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http://seqanswers.com/wiki/

Wiki forum providing an extensive catalogue of manually categorized analysis tools, technologies and information about service providers, maintained by the members of the SEQanswers community. * Minimum Information about a high-throughput Sequencing Experiment * Software Hub: The place to add to, edit or browse the software database on SEQwiki. * Service Providers: Browse or edit the list of NGS service facilities. * How-to Hub: Mini reviews for the most used tools broken down by common tasks. * Developers Hub: The place to discuss the development of the SEQwiki site and its associated data. See also publishing SEQ*. * Publications: Publication about SEQwiki and selected citations.

Proper citation: SEQanswers Wiki (RRID:SCR_004810) Copy   

•   Source: SciCrunch Registry

http://www.ibcresearch.org/

The Inflammatory Breast Cancer Research Foundation is a non-profit corporation dedicated to the support of research and public awareness. It is dedicated to researching the cause of Inflammatory Breast Cancer, also known as IBC, an advanced and accelerated form of breast cancer usually not detected by mammograms or ultrasounds. Inflammatory breast cancer requires immediate aggressive treatment with chemotherapy prior to surgery and is treated differently than more common types of breast cancer. Our mission is to assist scientists and researchers in their quest to determine the definitive causes of inflammatory breast cancer. The Inflammatory Breast Cancer Research Foundation seeks to assist them in their work so effective and meaningful detection and diagnosis, prevention and treatment can be pursued and achieved. Our Goals Include: * To ignite interest in the study and research of inflammatory breast cancer at every level. From researchers to physicians, educators and scientists, the IBC Research Foundation seeks to support and inspire those seeking to identify the cause(s) of inflammatory breast cancer. * To support research, the purpose of which is to reach an unambiguous definition of inflammatory breast cancer. The clinical/pathological definition in use since the late 1800s with little change in the 1900s is ambiguous and doesn''t result in a diagnosis of all cases of IBC. By using research methods available in the 21st Century, an unambiguous definition is now possible, assuring with high certainty that all cases of IBC will be correctly diagnosed, and possible sub-types of IBC identified, which may lead to better treatment outcomes. * To increase awareness of IBC for primary care physicians, nursing professionals, and medical technicians in order to minimize the time from presentation of symptoms to correct diagnosis of inflammatory breast cancer. * To increase public awareness in an effort to encourage women to seek medical attention for common inflammatory breast cancer symptoms soon after they appear and to empower patients, caregivers, families and friends to pursue meaningful paths in support of diagnosis and treatment of inflammatory breast cancer.

Proper citation: Inflammatory Breast Cancer Research Foundation (RRID:SCR_004898) Copy   

•   Source: SciCrunch Registry

http://www.open.ac.uk/

Public research university and the largest university in the UK for undergraduate education. The majority of the OU's undergraduate students are based in the United Kingdom and principally study off-campus; many of its courses can also be studied anywhere in the world.

Proper citation: Open University; Milton Keynes; United Kingdom (RRID:SCR_004931) Copy   

•   Source: SciCrunch Registry

http://www.youtube.com/watch?v=0OnwOKiMVb8

GENEticS is arap video about genetics. So let''s talk about genes, and I don''t mean trousers, go the lyrics to this catchy rap video created for The GAMY (Genetics and Merthyr Youth) Project. It is one of the many videos, games, and digital media used by researchers at the University of Glamorgan in the United Kingdom use to engage local teenagers in a conversation about genetics. Video produced by Jon Chase (aka Oort Kuiper).

Proper citation: GENEtics Video (RRID:SCR_004770) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/sra

Repository of raw sequencing data from next generation of sequencing platforms including including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT. In addition to raw sequence data, SRA now stores alignment information in form of read placements on reference sequence. Data submissions are welcome. Archive of high throughput sequencing data,part of international partnership of archives (INSDC) at NCBI, European Bioinformatics Institute and DNA Database of Japan. Data submitted to any of this three organizations are shared among them.

Proper citation: NCBI Sequence Read Archive (SRA) (RRID:SCR_004891) Copy   

•   Source: SciCrunch Registry

http://clams.jgi-psf.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2nd, 2023. Sequence composition based classifier for metagenomic sequences. It works by capturing signatures of each sequence based on the sequence composition. Each sequence is modeled as a walk in a de Bruijn graph with underlying Markov chain properties. ClaMS captures stationary parameters of the underlying Markov chain as well as structural parameters of the underlying de Bruijn graph to form this signature. In practice, for each sequence to binned, such a signature is computed and matched to similar signatures computed for the training sets. The best match that also qualifies the normalized distance cut-off wins. In the case that the best match does not qualify this cut-off, the sequence remains un-binned.

Proper citation: Classifier for Metagenomic Sequences (RRID:SCR_004929) Copy   

•   Source: SciCrunch Registry

http://sri.com/

Independent, nonprofit research institute conducting client sponsored research and development for government agencies, commercial businesses, foundations, and other organizations. SRI also brings its innovations to the marketplace by licensing its intellectual property and creating new ventures. SRI was founded as Stanford Research Institute in 1946 by a group of West Coast industrialists and Stanford University. SRI formally separated from the University in 1970, and we changed our name to SRI International in 1977.

Proper citation: Stanford Research Institute International (RRID:SCR_004926) Copy   

•   Source: SciCrunch Registry

http://snrp.utsa.edu/POD_html/Podcast/Podcast.html

The University of Texas at San Antonio''s (UTSA) Neurobiology Podcast, showcasing the current research of internationally renowned guest Neuroscientists. Each episode features a moderated discussion with a cross section of UTSA Neurobiology faculty, highlighting the featured guest''s research, and the state of the art in the field at hand.

Proper citation: Neuroscientists Talk Shop (RRID:SCR_004806) Copy   

•   Source: SciCrunch Registry

http://openflydata.org/

A cross-database search service for Drosophila gene expression data, including microarray data from FlyAtlas and in situ images from BDGP and Fly-TED. The applications provide different ways to search for and compare gene expression data for the fruit fly Drosophila melanogaster. You may Search Gene Expression Data by Gene, Gene Batch, and by Tissue Expression Profile. A number of Web services (SPARQL endpoints) are provided from this site which may be queried programmatically for data.

Proper citation: OpenFlyData.org (RRID:SCR_004807) Copy   

•   Source: SciCrunch Registry

http://www.methodbox.org/

Collaboration environment for sharing variable sets and statistical methods for analysis across social science survey data. MethodBox enables you to browse and download datasets, share methods and scripts, find fellow researchers with similar interests and share your knowledge. MethodBox source available on Google code. Finding the variables you need to support a particular research question can be time consuming. Wading through hundreds of pages of PDF documents, codebooks and metadata and then trying to find the exact column in a huge spreadsheet can be very frustrating. MethodBox gets you to the variables faster and lets you download only the data you need. You can also share your scripts with others to allow them to adopt best practice quicker than before.

Proper citation: MethodBox (RRID:SCR_004928) Copy   

•   Source: SciCrunch Registry

http://www.anatomyatlases.org/

An anatomy digital health sciences library to educate patients, healthcare providers, and students in a free and anonymous manner while using current, authoritative, trustworthy health information. Anatomy Atlases addresses the continuum of anatomy education and may be of use primarily to three distinct populations. It is written for and intended primarily for use by Medical Students, Residents, Fellows, or Attending Physicians studying anatomy. Other Health Care Providers studying anatomy should find it useful. Finally, Patients (including patient''s family members or friends) may find it helpful. Anatomy Textbooks and Anatomy Atlases: * Atlas of Human Anatomy * Atlas of Human Anatomy in Cross Section * Illustrated Encyclopedia of Human Anatomic Variation * Atlas of Microscopic Anatomy - A Functional Approach: Companion to Histology and Neuroanatomy: Second Edition * Anatomy of First Aid - A Case Study Approach * Lessons From a Bone Box Lessons From a Bone Box

Proper citation: Anatomy Atlases (RRID:SCR_004888) Copy   

•   Source: SciCrunch Registry

https://www.saintluc.be/en/node/2561

An essential reference center in Europe and a leader in French-speaking Belgium that treats all types of adult and childhood cancer. They fight against cancer while giving patients comprehensive and humane care. Their quest for excellence is in three main academic fields: clinical care, research and teaching.

Proper citation: Cliniques Universitaires Saint-Luc Cancer Centre (RRID:SCR_004922) Copy   

•   Source: SciCrunch Registry

http://www.proconsortium.org/pro/

An ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). NOTICE: The PRO ID format has changed from PRO: to PR: (e.g. PRO:000000563 is now PR:000000563).

Proper citation: PR (RRID:SCR_004964) Copy   

•   Source: SciCrunch Registry

http://wiki.iop.kcl.ac.uk/default.aspx/Neurodegeneration/Neurodegeneration%20Research%20Wiki.html

A wiki which provides information on neurodegenerative diseases to caregivers, students, and researchers.

Proper citation: Neurodegeneration Research Wiki (RRID:SCR_005015) Copy   

•   Source: SciCrunch Registry

http://www.uiowa.edu/

Public research university in Iowa City, Iowa. Founded in 1847, it is the oldest and the second-largest university in the state.

Proper citation: University of Iowa; Iowa; USA (RRID:SCR_005011) Copy   

•   Source: SciCrunch Registry

http://yost.genetics.utah.edu/software.php

A software analysis pipeline for mapping mutations using RNA-seq that works without parental strain information, without the requirement of a pre-existing snp map of the organism, and without erroneous assumptions that recombination occurs at the same frequency across the genome. In addition, it compensates for the considerable amount of noise in RNA-seq datasets and simultaneously identifies the region where the mutation lies and generates a list of putative coding region mutations in the linked genomic segment. MMAPPR can utilize RNA-seq datasets from isolated tissues or whole organisms that are often generated for phenotypic analysis and gene network analysis in novel mutants.

Proper citation: MMAPPR (RRID:SCR_005092) Copy   

•   Source: SciCrunch Registry

http://xml.coverpages.org/

Public reference database supporting the XML family of markup language standards, XML vocabularies, and related structured information standards. It promotes and enables the use of open, interoperable, standards-based solutions which protect digital information and enhance the quality of data processing. The Cover Pages web site provides reference material on enabling technologies compatible with SGML/XML descriptive markup language standards and applications: object modeling, semantic nets, ontologies, authority lists, document production systems, and conceptual modeling. It also supplies references for social aspects of distributed and public sector concerns: privacy, open standards, patented technology embedded in standards, etc. NB. This statement and the resource itself are works in progress, subject to continuous revision.

Proper citation: Cover Pages (RRID:SCR_004955) Copy   

•   Source: SciCrunch Registry

http://wellness.wikispaces.com/

Wellness Wiki is offered to help clarify the complex problems plaguing the U.S. healthcare system and develop sustainable ways to improve the health and well-being of all people. This virtual encyclopedia of the healthcare crisis and potential remedies welcomes your comments! The Wellness Wiki Book (Understanding & Curing American Healthcare: A Wise Way to Better Outcomes and Lower Costs) is available for purchase as a softcover book or pdf download. Table of contents: *Introduction & Executive Summary *Defining the Problem *Examining Three Proposed Solutions *Introducing a New Solution - Overview and Benefits, Wellness-Plus Solution Tactics, Barriers and Drivers to Implementing the Wellness-Plus Solution *Conclusion & Epilogue *Appendix *Wellness Model Technology Blueprint

Proper citation: Wellness Wiki (RRID:SCR_004957) Copy   

•   Source: SciCrunch Registry

http://www.mycobank.org/

Database documenting mycological nomenclatural novelties (new names and combinations) and associated data, for example descriptions and illustrations. The nomenclatural novelties will each be allocated a unique MycoBank number that can be cited in the publication where the nomenclatural novelty is introduced. These numbers will also be used by the nomenclatural database Index Fungorum, with which MycoBank is associated and will also serve as Life Science Identifiers (LSIDs). Nomenclatural experts will be available to check the validity, legitimacy and linguistic correctness of the proposed names in order to avoid nomenclatural errors; however, no censorship whatsoever, (nomenclatural or taxonomic) will be exerted by MycoBank. Deposited names will remain -when desired- strictly confidential until after publication, and will then be accessible through MycoBank, Index Fungorum, GBIF and other international biodiversity initiatives, where they will further be linked to other databases to realize a species bank that eventually will link all databases of life. MycoBank will (when applicable) provide onward links to other databases containing, for example, living cultures, DNA data, reference specimens and pleomorphic names linked to the same holomorph. Authors intending to publish nomenclatural novelties are encouraged to contribute to this new initiative. For the moment 2 search engines are available from the MycoBank website. The first one permits to search for fungal names (at any rank level), the authority or the MycoBank unique number. The second is dedicated to bibliographic queries related to fungal name''''s publications. MycoBank users willing to deposit their data will have to register so that they willbe able to contact the depositor for specific information (e.g. MycoBank number, possible points of attention regarding the name, actual publication, etc), and to avoid fake entries.

Proper citation: MycoBank (RRID:SCR_004950) Copy   

•   Source: SciCrunch Registry

http://brainliner.jp

Portal and tools for sharing and editing neurophysiological and behavioral data for brain-machine interface research. Users can search for existing data or login with their Google, Facebook, or Twitter account and upload new data. Their main focus is on supporting brain-machine interface research, so we encourage users to not just provide recordings of brain activity data, but also information about stimuli, etc., so that statistical relationships can be found between stimuli and/or subject behavior and brain activity. The Matlab tools are for writing, reading, and converting Neuroshare files, the common file format. A free, open source desktop tool for editing neurophysiological data for brain-machine interface research is also available: https://github.com/ATR-DNI/BrainLiner Since data formats aren''''t standardized between programs and researchers, data and analysis programs for data cannot be easily shared. Neuroshare was selected as the common file format. Neuroshare can contain several types of neurophysiological data because of its high flexibility, including analog time-series data and neuronal spike timing. Some applications have plug-ins or libraries available that can read Neuroshare format files, thus making Neuroshare somewhat readily usable. Neuroshare can contain several types of neurophysiological data, but there were no easy tools to convert data into the Neuroshare format, so they made and are providing a Neuroshare Converter Library and Simple Converter using the library. In future work they will make and provide many more useful tools for data sharing. Shared experiments include: EMG signal, Takemiya Exp, Reconstruct (Visual image reconstruction from human brain activity using a combination of multi-scale local image decoders), SPIKE data, Speech Imagery Dataset (Single-trial classification of vowel speech imagery using common spatial patterns), Functional Multineuron Calcium Imaging (fMCI), Rock-paper-scissors (The data was obtained from subject while he make finger-form of rock/paper/scissors). They also have a page at https://www.facebook.com/brainliner where you can contact us

Proper citation: BrainLiner (RRID:SCR_004951) Copy   

•   Source: SciCrunch Registry