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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.meduniwien.ac.at/kin/index.html

The (Clinical) Institute of Neurology (IN) of the Medical University Vienna was founded in 1882 by Heinrich Obersteiner. It is the oldest institution embracing the multidisciplinarity of neurosciences and has served as model for the establishment of similarly designed institutions in many countries. The original location of the then Neurological Institute in Vienna was at Schwarzspanierstrasse. Since 1993, IN is located in the Vienna General Hospital in top-class laboratory facilities. IN is committed to its proud tradition as Obersteiner Institute and to a promising future of a nationally and internationally leading institution in the clinical neurosciences. Our work aims to translate the understanding of nervous diseases to the development of novel therapeutics and diagnostics. IN''''s tasks include diagnostic patient service, research and graduate / postgraduate teaching in neuropathology, neurochemistry, and neuro-molecular biology in an integrated way. Neuropathology is a recognized medical specialty in Austria. It analyzes structural changes of nervous tissues in disease. Diagnostic neuropathology makes use of most modern morphological techniques applied to diseased central, peripheral and vegetative nervous tissues and fluids, and muscle. Neuropathological diagnoses are a basis for disease classification and rational therapies. Neurodegenerative disorders, in particular prion diseases, virus diseases affecting the nervous system, and brain tumors (neuro-oncology) are research priorities. In the highly publicized area of prion diseases, IN has developed into a national and international center of excellence and expertise that leads several European, EU-funded networks in prion research. As an indispensable asset, the IN possesses a large brain bank that has systematically collected neuropathological specimens since 1948. Most samples are fixed and paraffin-embedded tissue only, but in a part of neurosurgical, nerve and muscle biopsies and autopsies, also fresh tissue is obtained, frozen and stored at -80 degrees C. Occasionally blood and CSF are also available. The unique neuropathological collection of histological slides, paraffin blocks and formol-fixed nervous tissues now comprises about 16.000 brain autopsies, 30.000 neurosurgical and 7.500 nerve/muscle biopsies. Also a number of cell cultures have been stored, mainly fibroblasts from patients with rare neurometabolic diseases, and primary cultures of brain tumors. IN participates in the EU-supported European Network of Brain Banks BrainNet Europe.

Proper citation: Medical University of Vienna Institute of Neurology (RRID:SCR_005030) Copy   

•   Source: SciCrunch Registry

http://cbil.upenn.edu/BEERS/

A simulation engine for generating RNA-Seq data that was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data. By default BEERS simulates either mouse or human paired-end RNA-Seq data modeled on the illumina platform. It starts with a large number of gene models (approx 500K) taken from about ten different published annotation efforts, and then chooses a fixed number of these genes at random (30,000 by default). This avoids biasing for or against any particular set of annotations. BEERS then introduces substitutions, indels, alternate spice forms, sequencing errors, and intron signal. BEERS can also simulate strand specific reads. BEERS does not simulate quality scores. There are four configuration files required, these are available for human and mouse. BEERS can also be configured to use any set of gene models. Pre-built indexes for human refseq are given. Using these indexes will generate a much tamer set of transcripts. BEERS is written in perl.

Proper citation: BEERS (RRID:SCR_005090) Copy   

•   Source: SciCrunch Registry

http://anntools.sourceforge.net/

Software tool for annotating single nucleotide substitutions (SNP/SNV), small insertions/deletions (indels), and copy number variations (CNV) calls generated from sequencing and microarray data. Only human genome build 37/hg19 can be annotated at this time.

Proper citation: AnnTools (RRID:SCR_005170) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/software/pathseq/

A computational tool for the identification and analysis of microbial sequences in high-throughput human sequencing data that is designed to work with large numbers of sequencing reads in a scalable manner. This process is composed of a subtractive phase in which input reads are subtracted by alignment to human reference sequences, and an analytic phase in which the remaining reads are aligned to microbial reference sequences (viral, fungal, bacterial, archaeal) and de novo assembled. PathSeq is currently available in a cloud computing environment via Amazon Web Services The typical approach one would take to pathogen discovery with PathSeq: RNA or DNA is extracted from the tissue of interest and sequencing libraries are constructed to be run on the next-generation DNA sequencing platform of choice. The resulting sequence data is run through the PathSeq pipeline in a cloud computing environment. PathSeq reports potential microbes in the sequence data as well as the complete set of reads that could not be identified as human or microbial sequences.

Proper citation: PathSeq (RRID:SCR_005203) Copy   

•   Source: SciCrunch Registry

http://cbrc.kaust.edu.sa/readscan/

A highly scalable parallel software program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets.

Proper citation: READSCAN (RRID:SCR_005204) Copy   

•   Source: SciCrunch Registry

http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html

An algorithmic software tool for detecting known viruses and their integration sites using next-generation sequencing of human cancer tissue. VirusSeq takes FASTQ files (paired-end reads) as input.

Proper citation: VirusSeq (RRID:SCR_005206) Copy   

•   Source: SciCrunch Registry

http://omrf.org/

A biomedical research institute that aims to understand and develop more effective treatments for human disease, focusing on critical research areas such as heart disease, cancer, lupus and Alzheimer's disease.

Proper citation: Oklahoma Medical Research Foundation (RRID:SCR_005287) Copy   

•   Source: SciCrunch Registry

http://research.cs.wisc.edu/wham/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. High-throughput sequence alignment tool that aligns short DNA sequences (reads) to the whole human genome at a rate of over 1500 million 60bps reads per hour, which is one to two orders of magnitudes faster than the leading state-of-the-art techniques. Feature list for the current version (v 0.1.5) of WHAM: * Supports paired-end reads * Supports up to 5 errores * Supports alignments with gaps * Supports quality scores for filtering invalid alignments, and sorting valid alignments * finds ALL valid alignments * Supports multi-threading * Supports rich reporting modes * Supports SAM format output

Proper citation: WHAM (RRID:SCR_005497) Copy   

•   Source: SciCrunch Registry

https://alleninstitute.org/

Non profit bioscience research organization in Seattle, Washington dedicated to accelerating research globally and sharing that data within the science community. Allen Institute for Brain Science, Allen Institute for Cell Science, Allen Institute for Immunology, and The Paul G. Allen Frontiers Group are four divisions of this Institute with commitment to open science model within its research institutes.

Proper citation: Allen Institute (RRID:SCR_005435) Copy   

•   Source: SciCrunch Registry

http://apps.cytoscape.org/apps/jepetto

A Cytoscape plugin that performs integrated gene set analysis using information from interaction, pathways and processes databases. The plugin integrates information from three separate web servers specializing in enrichment analysis, pathways expansion and topological matching. It uses the TopoGSA server to identify topological analogies between the user selected gene set and the known pathways and processes. TopoGSA finds the most similar biological mechanism using the topological features of the interaction network of a user selected gene set. It is also able to suggest genes related to the query gene set using two pathway analysis servers EnrichNet and PathExpand. Both these servers are using a different topological matching algorithms that extends the query gene set with genes from the pathway databases. This integration substantially simplifies the analysis of user gene sets and the interpretation of the results.

Proper citation: JEPETTO (RRID:SCR_005909) Copy   

•   Source: SciCrunch Registry

http://www.mirecc.va.gov/

The Mental Illness Research, Education and Clinical Centers (MIRECC) were established by Congress with the goal of researching the causes and treatments of mental disorders and using education to put new knowledge into routine clinical practice in the VA. Congress established MIRECCs in October 1996 through Public Law 104-262. There are currently 10 MIRECCs. Each MIRECC focuses on mental illnesses or conditions that are common in Veterans. MIRECCs investigate the causes of mental illness, develop new treatments for mental illness, and evaluate both established and new treatments with the goal of identifying best practices. The MIRECCs also develop educational and training initiatives to implement best practices into the clinical settings of the VA. Each MIRECC works with all the facilities in its network (region) on research, education and clinical initiatives, evaluating services offered to the Veteran and helping the networks implement improved treatments, services, or practices. Several educational products are posted on this site on the Products page. These materials are in the public domain and available for your use. Many MIRECCs have additional materials that can be downloaded from their web sites or are available by request.

Proper citation: Mental Illness Research Education and Clinical Center (RRID:SCR_006956) Copy   

•   Source: SciCrunch Registry

http://www.alz.org/

A non profit organization dedicated to providing support for patients and families with Alzheimer's disease, to educating the public about the disease, to funding a wide range of Alzheimer's disease related research and to finding ways to treat and eventually to prevent Alzheimer's disease. Resources include: the Alzheimer's Association Green-Field Library, a research grants program, and the Journal of the Alzheimer's Association.

Proper citation: Alzheimers Association (RRID:SCR_007398) Copy   

•   Source: SciCrunch Registry

http://www.arvo.org/

An eye and vision research organization whose goal is to encourage and assist research, training, publication, and dissemination of knowledge in vision and ophthalmology. ARVO membership is comprised of more than 11,500 individuals. Some 42% of members reside in over 70 countries outside the U.S. The membership is multidisciplinary and consists of both clinical and basic researchers (approximately 44% MD/Ophthalmologists, 26% PhDs, and 30% Other, including optometrists, osteopaths, and veterinarians). ARVO is governed by a Board of Trustees, who are elected from candidates put forth by the 13 Scientific Sections.

Proper citation: Association for Research in Vision and Ophthalmology (RRID:SCR_007400) Copy   

•   Source: SciCrunch Registry

http://www.kreftregisteret.no/en/

Comprises 3 registries of cancer patients in Norway: the Incidence Registry, the Clinical Registry and Cancer Statistics. The Incidence Registry contains the basic data items collected from clinicians and pathologists, as well as from administrative discharge and mortality sources. It is updated continuously with information on both new cases, as well as cases diagnosed in previous years. All medical doctors in the country are instructed by law to notify new cancer cases. Clinical Registries: Registration of treatment and follow-up of Norwegian cancer patients. Clinical registries comprehensive registration schemes dedicated to specific cancers have been established to include detailed information on diagnostic measures, therapy, and follow-up. Cancer Statistics: Database of cancer statistics. The Cancer Registry of Norway is maintained by the Institute of Population-based Cancer Research and established in 1951. It is one of the oldest national cancer registries in the world. This, combined with the unique personal identification number used in Norway, makes the Cancer Registry''s data suitable, also internationally; by establishing new knowledge through research and spreading information on cancer.

Proper citation: Cancer Registry of Norway (RRID:SCR_008879) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/antsr

An R extension to ANTs that performs multivariate statistical parametric mapping of DTI, T1 and other datatypes for the purpose of both performing clinical studies and for tracking the performance of ANTs (and other) image processing methodologies. ANTsR depends upon the R statistical language, bash scripts and the ANTs toolkit. Some branches of ANTsR will also depend upon pipedream and specific datasets. Some of these datasets will be open access and, in that case, ANTsR will provide a 100% reproducible neuroimaging study on that data.

Proper citation: ANTsR (RRID:SCR_008891) Copy   

•   Source: SciCrunch Registry

http://www.fisherbioservices.com/

Biological material management services provider including biospecimen storage, biobanking services, specimen collection kits, sample processing, DNA /RNA extraction and amplification, sample storage, distribution, and clinical trial support. They also offer transport and storage of active pharmaceutical ingredient(s) (API and bio-API), including cryogenic. They can assist with public health research, phase I???????????????IV studies, prospective and retrospective studies, IND/NDA submissions to the FDA, and entry of biotherapeutics into the commercial marketplace.

Proper citation: Fisher BioServices (RRID:SCR_010528) Copy   

•   Source: SciCrunch Registry

http://www.surgicalbio.com

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 2nd, 2022. Tissue bank and service organization for bioimplants.

Proper citation: Surgical Biologics - a MiMedx Group Company (RRID:SCR_010661) Copy   

•   Source: SciCrunch Registry

http://www.abh.com

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 2nd, 2022. Manufacturer of Dermagraft, a bio-engineered skin substitute that assists in restoring damaged tissue and supports the body's natural healing process.

Proper citation: Advanced Biohealing, Inc. (RRID:SCR_010630) Copy   

•   Source: SciCrunch Registry

https://esp.gs.washington.edu/

Project focused on understanding the contribution of rare genetic variation to heart, lung and blood disorders through the sequencing of well-phenotyped populations.

Proper citation: NHLBI Grand Opportunity Exome Sequencing Project (RRID:SCR_010798) Copy   

•   Source: SciCrunch Registry