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on page 1 showing 20 out of 31 results

Cite this (Apache Hadoop, RRID:SCR_011879)

URL: http://hadoop.apache.org/

Resource Type: Resource, software resource, software toolkit

Software library providing a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage. Rather than rely on hardware to deliver high-availability, the library itself is designed to detect and handle failures at the application layer, so delivering a highly-available service on top of a cluster of computers, each of which may be prone to failures. The project includes these modules: * Hadoop Common: The common utilities that support the other Hadoop modules. * Hadoop Distributed File System (HDFS): A distributed file system that provides high-throughput access to application data. * Hadoop YARN: A framework for job scheduling and cluster resource management. * Hadoop MapReduce: A YARN-based system for parallel processing of large data sets.

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Cite this (Argo Genome Browser, RRID:SCR_011763)

URL: http://www.broadinstitute.org/annotation/argo/

Resource Type: Resource, software resource, data set, data or information resource

A tool for visualizing and manually annotating whole genomes that can be run as Applet or Webstart application as well as standalone application.

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    Arvados

Cite this (Arvados, RRID:SCR_002223)

URL: https://arvados.org/

Resource Type: Resource, service resource, data repository, storage service resource

A free and open source bioinformatics platform for storing, organizing, processing, and sharing genomic and other biomedical big data. The platform is designed to make it easier for bioinformaticians to develop analyses, developers to create genomic web applications and IT administers to manage large-scale compute and storage genomic resources. The platform is designed to run on top of cloud operating systems such as Amazon Web Services and OpenStack. Currently, there are implementations that work on AWS and Xen+Debian/Ubuntu. Functionally, Arvados has two major sets of capabilities: (a) data management and (b) compute management.

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Cite this (AutoDock Vina, RRID:SCR_011958)

URL: http://vina.scripps.edu/

Resource Type: Resource, software resource

An open-source program for doing molecular docking.

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    Bambus

Cite this (Bambus, RRID:SCR_005068)

URL: http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus2

Resource Type: Resource, software resource

Software for scaffolding to address some of the challenges encountered when analyzing metagenomes. Scaffolding represents the task of ordering and orienting contigs by incorporating additional information about their relative placement along the genome. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

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Cite this (Binding and Expression Target Analysis, RRID:SCR_005396)

URL: http://cistrome.org/BETA/

Resource Type: Resource, software resource, analysis service resource, data analysis service, service resource, production service resource

A software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes. BETA has three functions: (1) to predict whether the factor has activating or repressive function; (2) to infer the factor''''s target genes; and (3) to identify the motif of the factor and its collaborators which might modulate the factor''''s activating or repressive function. BETA requires ~2GB RAM and 1h for the whole procedure. BETA may run on the web server at Cistrome or may be downloaded.

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Cite this (Bio-Linux, RRID:SCR_005399)

URL: http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info

Resource Type: Resource, software resource

A free, fully featured, powerful, configurable and easy to maintain bioinformatics workstation that provides more than 500 bioinformatics programs on an Ubuntu Linux 12.04 LTS base. Install it or run it live. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs. You can run a Bio-Linux system on Amazon EC2 or other cloud computing architectures by using CloudBioLinux.

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Cite this (Bisulfighter, RRID:SCR_005440)

URL: https://code.google.com/p/bisulfighter/

Resource Type: Resource, software resource

A software package for detecting methylated cytosines (mCs) and differentially methylated regions (DMRs) from bisulfite sequencing data.

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    comrad

Cite this (comrad, RRID:SCR_005101)

URL: http://code.google.com/p/comrad/

Resource Type: Resource, software resource

A novel algorithmic framework for the integrated analysis of RNA-Seq and Whole Genome Shotgun Sequencing (WGSS) data for the purposes of discovering genomic rearrangements and aberrant transcripts. The Comrad framework leverages the advantages of both RNA-Seq and WGSS data, providing accurate classification of rearrangements as expressed or not expressed and accurate classification of the genomic or non-genomic origin of aberrant transcripts. A major benefit of Comrad is its ability to accurately identify aberrant transcripts and associated rearrangements using low coverage genome data. As a result, a Comrad analysis can be performed at a cost comparable to that of two RNA-Seq experiments, significantly lower than an analysis requiring high coverage genome data.

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    deStruct

Cite this (deStruct, RRID:SCR_004747)

URL: https://code.google.com/p/destruct/

Resource Type: Resource, software resource

A software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing.

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Cite this (Eucalyptus, RRID:SCR_011872)

URL: http://www.eucalyptus.com/

Resource Type: Resource, software resource, service resource

Open source software for building AWS-compatible private and hybrid clouds for IT organizations in enterprises and technology businesses.

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    Gaggle

Cite this (Gaggle, RRID:SCR_011780)

URL: http://gaggle.systemsbiology.net/docs/geese/genomebrowser/

Resource Type: Resource, software resource

An open source software tool for visualizing high-density data plotted against coordinates on the genome.

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Cite this (GeneStitch, RRID:SCR_011910)

URL: http://omics.informatics.indiana.edu/GeneStitch/

Resource Type: Resource, software resource

Network Matching Algorithm using the de Bruijn graph assembly of metagenomes to improve the assembly of genes.

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    Genometa

Cite this (Genometa, RRID:SCR_001181)

URL: http://genomics1.mh-hannover.de/genometa/index.php?Site=Home

Resource Type: Resource, software resource

A Java based bioinformatics program which allows rapid analysis of metagenomic short read datasets. Millions of short reads can be accurately analysed within minutes and visualised in the browser component. A large database of diverse bacteria and archaea has been constructed as a reference sequence. The approach is based upon the established open source visualisation tool IGB and supported by the rapid alignment program bowtie. The Picard toolset for SAM files is also made use of.

  • From Current Category

Cite this (GenomeView, RRID:SCR_012968)

URL: http://genomeview.org/

Resource Type: Resource, software resource, data or information resource, database

A next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute.

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Cite this (Glimmer-MG, RRID:SCR_011932)

URL: http://www.cbcb.umd.edu/software/glimmer-mg/

Resource Type: Resource, software resource

A software system for finding genes in environmental shotgun DNA sequences.

  • From Current Category

    Glimmer

Cite this (Glimmer, RRID:SCR_011931)

URL: http://ccb.jhu.edu/software/glimmer/index.shtml

Resource Type: Resource, software resource, analysis service resource, data analysis service, service resource, production service resource

A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.

  • From Current Category

    LMAT

Cite this (LMAT, RRID:SCR_004646)

URL: https://computation-rnd.llnl.gov/lmat/

Resource Type: Resource, software resource

Open-source software tool to assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick "single pass" analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads.

  • From Current Category

Cite this (MUMmerGPU, RRID:SCR_001200)

URL: http://sourceforge.net/apps/mediawiki/mummergpu/index.php?title=MUMmerGPU

Resource Type: Resource, software resource, software application, data processing software

An open-source high-throughput parallel pairwise local sequence alignment software program that runs on commodity Graphics Processing Units (GPUs) in common workstations. It uses the Compute Unified Device Architecture (CUDA) from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, it achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies.

  • From Current Category

    MZmine

Cite this (MZmine, RRID:SCR_012040)

URL: http://mzmine.sourceforge.net/

Resource Type: Resource, software resource

Software for mass-spectrometry data processing, with the main focus on LC-MS data.

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