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http://dgv.tcag.ca/dgv/app/home

Public repository that accepts direct submissions and provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species. Variants are accessioned at the study and sample level, granting stable identifiers that can be used in publications. DGVa data is integrated with other EBI resources, including comprehensive EBI search and Ensembl genome browser. Exchanges data with companion database, dbVar, at National Center for Biotechnology Information.NOTE: since 2019 DGVa doesn't accept submissions. Please send the data for submission to European Variation Archive (EVA).

Proper citation: Database of Genomic Variants Archive (DGVa) (RRID:SCR_004896) Copy   

•   Source: SciCrunch Registry

http://svmerge.sourceforge.net/

Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available.

Proper citation: SVMerge (RRID:SCR_004777) Copy   

•   Source: SciCrunch Registry

http://jaxmice.jax.org/strain/007910.html

These Brainbow 1.0 (founder line L) mice allow labeling of individual neuronal types (specifically hippocampal neuron cell bodies, and including motor neurons, dentate gyrus granule cells, pyramidal neurons of the cortex and CA1 area) with approximately 166 distinguishable color variations in cre recombined cells, and may also be useful in conjunction with other Brainbow strains (Stock No. 007901, Stock No. 007911, Stock No. 007921) for neurobiological studies. These Thy1-Brainbow 1.0 (line L) transgenic mice are viable and fertile. The mice possess multiple fluorescent protein sequences uniquely flanked with pairs of incompatible Lox sites alternated to create mutually exclusive recombination events; allowing stochastic expression of multiple fluorescent proteins from a single transgene. Prior to Cre-mediated recombination, the fluorescent protein immediately adjacent to the promoter, dTomato (RFP), is expressed in peripheral and central neurons. When bred to Cre recombinase expressing mice, the resulting offspring can have one of three expression outcomes for each transgene in each cell of the cre expressing tissue(s): dTomato (RFP) (no recombination), mCerulean (CFP), or mYFP. Integration of tandem transgene copies yields combinatorial fluorescent protein expression in each cell, and thus many possible cell colors, providing a way to distinguish adjacent neurons and visualize other cellular interactions. Of note, the single FRT site inserted in the transgene allows tandem transgene copy number reduction through Flp-mediated recombination if desired. These Brainbow 1.0 (founder line L) mice were found to have multiple transgene copies that allow labeling of individual neuronal types (specifically hippocampal neuron cell bodies, and including motor neurons, dentate gyrus granule cells, pyramidal neurons of the cortex and CA1 area) with approximately 166 distinguishable color variations in cre recombined cells, and may also be useful in conjunction with other Brainbow strains (Stock No. 007901, Stock No. 007911, Stock No. 007921) for neurobiological studies. This mouse can be used to support research in many areas including:
Neurobiology Research
* Cre-lox System (loxP-flanked Sequences)
* Fluorescent protein expression in neural tissue
Research Tools
* Cre-lox-System (loxP-flanked Sequences: Test/Reporter)
* Developmental Biology Research (Cre-lox system)
* Developmental Biology Research (transplantation marker for embryonic and adult tissue)
* FLP-FRT System (FRT-flanked Sequences)
* Fluorescent Proteins * Genetics Research (Mutagenesis and Transgenesis: Cre-lox system) * Genetics Research (Tissue/Cell Markers: Cre-lox system) * Genetics Research (Tissue/Cell Markers: astrocyte-specific marker) * Genetics Research (Tissue/Cell Markers: astrocytes) * Genetics Research (Tissue/Cell Markers: astrocytes, neurons) * Genetics Research (Tissue/Cell Markers: glial cells) * Genetics Research (Tissue/Cell Markers: multiple) * Genetics Research (Tissue/Cell Markers: neurons) * Genetics Research (Tissue/Cell Markers: transplantation marker for embryonic and adult tissue) * Neurobiology Research (astrocyte-specific marker) * Neurobiology Research (cell marker) * YFP related Research Tools * Fluorescent Proteins Control: 000664 C57BL/6J (approximate)

Proper citation: Brainbow mouse resource at Jackson Labs (RRID:SCR_004894) Copy   

•   Source: SciCrunch Registry

http://seqanswers.com/

An information resource and user-driven community focused on all aspects of next-generation genomics. They hope to become the central location for next generation sequencing technology discussion and education. The site will always attempt to cater to everyone, regardless of scientific background or knowledge. The High-Throughput Sequencing Map site was conceived by James Hadfield (Cancer Research UK, Cambridge) and built by Nick Loman (University of Birmingham). The database is as only as good as you, the users.

Proper citation: SEQanswers (RRID:SCR_004808) Copy   

•   Source: SciCrunch Registry

http://www.engr.uconn.edu/~jiz08001/svseq2.html

Software for accurate and efficient calling of structural variations with low-coverage sequence data. Version 2 uses the BAM files of paired Illumina reads with soft-clip signature as input. It calls both deletions and insertions.

Proper citation: SVseq (RRID:SCR_004804) Copy   

•   Source: SciCrunch Registry

http://www.science3point0.com/coaspedia/index.php/Welcome

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. Wiki serving as a demo for integrating wikis with scientific workflows, extending peer review and open access from formal scholarly publishing to the whole research cycle. Just imagine you could browse science as it happens. It is intended to be launched, as a prototype, in early 2011, and any help with it is welcome just create an account and mention here how you would like to get involved. In the initial phase, the platform will primarily be used to simply archive copies of scholarly articles that were formally published under an Open license. This WikiRepository shall provide a unified front-end to search, discover and sort all these Open Access papers, and to annotate, share, bookmark and discuss them. Later on, it is intended to be complemented by a formal publishing platform, WikiJournal. From the start on, emphasis will be placed on updatability of published research, on placing new research in the context of existing knowledge as well as ongoing and even planned research on the matter, and of the communities concerned.

Proper citation: Daniel Mietchens demo wiki: What would scholarly communication look like if it were invented today? (RRID:SCR_004805) Copy   

•   Source: SciCrunch Registry

http://www.biobanks.se/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. The National Biobank Program is a joint national program of two Swedish investments on functional genomics, Swegene and Wallenberg Consortium North. This web-site is intended as an information resource on biobanks in Sweden, where knowledge about the Swedish biobanking system is mediated and the progress of the National Biobanking Program is presented. You will also find a list of individual Swedish biobanks. The main objectives of the National Biobank Program are: * to increase the knowledge of the Swedish biobanking system * to increase the quality of Swedish biobanks * to increase usability and availability of samples stored in Swedish biobanks for use in research, diagnosis and treatment * to increase the safety of the providers of samples by stimulating increased protection of the personal integrity and increased ethical awareness The National Biobank Program works through financing of strategic investments to improve biobanking systems of national interest. The program has a budget of SEK 26.4 million for the period of 2002 to 2003.

Proper citation: Swedish National Biobank Program (RRID:SCR_004889) Copy   

•   Source: SciCrunch Registry

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://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   

•   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://www.jcamp-dx.org/

An International Union of Pure and Applied Chemistry (IUPAC) subcommittee that deals with individual projects related to technique-specific data standards as well as generic issues. There are worrying gaps in the coverage of known chemistry by reference spectroscopic databases, which are unlikely to be filled by the activities of the commercial sector alone. The IS-DB offers the scientific community the opportunity to share their spectra and develop a vital resource for future generations. Such a collection of spectra will help to provide significant improvements in human health, new materials, environmental protection, sustainable development and educational progress. XML in Chemistry is a new IUPAC initiative to bring a degree of regulation to this important and rapidly expanding field. They aim to facilitate the validation of data dictionaries for various groups developing ontologies expressed in XML in the broad field of Chemistry. This will help to reduce duplication of effort around the world and allow development projects to build on the work previous groups concentrating on their own innovative goals rather than wasting time and effort re-inventing wheels. IUPAC encourages the submission of projects in all areas of chemistry relevant to its work. If you believe there is a need for a new scientific data standard in your field and wish to know more about how to form a limited term task group to get the standard developed please contact the subcommittee.

Proper citation: IUPAC CPEP Subcommittee on Electronic Data Standards (RRID:SCR_005082) Copy   

•   Source: SciCrunch Registry

http://krasnow1.gmu.edu/cn3/hippocampus3d/

Data files for a high resolution three dimensional (3D) structure of the rat hippocampus reconstructed from histological sections. The data files (supplementary data for Ropireddy et al., Neurosci., 2012 Mar 15;205:91-111) are being shared on the Windows Live cloud space provided by Microsoft. Downloadable data files include the Nissl histological images, the hippocampus layer tracings that can be visualized alone or superimposed to the corresponding Nissl images, the voxel database coordinates, and the surface rendering VRML files. * Hippocampus Nissl Images: The high resolution histological Nissl images obtained at 16 micrometer inter-slice distance for the Long-Evans rat hippocampus can be downloaded or directly viewed in a browser. This dataset consists of 230 jpeg images that cover the hippocampus from rostral to caudal poles. This image dataset is uploaded in seven parts as rar files. * Hippocampus Layer Tracings: The seven hippocampus layers ''ML, ''GC'', ''HILUS'' in DG and ''LM'', ''RAD'', ''PC'', ''OR'' in CA were segmented (traced) using the Reconstruct tool which can be downloaded from Synapse web. This tool outputs all the tracings for each image in XML format. The XML tracing files for all these seven layers for each of the above Nissl images are zipped into one file and can be downloaded. * Hippocampus VoxelDB: The 3D hippocampus reconstructed is volumetrically transformed into 16 micrometer sized voxels for all the seven layers. Each voxel is reported according to multiple coordinate systems, namely in Cartesian, along the natural hippocampal dimensions, and in reference to the canonical brain planes. The voxel database file is created in ascii format. The single voxel database file was split into three rar archive files. Please note that the three rar archive files should be downloaded and decompressed in a single directory in order to obtain the single voxel data file (Hippocampus-VoxelDB.txt). * 3D Surface Renderings: This is a rar archive file with a single VRML file containing the surface rendering of DG and CA layers. This VRML file can be opened and visualized in any VRML viewer, e.g. the open source software view3dscene. * 3D Hippocampus Movie: This movie contains visualization of the 3D surface renderings of CA (blue) and DG (red) inner and outer boundaries; neuronal embeddings of DG granule and CA pyramidal dendritic arbors; potential synapses between CA3b interneuron axon and pyramidal dendrite, and between CA2 pyramidal axon and CA pyramidal dendrites.

Proper citation: Hippocampus 3D Model (RRID:SCR_005083) Copy   

•   Source: SciCrunch Registry

http://www.iupac.org/

Recognized as the world authority on chemical nomenclature, terminology, standardized methods for measurement, atomic weights and many other critically evaluated data, this scientific, international, non-governmental and objective body addresses many global issues involving the chemical sciences. It serves to advance the worldwide aspects of the chemical sciences and to contribute to the application of chemistry in the service of Humankind. The Union sponsors major international meetings that range from specialized scientific symposia to CHEMRAWN meetings with societal impact. * Projects: IUPAC encourages the submission of projects in all areas of chemistry relevant to its work. * Publications: IUPAC publishes books, journals, electronic resources, and issues many reports in all areas of chemistry * Conferences: Each year IUPAC sponsors a large number of symposia that cover a wide range of specialized topics in chemistry. * Members and bodies: Chemists throughout the world are engaged on a voluntary basis in the scientific work of IUPAC.

Proper citation: IUPAC (RRID:SCR_005084) Copy   

•   Source: SciCrunch Registry

http://minia.genouest.org/

A short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.

Proper citation: Minia (RRID:SCR_004986) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.huji.ac.il/NucPosition/TemplateFiltering/Home.html

A software pipeline for analyzing deep sequencing maps of chromatin structure.

Proper citation: TemplateFilter (RRID:SCR_004980) Copy   

•   Source: SciCrunch Registry

http://www.anthonynolan.org/

Stem cell and bone marrow register in the United Kingdom, managing and recruiting donors internationally for patients who require stem cell transplants. A database of tissue-typing results of all prospective donors is maintained. A national cord blood program consisting of both a cord blood bank and a research institute provides donated umbilical cord blood for use in clinical transplants and research. Research is conducted in immunogenetics, immunotherapy, bioinformatics (curating the World Health Organisation HLA Nomenclature database, ensuring that all new tissue types are consistently documented), and immune reconstitution.

Proper citation: Anthony Nolan (RRID:SCR_004982) Copy   

•   Source: SciCrunch Registry

http://www.flyatlas.org/

FlyAtlas gives you a quick answer to the question: where is my gene of interest expressed/enriched in the adult fly? For each gene and tissue, you''re given the mRNA SIGNAL (how abundant the mRNA is), the mRNA ENRICHMENT (compared to whole flies), and the Affymetrix PRESENT CALL (out of 4 arrays, how many times it was detectably expressed). The dataset so far comprises 44 Affymetrix Dros2 expression arrays, each mapping the expression of 18770 transcripts - corresponding to the vast majority of known Drosophila genes. The dataset thus contains over 822800 separate datapoints. This website is intended to make the data easily accessible and comprehensible to mere mortals. FlyAtlas provides the most comprehensive view yet of expression in multiple tissues of Drosophila melanogaster. Meta-analysis of the data shows that a significant fraction of the genome is expressed with great tissue specificity in the adult, demonstrating the need for the functional genomic community to embrace a wide range of functional phenotypes. Well-known developmental genes are often reused in surprising tissues in the adult, suggesting new functions. The homologs of many human genetic disease loci show selective expression in the Drosophila tissues analogous to the affected human tissues, providing a useful filter for potential candidate genes. Additionally, the contributions of each tissue to the whole-fly array signal can be calculated, demonstrating the limitations of whole-organism approaches to functional genomics and allowing modeling of a simple tissue fractionation procedure that should improve detection of weak or tissue-specific signals.

Proper citation: FlyAtlas: the Drosophila gene expression atlas (RRID:SCR_005032) Copy   

•   Source: SciCrunch Registry

http://www.wikidoc.org/index.php/Main_Page

WikiDoc is the Original Medical Wiki / Encyclopedia. 71,700 Textbook Chapters and News Articles in English are available and anyone may edit this medical news service and textbook of medicine. Major sections include WikiDoc News: Today in Medicine, Co-Author The World''s Largest Textbook of Medicine, Community, and Care. WikiDoc is available in other languages including Espa��ol, Fran��ais, Polski, , Rom��n, , and T��rk��e.

Proper citation: WikiDoc The Living Textbook of Medicine (RRID:SCR_004978) Copy   

•   Source: SciCrunch Registry

http://www.fccc.edu/index.html

Fox Chase Cancer Center is the region''s only hospital devoted entirely to cancer treatment, research and prevention. Our 100-bed hospital, located in Philadelphia, is consistently ranked by U.S. News and World Report among the top cancer centers in the nation. Our nationally and internationally recognized staff provides consultations and treatment recommendations for all types of adult cancer. Fox Chase Cancer Center is an independent, nonprofit institution formed in 1974 by the union of American Oncologic Hospital (one the the nation''s first cancer hospitals, established in 1904) and the Institute for Cancer Research (founded in 1927). Fox Chase was also among the first institutions to be designated a National Cancer Institute Comprehensive Cancer Center in 1974. In September 2000, the Hospital of Fox Chase Cancer Center became the nation''s first comprehensive cancer center and Pennsylvania''s first hospital to receive Magnet status for nursing excellence from the American Nurses Credentialing Center, which renewed this honor in 2004 and again in 2009, making it the first hospital in Pennsylvania to have achieved two successful Magnet renewals. The Women''s Cancer Center builds on Fox Chase''s world-renowned expertise in breast and gynecologic cancers. The Center offers women a place where they can receive coordinated, state-of-the-art care, support services, and education all under one roof.

Proper citation: Fox Chase Cancer Center (RRID:SCR_004974) Copy   

•   Source: SciCrunch Registry

http://www.uma.es/

Public university ranked established in 1972. Courses taught entirely in English, related to the world of business, engineering, culture, art and Spanish society.

Proper citation: University of Malaga; Andalusia; Spain (RRID:SCR_004975) Copy   

•   Source: SciCrunch Registry