Scientific/Engineering Software

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Scientific/Engineering Software

  • Searching for Affordable Business Phone Service? Searching for Affordable Business Phone Service? Icon
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  • SAM tools

    SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format. The main samtools source code repository moved to GitHub in March 2012. For ongoing development since then, see http://github.com/samtools/samtools

  • Universal JTAG library, server and tools

    UrJTAG aims to create an enhanced, modern tool for communicating over JTAG with flash chips, CPUs, and many more. It is a descendant of the popular openwince JTAG tools with a lot of additional features and enhancements.

  • scalpel

    Genetic variants discovery tool

    Bioinformatics pipeline for discovery of genetic variants from NGS reads.

  • General Graphics Interface

    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.

    Downloads: 23 This Week Last Update: See Project
  • Pretty Damn Quick Queueing Model Package

    Pretty Damn Quick (PDQ) analytically solves queueing network models of computer and manufacturing systems, data networks, etc., written in conventional programming languages. Generic or customized reports of predicted performance measures are output.

    Downloads: 23 This Week Last Update: See Project
  • License This HTML5 Speed Test for Your ISP or Network License This HTML5 Speed Test for Your ISP or Network Icon
    License This HTML5 Speed Test for Your ISP or Network Icon

    Are you an ISP or network administrator looking for a reliable, accurate, & affordable HTML5 speed test that works on all devices?

    The SourceForge Speed Test measures Latency/Ping, Jitter, Download Speed, Upload Speed, Buffer Bloat, and Packet Loss. Upon completion, you can view detailed reports about your connection. This HTML5 speed test does not require Flash or Java, and works on all devices including tablets and smartphones. Host on your own infrastructure or use ours. For licensing, inquire today.
  • BamBam

    Tools for genomic analysis

    BamBam includes numerous tools for analyzing DNA next-generation sequencing data. Tools are provided for calling SNPs and indels, identifying large scale deletions, tabulating counts of mapped reads, methylation analysis, and more. Depends on SAMtools (http://samtools.sourceforge.net/) and BAMtools (https://github.com/pezmaster31/bamtools). Also uses BioPerl, which is included in the download tarball.

    Downloads: 9 This Week Last Update: See Project
  • BisSNP

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

    BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously. It works for both of single-end and paired-end reads.Specificity and sensitivity has been validate by Illumina IM SNP array. In default threshold 30X data (Phred scale score > 20), it could detect 92.21% heterozygous SNPs with 0.14% false positive rate Cytosine calling is not only based on reference context, so it could detect non-reference cytosine context. Google group for help: http://goo.gl/zL7Nj

    Downloads: 9 This Week Last Update: See Project
  • CSBB-v2.1 Icon

    CSBB-v2.1

    Computational Suite For Bioinformaticians and Biologists

    CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX and Windows platforms. Currently CSBB provides 17 modules focused on analytical tasks like normalization, visualization, statistics, RNA-SEQ etc.

    Downloads: 5 This Week Last Update: See Project
  • MutationFinder

    MutationFinder is a biomedical natural language processing (NLP) system for extracting mentions of point mutations from free text. MutationFinder achieves high performance (99% precision, 81% recall on blind test data) as an information extraction system

    Downloads: 4 This Week Last Update: See Project
  • OncoIMPACT

    Cancer driver prediction via integrative omics

    OncoIMPACT is a model-driven approach to integrate omics profiles (genomics, transcriptomics etc.) and provides patient-specific cancer driver gene predictions.

    Downloads: 2 This Week Last Update: See Project
  • math-linux

    This project is for maintaining a linux system that concentrates on math, logic, and geometry related softwares.

    Downloads: 2 This Week Last Update: See Project
  • 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).

  • mged

    Microarray Gene Expression Database Group and OMG Gene Expression Standard (MAGE)

    Downloads: 1 This Week Last Update: See Project
  • CSBB-v2.0 Icon

    CSBB-v2.0

    Computational Suite for Bioinformaticians and Biologists

    CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX and Windows platforms. Currently CSBB provides 16 modules focused on analytical tasks like normalization, visualization, statistics, RNA-SEQ etc.

    Downloads: 0 This Week Last Update: See Project
  • Chromatin Consortium Tools

    A collection of utilities, developer tools and libraries developed by the Maize Functional Genomics of Chromatin Consortium

    Downloads: 0 This Week Last Update: See Project
  • EACO

    Enrichment analysis for customized organisms

    Downloads: 0 This Week Last Update: See Project
  • Evoker

    Evoker is a graphical tool for plotting genotype intensity data in order to assess quality of genotype calls. It implements a compact, binary format which allows rapid access to data, even with hundreds of thousands of observations. PLEASE NOTE: This source repository is no longer active. See the github link above for the latest version.

  • Laboratory for Genome Bioinformatics

    Code repository for the Laboratory for Genome Bioinformatics at Texas A&M. The LGB project was initiated primarily to support biologists at Texas A&M needing help with bioinformatics in order to use new genomic technologies.

    Downloads: 0 This Week Last Update: See Project
  • 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.

    Downloads: 0 This Week Last Update: See Project
  • Sabeti Lab Data System

    An open-source data management, analysis and visualization system to make the process of the scientific data development clean, easily reproducible, and easily sharable with the outside world.

    Downloads: 0 This Week Last Update: See Project
  • Scenario Data Selector

    The Scenario Data Selector is a Perl script that serves up scenario data on the web. Users can browse data and choose to show by value or as growth rates or indices. Data can be shown by region or indicator - the script takes care of regional aggrega

    Downloads: 0 This Week Last Update: See Project
  • Solanaceae Phenotypes

    This project is for the developing Solanaceae Phenotype descriptors and ontology. The vocabulary is being used at the Sol Genomics database (sgn.cornell.edu).

    Downloads: 0 This Week Last Update: See Project
  • TaxoAssignement

    Taxonomic assignement of sequences

    TANGO is one of the most accurate tools for the taxonomic assignment of Next Generation Sequencing reads using multiple reference taxonomy

    Downloads: 0 This Week Last Update: See Project
  • TaxoAssignment

    TANGO is one of the most accurate tools for the taxonomic assignment of Next Generation Sequencing reads using multiple reference taxonomy

    Downloads: 0 This Week Last Update: See Project
  • Thermocouple Scripts

    Thermocouple Scripts. Thermocouples generate a voltage at a given temperature. The relationship isn't simple. There are published tables, but the format can be awkward. This project supplies tools to find, parse, plot, and curve-fit thermocouple data.

    Downloads: 0 This Week Last Update: See Project
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