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http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_indels_SomaticIndelDetector.html

Tool for calling indels in Tumor-Normal paired sample mode.

Proper citation: SomaticIndelDetector (RRID:SCR_005107) Copy   

•   Source: SciCrunch Registry
  

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

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.

Proper citation: comrad (RRID:SCR_005101) Copy   

•   Source: SciCrunch Registry
  

http://service.iris.edu/fdsnws/dataselect/1/

Web service to access seismic time-series data for specified channels and time ranges that are selected using SEED time series identifiers (network, station, location & channel). Data are returned in miniSEED format. This service is an implementation of the International Federation of Digital Seismograph Networks (FDSN) web service specification version 1.

Proper citation: IRIS DMC FDSNWS dataselect Web Service (RRID:SCR_005103) Copy   

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http://biohaskell.org/Applications/FlowSim

A suite of tools for simulating the 454 pyrosequencing process. It is based on the characteristics of real 454 data, and attempts to model the known aspects of the process.

Proper citation: FlowSim (RRID:SCR_005224) Copy   

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http://purl.bioontology.org/ontology/PHENOMEBLAST

A cross-species phenotype and anatomy ontology resulting from combining available anatomy and phenotype ontologies and their definitions. The ontology includes phenotype definitions for yeast, mouse, fish, worm, fly and human phenotypes and diseases.

Proper citation: PhenomeBLAST Ontology (RRID:SCR_005139) Copy   

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http://narc.wustl.edu/narc/default.aspx

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The Neurologic AIDS Research Consortium (NARC) is supported by the National Institutes of Health to design and carry out clinical trials to improve the therapy for HIV induced neurologic disease, and neurologic conditions associated with the AIDS virus. This consortium was established in 1993 when the NARC grant submitted by David B. Clifford, M.D. of Washington University School of Medicine was funded by the National Institute of Neurologic Disorders and Stroke (NINDS) to establish the consortium. Since that time the grant has supported studies of the natural history of neurologic performance in advanced AIDS, treatment of HIV associated peripheral neuropathy, progressive multifocal leukoencephalopathy, and cytomegalovirus.

Proper citation: Neurologic AIDS Research Consortium (RRID:SCR_005019) Copy   

•   Source: SciCrunch Registry
  

http://alt.kompetenznetz-parkinson.de/englisch/englisch.html

A medical network comprised of university clinics, special clinics, and special practices working together to collect data, gene samples, and execute clinical trials in order to bring about diagnoses and therapy methods. Research projects are done in cure research, diagnostic and therapeutic research. The care network includes university clinics, town clinics, special clinics for Parkinson's disease, specialists, and general practitioners.

Proper citation: Competence Network on Parkinson's Disease (RRID:SCR_005013) Copy   

•   Source: SciCrunch Registry
  

http://petrov.stanford.edu/cgi-bin/Tlex.html

Software package for fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements using Next-Generation Sequencing data.

Proper citation: T-lex (RRID:SCR_005134) Copy   

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http://www.uoi.gr/en/

University was founded in 1964, as a charter of the Aristotle University of Thessaloniki and became an independent university in 1970.

Proper citation: University of Ioannina; Ioannina; Greece (RRID:SCR_005010) Copy   

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https://code.google.com/p/popoolationte/

A quick and simple pipeline for the analysis of transposable element (TE) insertions in (natural) populations using next generation sequencing. It calculates TE insertion frequencies for TEs that are present in the reference genome as well as for novel TE insertions. PoPoolation TE requires paired-end reads from a pooled population, a reference sequence and transposable element sequences (fasta-file).

Proper citation: PoPoolation TE (RRID:SCR_005131) Copy   

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http://www.uga.edu/

Public research university with its main campus in Athens, Georgia. Founded in 1785, it is one of the oldest public universities in the United States.

Proper citation: University of Georgia; Georgia; USA (RRID:SCR_004954) Copy   

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http://www.bmg.bund.de/ministerium/presse/english-version.html

Proper citation: German Federal Ministry of Health (RRID:SCR_005247) Copy   

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http://www.uni-kiel.de/index-e.shtml

A university in Germany.

Proper citation: University of Kiel; Schleswig-Holstein; Germany (RRID:SCR_005127) Copy   

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http://www.ctsasharecenter.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 5th, 2022. An open-source platform designed for organic sharing and collaborative work, it provides the CTSA Consortium with a convenient web platform for networking, exchanging resources, and collaborating. Created and maintained as a tool for the CTSA Consortium, it can be implemented by organizations, either in a standalone installation or via cloud-based hosting provided by Zaloni, Inc. The installation package is available at http://www.getsharecenter.org/, including a package optimized for research networks. ShareCenter integrates with VIVO and is a demonstration site for the new CTSAconnect project that will coalesce the VIVO and eagle-i ontologies. CTSA personnel can use ShareCenter to connect and share with each other, while CTSAs can (a) set up the open-source package, which includes a version optimized for research networks or (b) easily create their own private ''''channel'''' on CTSA ShareCenter. * Search for resources and people. * Contribute your institute''''s gems. * Look cool for being a top contributor! ShareCenter Features * Easy search and access: Find content easily using faceted search. * Team based workspaces: Easily create and manage private collaboration spaces. * Connect with other users and follow their activities: Connect with other CTSA members. Follow their activities. * Subscriptions and Notifications: Subscribe to interesting content and receive notifications when your requests are filled. * Sophisticated categorization of information: Content can be categorized by key function areas, taxonomy and keywords. * Incentives for sharing: Reward users for sharing resources, ideas, expertise, skills.

Proper citation: CTSA ShareCenter (RRID:SCR_005248) Copy   

•   Source: SciCrunch Registry
  

http://en.wikiversity.org/wiki/School:Medicine

The Wikiversity School of Medicine is a free online educational resource for the study of medicine. It is a member of the Faculty of Life Sciences and aims to maximize collaboration with other schools within the faculty and elsewhere. Prospective students may study medicine at Wikiversity by registering with the site and joining the school. Students may study via the proposed curriculum pathway, by picking and choosing modules or lessons from the different departments or by joining the school in creating lessons. The school''s medical course is currently divided into pre-clinical and clinical sets of modules. Access to these modules is via the school curriculum. This resource is available in other languages including Deutsch, Espa��ol, Fran��ais, Italiano, Portugu��s, and .

Proper citation: Wikiversity School of Medicine (RRID:SCR_005008) Copy   

•   Source: SciCrunch Registry
  

http://www.scientificamerican.com/

Scientific American, the oldest continuously published magazine in the U.S., has been bringing its readers unique insights about developments in science and technology for more than 160 years. It is the leading source and authority for science, technology information and policy for a general audience. In an era of rapid innovation, Scientific American founded the first branch of the U.S. Patent Agency, in 1850, to provide technical help and legal advice to inventors. A Washington, D.C., branch was added in 1859. By 1900 more than 100,000 inventions had been patented thanks to Scientific American. * Read in print by 3.5 million worldwide consumers * On average, 2.7 million unique users visit ScientificAmerican.com every month * 14 local language editions worldwide, including the U.S. edition of Scientific American, read in more than 30 countries, with a worldwide audience of more than 5 million people * A third of Scientific American readers hold postgraduate degrees * 144 Nobel Prize Scientists have contributed 234 articles to Scientific American * Part of Macmillan Publishers, owned by Holtzbrinck Group of companies; acquired by Holtzbrinck in 1986 * Three Scientific American features in the Federal Record * Scientific American won the 2011 National Magazine Award for General Excellence.

Proper citation: Scientific American (RRID:SCR_005243) Copy   

•   Source: SciCrunch Registry
  

http://oncowiki.info/index.php?title=Main_Page

A free repository for oncology information, chemotherapy protocols, and cancer treatment regimens. It is meant for Healthcare providers working in the field of Oncology.

Proper citation: Onco Wiki (RRID:SCR_005002) Copy   

•   Source: SciCrunch Registry
  

http://en.bioinformatica-na-escola.org/

Project to use bioinformatics-based research activities in high schools that provides teachers and students training materials to support the teaching of Life Sciences, particularly in the area of Biology. Their aims include new ways to learn biology, adapting Bioinformatics exercises to the curricula of practical classes, and encouraging the acquisition of new scientific and technological knowledge.

Proper citation: Bioinformatics(at)school (RRID:SCR_005245) Copy   

•   Source: SciCrunch Registry
  

http://vivoweb.org/

Open source semantic web application that enables the discovery of research and scholarship across disciplines at a particular institution and across institutions by creating a semantic cloud of information that can be searched and browsed. Participants include institutions with local installations of VIVO or those with research discovery and profiling applications that can provide semantic web-compliant data. The information accessible through the national network''''s search and browse capability will therefore reside and be controlled locally within institutional VIVOs or other semantic web applications. The VIVO ontology provides a set of types (classes) and relationships (properties) to represent researchers and the full context of their experience, outputs, interests, accomplishments, and associated institutions. https://wiki.duraspace.org/display/VIVO/VIVO-ISF+Ontology VIVO is populated with detailed profiles of faculty and researchers including information such as publications, teaching, service, and professional affiliations. It also supports browsing and a search function which returns faceted results for rapid retrieval of desired information. The rich semantically structured data in VIVO support and facilitate research discovery. Examples of applications that consume these rich data include: visualizations, enhanced multi-site search through VIVO Search, and applications such as VIVO Searchlight, a browser bookmarklet which uses text content of any webpage to search for relevant VIVO profiles, and the Inter-Institutional Collaboration Explorer, an application which allows visualization of collaborative institutional partners, among others. Institutions are free to participate in the national network by installing and using the application. The application provides linked data via RDF data making users a part of the semantic web! or any other application that provides linked data can be used. Users can also get involved with developing applications that provide enhanced search, new collaboration capabilities, grouping, finding and mapping scientists and their work.

Proper citation: VIVO (RRID:SCR_005246) Copy   

•   Source: SciCrunch Registry
  

http://woldlab.caltech.edu/rnaseq

Software for Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Its functions are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (''multireads''), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candidate exons or parts of exons; and (iv) calculate the prevalence of transcripts from each known or newly proposed RNA, based on normalized counts of unique reads, spliced reads and multireads. The new candidate RNA regions produced can be thought of as ESTs, and, like ESTs, some are provisionally appended to existing gene models if they meet several additional criteria. Remaining unassigned candidate transcribed regions (labeled RNAFAR features) can then be used in conjunction with other confirming data to develop new or revised gene models.

Proper citation: ERANGE (RRID:SCR_005240) Copy   

•   Source: SciCrunch Registry