Search Results for "reference" - Page 5
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Showing 290 open source projects for "reference"
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Brainstorm Network
Software to organize a brainstorm as a complex network.
...With this organization the users are able to visualize the main points of the brainstorm (the hubs in the network). Moreover, they can access the information through the rede, interactively, clicking on the edges or nodes! All information is associated with a reference list (imported from a bibtex file). This project uses Python, Web2py, MariaDB and VIS.js (D3.js). -
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TAG
A tool for metatranscriptome assembly using metagenome graph
TAG is a tool for metatranscriptome assembly using de Bruijn graph of matched metagenome as the reference. TAG is an application of a reads mapping algorithm that we developed for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction k-mers (k-mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph. We have shown that TAG helps to assemble substantially more transcripts from metatranscriptomic datasets that otherwise would have been missed or truncated because of the fragmented nature of the reference metagenome. ... -
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Periodic Table of Elements
Periodic Table of Elements a quick reference tool
Periodic Table of Elements is a quick reference tool that allows you a quick glance to get general information about an element. The program is for educational purposes. -
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riboFR-seq
A novel approach to linking 16S rRNA amplicon profiles to metagenomes
...Here we propose a novel approach, RiboFR-Seq (Ribosomal RNA gene Flanking Region Sequencing), for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. We demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S rRNA and metagenomic contigs to make a consensus classification. -
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# ASPI Kit - Adaptive Identification and Control Software This software is under development by the ASPICC group. Its purpose is to allow users to learn and experiment the use of Neural Networks (NN's) and related Computational Intelligence algorithms on their own data. Users can upload their own data and experiment with various algorithms of various setups to see how the algorithms performs on their data. Users can also investigate and familiarize themselves with the Python code of...
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Resistor Value Identifier
Identify electronic resistor values
This HTML utility allows the user to select standard color codes or surface mount numbers, then it identifies the resistor value. There is no need to memorize color codes or multipliers. An online working example of this program can be used at ZoomAviation.com/programs. -
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Reference implementation of the Systems Biology Graphical Notation: map exchange format and library handling import/export and validation. Resource of the libSBGN project have been migrated from SourceForge to GitHub. Latest changes can be found on GitHub now. The code repository can be found here now https://github.com/sbgn/libsbgn The files (releases) can be found here now https://github.com/sbgn/libsbgn/releases The bugs and features (issues) can be found here now https://github.com/sbgn/libsbgn/issues
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The Genome Mappability Analysis suite is used for measuring how well NGS reads can be mapped to reference genomes, especially for discovering variations
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ChIP-RNA-seqPRO
ChIP-RNA-sequencing-processing (ChIP-RNA-seqPRO)
ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites. Runnable python scripts packaged together with customized annotation libraries, demo data input and README guide. 9/26 : v1.1 Updated MAIN_IV to debug error thrown by python pandas no longer supporting 'subset'. This code will no longer be actively maintained/updated here. A cloud-based resource for comparative analysis of epigenetic,... -
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CNVision
CNV prediction from Illumina genotyping data
...CNVision was written to analyze data for the Simons Simplex Collection (SSC) autism data. A fill description of methods are given in the following paper which can be used to reference CNVision: http://www.ncbi.nlm.nih.gov/pubmed/21658581 -
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Tardyon Drive AVR Stepper Controller
AVR-based single axis stepper motor controller
This project provides an AVR-based, USB accessible, single-axis motion controller that can fit into an USB-connector completely and therefore is probably the worlds smallest stepper motor controller. Here both, hardware schematics and all software components are provided. -
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This is the reference library for ICS (Image Cytometry Standard), an open standard for writing images of any dimensionality and data type to file, together with associated information regarding the recording equipment or recorded subject.
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Flexbar
flexible barcode and adapter removal for sequencing platforms
...Moreover, trimming and filtering features are provided. Flexbar supports next-generation sequencing data in fasta and fastq format, e.g. from the Illumina platform. Reference: Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905. -
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MassWiz
Proteomics MS/MS database search engine
Open Source MS/MS algorithm with integrated target-decoy based FDR. Reference- http://pubs.acs.org/doi/abs/10.1021/pr200031z , Check out the wiki site for help and support - https://sourceforge.net/apps/mediawiki/masswiz/index.php?title=Main_Page -
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...This wrapper uses 'PInvoke' (like peek/poke) to 'martial' calls from managed to unmanaged code. It sounds complicated, and it is. IT IS ALSO TOTALLY UNNECESSARY. Why not have the DLL as managed code?? Why not simply reference the library in your project and just call its functions?? This project does just that Licence: LGPLV3.: In summary, the only thing we ask is if you improve / bugfix / extend the library then feed these changes back into the project by emailing jon_newcomb or requesting sourceforge access. Applications you develop that use this library are not covered by this licence and can remain closed source and commercial
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OpenTRV
Open-Source Thermostatic Radiator Valve
Retrofit completely-open reference mechanical/hardware/software design for zoned heating control not relying critically on any proprietary/hacked components. The aim is to include at least one complete mechanical and software design for a replacement TRV head that can be retrofitted without any plumbing plus at least one simple boiler control to allow end-to-end open soft heating zoning, with the ability to connect to home automation system or the Net if required. -
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Transcriptome assembly ORA
Reference-based transcriptome reconstruction software
Sofware for reference-based transcriptome reconstruction. It performs reconstruction starting from short reads obtained from RNA-seq. It is best suited to manage the transcriptomes of lower eukaryotes with a low number of introns per gene and it can be used also for procariotes. It needs a SAM file with the reads aligned on the reference genome and (optional) a gff file with the position of genes on the reference genome. -
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galprop
Cosmic-ray propagation and emission processes
...Current version (r2766) includes * accurate propagation scheme * polarized synchrotron * free-free emission and absorption * new convection models * anisotropic diffusion * primary positrons * free-escape boundary conditions * new hadronic gamma-ray production models * new injection spectral breaks * upwards compatible with latest HEALPix * improved HEALPix skymap format * full reference output for a sample run * deuterium production by pp fusion * JF12 B-field * hadronic losses Full details in the Explanatory Supplement and README. Now at https://gitlab.mpcdf.mpg.de/aws/galprop Older versions, datasets etc: http://galprop.stanford.edu. See also http://www.mpe.mpg.de/~aws/propagate.html https://sourceforge.net/projects/galplot http://sourceforge.net/projects/galpropskymapco https://sourceforge.net/projects/gcrconvert https://sourceforge.net/projects/galpropsynchrotron synchrotron routines. -
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MD PnP | OpenICE
Open Source Integrated Clinical Environment
As of 2015-06-23, this project may now be found at http://www.github.com/mdpnp/mdpnp. A prototype reference implementation of the standard for the Integrated Clinical Environment (ASTM F2761-2009) -
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SuRankCo
Supervised Ranking of Contigs in de novo Assemblies
SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet. For more details about SuRankCo and its functioning, please see "SuRankCo: Supervised Ranking of Contigs in de novo Assemblies" Mathias Kuhring, Piotr Wojtek Dabrowski, Andreas Nitsche and Bernhard Y. Renard (http://www.biomedcentral.com/1471-2105/16/240/abstract) PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using SuRankCo. ... -
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That project (RMOL) aims at giving developers concerned by the Revenue Management arena a library delivering a reference implementation for most of the published algorithms and methods. That library is intended to be used in simulated environment: it does not intend to be used in real world production systems.
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That project aims at delivering a reference implementation of a library, estimating and serving average prices paid for air travel products. It is not intended for use by an actual airline, but rather by simulators or other airline-related modules of
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GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded. This project has moved to GitHub: https://github.com/GenomeView/genomeview
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SplitMEM
Graphical pan-genome analysis with suffix skips
With the rise of improved sequencing technologies, genomics is expanding from a single reference per species paradigm into a more comprehensive pan-genome approach with multiple individuals represented and analyzed together. Here we introduce a novel O(n log n) time and space algorithm called splitMEM, that directly constructs the compressed de Bruijn graph for a pan-genome of total length n. To achieve this time complexity, we augment the suffix tree with suffix skips, a new construct that allows us to traverse several suffix links in constant time, and use them to efficiently decompose maximal exact matches (MEMs) during a suffix tree traversal. -
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fitGCP
Fitting genome coverage distributions with mixture models
...While the average genome coverage is frequently used within algorithms in computational genomics, the complete information available in coverage profiles (i.e. histograms over all coverages) is currently not exploited to its full extent. Thus, biases such as fragmented or erroneous reference genomes often remain unaccounted for. Making this information accessible can improve the quality of sequencing experiments and quantitative analyses. fitGCP is a framework for fitting mixtures of probability distributions to genome coverage profiles. Besides commonly used distributions, fitGCP uses distributions tailored to account for common artifacts. ...
