Linux GPIB Driver package (source)
The Linux GPIB Package is a support package for GPIB (IEEE 488.2) hardware. The package contains a development environment consisting of a GPIB library written in C, kernel driver modules, and bindings for several other languages.
Command-line operators for netCDF and HDF files
The netCDF Operators, or NCO, are a suite of file operators which facilitate manipulation and analysis of self-describing data stored in the (freely available) netCDF and HDF formats. Volunteers welcome! See homepage for details and download links.
The PDL module gives standard perl the ability to COMPACTLY store and SPEEDILY manipulate the large N-dimensional data sets that are the bread and butter of scientific computing.
GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.
Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.
A bioinformatics tool to PRe-process and show INformation of SEQuence data. The tool is written in Perl and can be helpful if you want to filter, reformat, or trim your sequence data. It also generates basic statistics for your sequences.
The home of the Gene Ontology project on SourceForge, including ontology requests, software downloads, bug trackers, and much, much more.
GPL-licensed Electronic Medical Record and Practice Management system for medical providers that runs in any web browser in multiple languages. It provides an XML-RPC backend and multiple import and export formats, as well as reporting and other features
Genetic variants discovery tool
Bioinformatics pipeline for discovery of genetic variants from NGS reads.
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.
Simple Event Correlator (SEC) is a lightweight event correlator for network management, log file monitoring, security management, fraud detection, and other tasks which involve event correlation.
openEAR is the Munich Open-Source Emotion and Affect Recognition Toolkit developed at the Technische Universität München (TUM). It provides efficient (audio) feature extraction algorithms implemented in C++, classfiers, and pre-trained models on well-known emotion databases. It is now maintained and supported by audEERING. Updates will follow soon.
Extract and reformat a sequence database search or multiple alignment
NOTE: The MView repository and web pages have moved to: https://github.com/desmid/mview https://desmid.github.io/mview/ Release tarballs will continue to be uploaded to SourceForge. ---- MView is a command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats. Inputs: - Sequence database search: BLAST, FASTA suites. - Multiple sequence alignment: CLUSTAL, HSSP, MSF, FASTA, PIR, MAF. Outputs: - HTML, FASTA, CLUSTAL, MSF, PIR, RDB (tab-separated). Found a bug? Please open an issue on the MView issue tracker at https://github.com/desmid/mview/issues or send an email to email@example.com.
Celera Assembler (CA) is a whole-genome shotgun (WGS) assembler for the reconstruction of genomic DNA sequence from WGS sequencing data.
The DeconSeq tool can be used to automatically detect and efficiently remove sequence contamination from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. More at http://deconseq.sourceforge.net
Multiplatform Ham Radio APRS and Mapping Program
NOTE: Code commits are FROZEN on SourceForge: New code is now at <http://github.com/Xastir/Xastir>. Real-time tracking & messaging of stations via radio/internet APRS data streams, w/125 map formats supported. Linux/FreeBSD/Solaris/MacOSX/Windows in any of 7 languages. Can also be used for mobile mapping w/GPS. MAILING LISTS ARE AT: PROJECT->WEB SITE.
Software tools for processing taxonomic descriptions in DELTA format
The Free DELTA Project is a free, open-source, software alternative for a generic system to the processing of taxonomic descriptions based on the DELTA (DEscription Language for TAxonomy) format.
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.
Tools for FPGA development and IP cores. This project provides tools, cores and documentation to develope FPGA applications. The project focuses on VHDL.
A neural network package for Octave! Goal is to be as compatible as possible to the one of MATLAB(TM).
Parse and decode METAR, TAF, SYNOP, BUOY, AMDAR and write data as XML
metaf2xml can download, parse and decode aviation routine weather reports (METAR, SPECI, SAO), aerodrome forecasts (TAF), synoptic observations (SYNOP), observations from buoys (BUOY) and meteorological reports from aircrafts (AMDAR). Data can also be taken from decoded BUFR messages. The extracted data can be written as XML or passed to a user-defined function (all done in Perl). It also provides XSLT style sheets to convert the XML to plain language (text, HTML), or XML with different schemas. A web-based (CGI) user interface can be used to download and display up-to-date weather data from NOAA, Ogimet, and other sources.
A multi-purpose extensible self-adaptive evolutionary algorithm
MicroGP (uGP) is a versatile optimizer able to outperform both human experts and conventional heuristics in finding the optimal solution of hard problems. It is an evolutionary algorithm since it mimics some principles of the Neo-Darwinian paradigm.
BreakDancer-0.0.1 is a Perl package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.
GGNFS is an open source implementation of General Number Field Sieve algorithm for factoring integers.
An automatic tool for binning metagenomics sequences
MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users could understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. For users' convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page. Users could use MEGAN or similar software on MaxBin bins to find out the taxonomy of each bin after the binning process is finished. The most current version is 2.2.4. MaxBin was published on Microbiome journal (2:26)! Please cite the Microbiome paper if you use MaxBin in your work. More information can be found at the official MaxBin website: http://downloads.jbei.org/data/MaxBin.html to