Progressive assembly tool using DNA, protein or profile HMMs as seeds.
GenSeed-HMM is a program for seed-driven progressive DNA assembly. It differs from the previously published GenSeed in many aspects, but more pointedly by being able to use an HMM profile as seed. Basically, GenSeed-HMM performs three operations, repeatedly: - recruit reads by matching them to a seed - assemble the recruited reads (including previously assembled contigs) - generate new seeds (for the next round of progressive assembly) from the extremities of all generated contigs The first seed is provided by the user, and can be a piece of DNA or protein sequence, or an HMM profile, for increased sensitivity. This program depends on BLAST+ or hmmsearch and a number of third-party support tools (EMBOSS' transeq and splitter, bowtie, 454's sfffile and sffinfo). Which tools will be mandatory depends on the kind of seed and assembler used. Assemblers currently supported include CAP3, Newbler, SOAPdenovo, Velvet, and Abyss.
Project moved to https://github.com/owfs/owfs/
Please note that OWFS source code, and all Issue/Tickets/merge requests have now been moved to https://github.com/owfs/owfs/. Developer mailing lists will still be kept at Sourceforge. ---- OWFS -- 1-Wire file system. Use the Dallas 1-Wire and iButton chips with standard filesystem commands. Create temperature loggers. Monitor everything. OWHTTPD -- same system, only used as a light weight web server. OWFS is also ported to embedded routers, Mac OSX and Windows. Basically you can use these inexpensive little sensors and other chips with very simple wiring to sense and control the physical environment. The interface is very flexible -- everything from a web browser, to read and writing directly to the chip's "file" to integrating with your programs -- even over the internet. There is a growing number of 1-wire sensors: temperature, voltage, humidity, light, ultraviolet, pressure, thermisters, thermocouples, programmable microcontrollers, relays, lights, LCD panels, etc
Text anonymiser for the Autshumato project.
A tool for the anonymisation of text corpora which entails the identification of entities that may convey confidential information and replacing those entities with with randomly selected entities of the same type.
Software for storing and analysing bacterial sequence data
The Bacterial Isolate Genome Sequence Database (BIGSdb) is a scalable, web-accessible database system designed to store and analyse linked phenotypic and genotypic information in a computationally efficient manner. Sequence data can range from single sequence reads to multiple contigs generated by whole genome sequencing technologies. The system incorporates the capacity to define and identify any number of loci and genetic variants at those loci within the stored nucleotide sequences. These loci can be further organised into schemes for isolate characterisation or for evolutionary or functional analyses. See Jolley and Maiden 2010, BMC Bioinformatics 11:595 (http://www.biomedcentral.com/1471-2105/11/595). You can report bugs or make enhancement requests using the issues tracker at https://github.com/kjolley/BIGSdb. The source code is also mirrored there.
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
Depth Conversion uncertainty analysis for the oil and gas industry. Incorporates cross-validation and multiple iterations.
ImageMagick is free software to create, edit, and compose bitmap images in many formats from the commandline or via programming interfaces. Images can be cropped, resized, and combined, effects can be applied, and text, polygons, and curves can be added.
Software Unit Tests (Language Independent Approach)
Automation of Unit and System Tests. Tests can be implemented in any language and on many platforms. The flexible approach enables the inclusion of many types of tests, such as memory leak checks (using valgrind), coding rule checks, complexity checks, etc. Tests are run by a simple call to hwut in a base directory of a project. In particular for C, HWUT supports make file generation using 'sos' and 'sols' modes. Remote control-able function stubs may be generated using the 'stub' mode. Test cases can be generated using the 'gen' mode, and state machine walkers by the 'sm_walker' mode. Over the last decade HWUT has matured towards a full fledged unit test tool for a wide variety of applications.
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
Now in Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP 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
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.
A loudspeaker phase linearization, EQ and filtering tool
rePhase is a FIR generation tool for building fully linear-phase active crossovers with arbitrary slopes. It also let you manually compensate for the phase shifts of your loudspeakers and existing crossovers, be it active or passive. Once generated, the FIR can be applied using any hardware (openDRC, miniSHARC, Najda, ...) or software (foobar, convolver, JRiver, ...), stereo or multi-way convolution engine. Donate: rePhase is free software. If you like it you can support its development with a donation. - paypal: https://goo.gl/v44mmD Tutorials: - miniDSP application note: http://goo.gl/9krGT8 - Pat Brown's prosoundweb article: http://goo.gl/gJG1Of - mwillems' tutorial: http://goo.gl/oKgmhx - Jimmy Thomas' tutorial (in French): http://goo.gl/7kBt7Q Support: - diyaudio forum thread: http://www.diyaudio.com/forums/multi-way/221434-rephase-loudspeaker-phase-linearization-eq-fir-filtering-tool.html - miniDSP forum section: http://goo.gl/U78IXD
City of Hope CpG Island Analysis Pipeline
COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values. Please note: 1) The standalone version of COHCAP is no longer being updated. Please see the Bioconductor version: http://bioconductor.org/packages/release/bioc/html/COHCAP.html 2) In addition to the original NAR paper, please see the following links: Benchmarks: http://www.nature.com/protocolexchange/protocols/2965#/introduction Protocol Exchange Files: http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip 3) Bioconductor Custom Annotation Files (including EPIC Array): https://sourceforge.net/projects/cohcap/files/additional_Bioconductor_annotations.zip/download
Classification Algorithm Based on a Bayesian method for Genomics
PAN And Core-gEnome Analysis
A tool to calculate the Pan-Genome of a set of annotated genomes
ParseCNV CNV call association software takes CNV calls as input and creates SNP based statistics for CNV occurrence in population study cases and controls then calls CNVRs based on neighboring SNPs of similar significance.
A useful collection of batch files and scripts for daily purposes (backup, security, system management, etc.) and development
A C++ unit testing framework, in the style of CxxUnit, for Symbian OS. (For more information, forums and mailing lists please visit the project Home Page http://symbianosunit.sourceforge.net)
myTemp is a thermometer for PalmOS PDAs. It uses a Dallas Semiconductor MicroLan sensor and provides logging functionality and multi-sensor support.
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.
PerlCE provides pre-built perl binaries and some popular extensions for various WinCE platforms
WOOP(c) is an Open-Source Software Architecture.
GUI for rayinvr modelling
PRay stands for 'Plot Rayinvr' and is a graphical user interface for the ray-tracing software rayinvr (Zelt & Smith, 1992). In principle it can also be used as viewer for seismic traveltime data from other software like tomo2D. Zelt, C. A. and Smith, R. B., 1992, Seismic traveltime inversion for 2-D crustal velocity structure, Geophysical Journal International, 108(1), 16--34, 10.1111/j.1365-246X.1992.tb00836.x SYSTEM/USER REQUIREMENTS: - Linux/Mac OS X - You do need to be familiar with command line operations. - a running rayinvr installation DOWNLOAD AND INSTALLATION: Please use the svn repository to download the code: svn checkout svn://svn.code.sf.net/p/pray-plot-rayinvr/code/trunk/ path/to/your/installation To install follow the instructions in the downloaded file 'install.readme'
Genetic variants discovery tool
Bioinformatics pipeline for discovery of genetic variants from NGS reads.
The OpenGEREA is a open enrichment analysis framework for gene expression regulation data analysis.
Tahoe is a research-oriented platform for the development of numerical methods and models for the simulation of complex material behavior.