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on page 1 showing 20 out of 217 results

    Aegean

Cite this (Aegean, RRID:SCR_015965)

URL: http://standage.github.io/AEGeAn

Resource Type: Resource, data analysis software, data processing software, software application, sequence analysis software, software resource, software toolkit

Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more.

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Cite this (AIDA Toolkit, RRID:SCR_005914)

URL: https://adaptivedisclosure.wordpress.com/aida/

Resource Type: Resource, software resource, software toolkit, data access protocol, web service

A generic set of components that can perform a variety of tasks, such as learn new pattern recognition models, perform specialized search on resource collections, and store knowledge in a repository. W3C standards are used to make data accessible and manageable with semantic web technologies such as OWL, RDF(S), and SKOS. The AIDA Toolkit is directed at groups of knowledge workers that cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. The server offers services for: text indexing and statistics, metadata storage and querying, thesaurus reasoning, annotation, text retrieval, spelling correction, synonym detection, and model learning.

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Cite this (AngioTool, RRID:SCR_016393)

URL: https://ccrod.cancer.gov/confluence/display/ROB2/Home

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

Software that performs quantitative analysis of angiogenesis. It specializes in quantitative assessment of various vessel morphometric and spatial parameters, including vessel length and density, branching index, lacunarity, etc.

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Cite this (AnimalTracker, RRID:SCR_014397)

URL: http://animaltracker.elte.hu/

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

A universal tracking application specifically designed to support animal behavioral analysis. AnimalTracker consists of three main modules which can be used independently: Tracker is responsible for image processing and providing the coordinates of the identified object; Zone Designer provides tools to create custom-made investigation areas in order to design a maze-setup; and Tracking Analyzer module serves to define and obtain the parameters needed for the evaluation.

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    ASaiM

Cite this (ASaiM, RRID:SCR_015878)

URL: http://asaim.readthedocs.io

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

Software that analyzes intestinal microbiota data. This environment is composed of a framework to process and analyze microbiota data from raw sequences to taxonomic and functional assignations.

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Cite this (Asciidoctor, RRID:SCR_014003)

URL: http://asciidoctor.org

Resource Type: Resource, software resource, software application

A software application which translates plain text written in AsciiDoc syntax to HTML5, DocBook 5, and other backends. Asciidoctor reads and parses text written in the AsciiDoc syntax, then feeds the parse tree into a set of built-in templates to produce HTML5. Users can write their own converter or provide Tilt-supported templates to customize the generated output or produce alternative formats. Asciidoctor also recognizes additional markup and formatting options, such as font-based icons and UI elements.

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Cite this (Atomify LAMMPS, RRID:SCR_015240)

URL: https://play.google.com/store/apps/details?id=com.compphys.atomify&hl=no

Resource Type: Resource, software resource, software application, simulation software, mobile app

Mobile simulation app for visualizing molecular interactions in liquids, solids and gases. The simulations are performed with the molecular dynamics code LAMMPS.

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Cite this (AutoAssemblyD, RRID:SCR_001087)

URL: http://sourceforge.net/projects/autoassemblyd/

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

Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers.

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    Avogadro

Cite this (Avogadro, RRID:SCR_015983)

URL: http://avogadro.cc/

Resource Type: Resource, data analysis software, data processing software, software application, data visualization software, software resource, software toolkit

Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

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    BAC

Cite this (BAC, RRID:SCR_001067)

URL: http://www.bioconductor.org/packages/release/bioc/html/BAC.html

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

R software package that uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments.

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Cite this (BCBtoolkit, RRID:SCR_015519)

URL: http://toolkit.bcblab.com/

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

Software toolkit that provides several multi-modal tools to assess brain disconnections and remote effects of lesions. All modules are designed to process brain lesion data with a normalization algorithm, a module to estimate the probability and the severity of white matter disconnections, and a tool to build a map of the disconnected areas.

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    BeCalm

Cite this (BeCalm, RRID:SCR_015021)

URL: http://www.becalm.eu/

Resource Type: Resource, software resource, software repository

Server that contains a registry of text mining tools primarily within the biomedical field. It includes resources for biomedical text annotation visualization, biomedical text annotation prediction, and benchmarking biomedical entity recognition between independent automatic prediction systems.

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Cite this (Berkeley Advanced Reconstruction Toolbox, RRID:SCR_016168)

URL: https://doi.org/10.5281/zenodo.592960

Resource Type: Resource, software resource, image reconstruction software, software application, data processing software, image analysis software

Image reconstruction software for MRI. Its library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms.

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    Binder

Cite this (Binder, RRID:SCR_016437)

URL: https://mybinder.org/

Resource Type: Resource, software resource, service resource, data repository, storage service resource, web application

Open-source web application for managing digital repositories. Allows to create custom computing environments that can be shared and used by many remote users.Turns a GitHub repository containing a collection of Jupyter Notebooks into a collection of interactive notebooks. With Binder, open those notebooks in an executable environment, making your code immediately reproducible by anyone, anywhere.

  • From Current Category

    BINOCh

Cite this (BINOCh, RRID:SCR_002778)

URL: http://liulab.dfci.harvard.edu/BINOCh/

Resource Type: Resource, software resource

Software that infers the identity of transcription factors used to regulate cell response to stimulus or determine a program of differentiation. It uses genome wide information on enhancer proximal nucleosome occupancy, acquired using ChIP-seq targeting enhancer related histone modifications.

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    Birdseed

Cite this (Birdseed, RRID:SCR_001122)

URL: http://www.broadinstitute.org/mpg/birdsuite/birdseed.html

Resource Type: Resource, software resource, algorithm resource

SNP genotyping algorithm that runs on the Affymetrix 500K, SNP5.0, and SNP6.0 platforms. This software runs a clustering algorithm and generally should be run on a sample at least 50 times. It utilizes an Expectation-Maximization (EM) algorithm to produce genotypes and confidence scores for every individual at every SNP.

  • From Current Category

Cite this (BLASTPLOT, RRID:SCR_000162)

URL: http://sourceforge.net/projects/blastplot/

Resource Type: Resource, software resource

A PERL module that can quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets. This software generates PNG graphs for all of the reference sequences associated with a BLAST result set.

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Cite this (BloodSpot, RRID:SCR_015563)

URL: http://servers.binf.ku.dk/bloodspot/

Resource Type: Resource, data or information resource, database

Database that provides gene expression profiles of genes and gene signatures in healthy and malignant hematopoiesis and includes data from both humans and mice. In addition to the default plot, which displays an integrated expression plot, two additional levels of visualization are available: an interactive tree showing the hierarchical relationship between the samples, and a Kaplan-Meier survival plot. The database is sub-divided into several datasets that are accessible for browsing.

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Cite this (BOINC - Berkeley Open Infrastructure for Network Computing, RRID:SCR_015896)

URL: http://boinc.berkeley.edu

Resource Type: Resource, data processing software, software application, data distribution software, portal, data acquisition software, software resource, project portal, data or information resource

Software to orchestrate the distribution of computational work units (data and applications) to volunteers and have results collected back. It supports diverse applications, including those with large storage or communication requirements, and addresses unsolved issues in biology, medicine, physics, astronomy and computer science.

  • From Current Category

Cite this (Bootstrap CSS, RRID:SCR_016096)

URL: https://getbootstrap.com/docs/3.3/

Resource Type: Resource, software resource, programming language

Programming language framework for HTML, CSS, and JS. It is used for developing responsive, mobile projects on the web.

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