annotation curation.
ZORRO is a probabilistic masking program that assigns confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines.
OECE is a Cisco IOS interface simulator. Useful for beginner to Cisco's IOS command line interface. Supports basic commands like 'enable', 'configure terminal'. It has FULL support for keyboard shortcuts, command shortcuts, history, errors and more.