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http://www.data.gov/

Catalog of data sets that are generated and held by the Federal Government, including data, tools and resources to conduct research, develop web and mobile applications, design data visualizations, etc. Data.gov provides descriptions of the Federal datasets (metadata), information about how to access the datasets, and tools that leverage government datasets. The data catalogs will continue to grow as datasets are added. Federal, Executive Branch data are included in the first version of Data.gov.

Proper citation: Data.gov (RRID:SCR_004712) Copy   

•   Source: SciCrunch Registry

http://www.rhea-db.org/

Manually annotated reaction database where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both elemental and charge balance of the reactions. The database has been populated with the reactions found in the Enzyme Commission (EC) list (and in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalyzed reactions, other biochemical reactions are also included. Rhea is a manually annotated resource and it provides: stable reaction identifiers for each of its reactions; directionality information if the physiological direction of the reaction is known; the possibility to link several reactions together to form overall reactions; extensive cross-references to other resources including enzyme-catalyzed and other metabolic reactions, such as the EC list (in IntEnz), KEGG, MetaCyc and UniPathway; and chemical substructure and similarity searches on compounds in Rhea.

Proper citation: RHEA (RRID:SCR_004713) Copy   

•   Source: SciCrunch Registry

https://www.biodiscovery.com/products/nexus-copy-number?hsLang=en

Software package provides statistical tools. Derives copy number and BAF from variety of NGS data including WES, WGS, targeted panel, and shallow sequencing as well as Microarray data. Multifaceted desktop software for rapid discovery of genomic alterations. Accepts data from various manufacturers and technologies including Infinium GSA and CytoScan XON.

Proper citation: BioDiscovery Nexus Copy Number (RRID:SCR_004557) Copy   

•   Source: SciCrunch Registry

http://www.brt.org.uk/

Brain Research Trust is a Registered Charity (no. 1137560) and a Company Limited by Guarantee (no. 7345516) promoting and supporting vital research. With the help of our donors, Brain Research Trust supports world-class research at University College London''''s Institute of Neurology (IoN), London. We were able to provide a record 2.3m pounds to research grants in the 09/10 financial year and has been supporting its vital research program for almost 40 years. Brain Research Trust comprises a dedicated fundraising team, a supportive Board of Trustees and a knowledgeable Scientific Advisory Panel who all work together closely to ensure your money goes towards the best neurological research projects. Some of the conditions into which we fund research include: Alzheimer''''s Disease, Ataxia, Brain Tumours, Creutzfeldt-Jakob Disease, Dystonia, Epilepsy, Huntington''''s Disease, Migraine, Motor Neurone Disease, Multiple Sclerosis, Parkinson''''s Disease, Progressive Supranuclear Palsy, Stroke. The Institute of Neurology also carries out research into Autism, Aphasia, Guillain-Barre Syndrome, M��ni��re''''s Disease, Multiple Systems Atrophy (MSA), Myasthenia Gravis, Niemann-Pick Disease, Shy-Drager Syndrome, Tay-Sachs Disease and Tourette Syndrome.

Proper citation: Brain Research Trust (RRID:SCR_004678) Copy   

•   Source: SciCrunch Registry

http://www.usidnet.org/

Research consortium to advance scientific research in the primary immune deficiency diseases (PIDD) and: * Assemble and maintain a registry of patients with primary immunodeficiency diseases to provide a minimum estimate of the prevalence of each disorder in the United States. Provide a comprehensive clinical picture of each disorder and act as a resource for clinical and laboratory research. * Establish a multifaceted mentoring program to introduce new investigators into the field and stimulate interest and research in primary immune deficiency diseases. * Establish an advisory/review committee to maintain a cell/DNA Repository of biologic material from well-characterized PIDD patients for the advancement of scientific research USIDNET operates a large database of patient information for your use. The purpose and scope of this project is to assemble and maintain a registry of residents with primary immunodeficiency diseases. The project was started with the Registry of U.S. Residents with Chronic Granulomatous Disease. Since then, the registry has been expanded and now collects data on all primary immunodeficiency disorders. The following are just a few of the diseases housed in the registry: Chronic Granulomatous Disease, Common Variable Immunodeficiency Disease, DiGeorge Anomaly, Hyper IgM Syndrome, Leukocyte Adhesion Defect, Severe Combined Immunodeficiency Disease, Wiskott-Aldrich Syndrome, X-Linked Agammaglobulinemia Physicians who would like to register their patients or access the registry are encouraged to contact Onika Davis or Lamar Hamilton, USIDNET team, at odavis (at) primaryimmune.org, or lhamilton (at) primaryimmune.org

Proper citation: USIDNET: US Immunodeficiency Network (RRID:SCR_004672) Copy   

•   Source: SciCrunch Registry

http://primaryimmune.org/

National non-profit patient organization dedicated to improving the diagnosis, treatment and quality of life of persons with primary immunodeficiency diseases through advocacy, education and research. One of the greatest challenges faced by individuals diagnosed with primary immunodeficiency disease is finding the right information and resources when they need it. With knowledge and foresight from their personal experience, the Immune Deficiency Foundation (IDF) was founded by families of children with primary immunodeficiency diseases and their physicians to help meet those needs. It is with the spirit and energy of this keen perspective that IDF exists today, thriving as an organization dedicated to individuals living with primary immunodeficiencies. Since 1980, IDF has provided accurate and timely information for the nearly quarter-million Americans who have been diagnosed with a primary immunodeficiency disease. Governed by a Board of Trustees and supported by a Medical Advisory Committee comprised of some of the world''s leading clinical immunologists, as well as hundreds of grassroots volunteers and a compassionate, professional staff IDF has provided individuals and their families with vital knowledge and made tremendous strides in: * Helping the patient and medical community gain a broader understanding of primary immunodeficiency diseases through education and outreach efforts; * Promoting, participating, and funding research that has helped characterize primary immunodeficiency diseases and given patients and physicians substantially improved treatment options; * Addressing patient needs through public policy programs by focusing on issues such as insurance reimbursement, patient confidentiality, ensuring the safety and availability of immune globulin therapy, and maintaining and enhancing patient access to treatment options. Today, thousands of individuals and families affected by primary immunodeficiency diseases depend on IDF for advocacy, education and empowerment.

Proper citation: Immune Deficiency Foundation (RRID:SCR_004674) Copy   

•   Source: SciCrunch Registry

http://metagenomics.atc.tcs.com/binning/ProViDE/

A similarity based binning algorithm that uses a customized set of alignment parameter thresholds / ranges, specifically suited for the accurate taxonomic labelling of viral metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ProViDE (RRID:SCR_004709) Copy   

•   Source: SciCrunch Registry

http://caintegrator-info.nci.nih.gov/rembrandt

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. REMBRANDT is a data repository containing diverse types of molecular research and clinical trials data related to brain cancers, including gliomas, along with a wide variety of web-based analysis tools that readily facilitate the understanding of critical correlations among the different data types. REMBRANDT aims to be the access portal for a national molecular, genetic, and clinical database of several thousand primary brain tumors that is fully open and accessible to all investigators (including intramural and extramural researchers), as well as the public at-large. The main focus is to molecularly characterize a large number of adult and pediatric primary brain tumors and to correlate those data with extensive retrospective and prospective clinical data. Specific data types hosted here are gene expression profiles, real time PCR assays, CGH and SNP array information, sequencing data, tissue array results and images, proteomic profiles, and patients'''' response to various treatments. Clinical trials'''' information and protocols are also accessible. The data can be downloaded as raw files containing all the information gathered through the primary experiments or can be mined using the informatics support provided. This comprehensive brain tumor data portal will allow for easy ad hoc querying across multiple domains, thus allowing physician-scientists to make the right decisions during patient treatments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Repository of molecular brain neoplasia data (RRID:SCR_004704) Copy   

•   Source: SciCrunch Registry

http://www.arabidopsis.org

Database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from data pages to other Arabidopsis resources. The data can be searched, viewed and analyzed. Datasets can also be downloaded. Pages on news, job postings, conference announcements, Arabidopsis lab protocols, and useful links are provided.

Proper citation: TAIR (RRID:SCR_004618) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/souravc/compostbin

A DNA-composition-based binning algorithm for classifying metagenomic reads. It has the ability to accurately bin raw sequence reads without need for assembly or training. It applies principal component analysis to project the data into an informative lower-dimensional space, and then uses the normalized cut clustering algorithm on this filtered data set to classify sequences into taxon-specific bins.

Proper citation: CompostBin (RRID:SCR_004619) Copy   

•   Source: SciCrunch Registry

http://www.genedb.org/Homepage/Lmajor

Database of the most recent sequence updates and annotations for the L. major genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The Pathogen Genomics group at the Wellcome Trust Sanger Institute played a major role in sequencing the genome of Leishmania major (see Ivens et al.) Details of the centres involved and which chromosomes they sequenced, are given. The sequence data were obtained by adopting several parallel approaches, including complete cosmid sequencing, whole chromosome shotguns and/or BAC sequencing/skimming. The Leishmania parasite is an intracellular pathogen of the immune system targeting macrophages and dendritic cells. The disease Leishmaniasis affects the populations of 88 counties worldwide with symptoms ranging from disfiguring cutaneous and muco-cutaneous lesions that can cause widespread destruction of mucous membranes to visceral disease affecting the haemopoetic organs. In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries.

Proper citation: GeneDB Lmajor (RRID:SCR_004613) Copy   

•   Source: SciCrunch Registry

https://github.com/HIITMetagenomics/dsm-framework

Software package providing distributed string mining for High-Throughput Sequencing data that provides a content-based exploration and retrieval method for whole metagenome sequencing samples.

Proper citation: Distributed String Mining Framework (RRID:SCR_004736) Copy   

•   Source: SciCrunch Registry

http://bioinfo.au.tsinghua.edu.cn/subMito/

SubMito is the first computational system for predicting protein submitochondria locations from its primary sequence. SubMito is designed and implemented with Java. This site is a web-like front end for SubMito system. Users can access SubMito on the server side by uploading a FASTA file or entering sequence below. The prediction result will be saved on server, and a link to the result file will be provided. Since there may be several sessions running at the same time on the server, the responding of the server side SubMito may be very slow. Another way to use SubMito is to download a local version of the software. The online service can accept 2 forms of input. One is single sequence, the other is uploaded FASTA file. If you want to predict submitochondria location for a single sequence, you can paste your sequence in the text box. Optionally, you can choose to write some remarks in the text field labeling Enter your remark. Then, press the Submit button to perform the prediction. The result will be saved in a FASTA format file, and you can download it at any time in the coming 48 hours.

Proper citation: SubMito (RRID:SCR_004572) Copy   

•   Source: SciCrunch Registry

http://dcoe.health.mil/

The Defense Centers of Excellence for Psychological Health and Traumatic Brain Injury (DCoE) was established in November 2007 to integrate knowledge and identify, evaluate and disseminate evidence based practices and standards for the treatment of psychological health and TBI within the Defense Department. DCoE is part of the Military Health System, which provides a ''continuum of care'' from initial accession to deployment to discharge. DCoE works across the entire continuum of care to promote resilience, rehabilitation and reintegration for warriors, families and veterans with psychological health concerns and traumatic brain injuries. DCoE leads a groundbreaking collaborative effort that includes the Department of Veterans Affairs (VA), civilian agencies, community leaders, advocacy groups, clinical experts and academic institutions that are dedicated to expanding the state of knowledge of psychological health and TBI. In addition, DCoE''s Real Warriors Campaign is working to encourage help-seeking behavior for warriors with post-traumatic stress or mTBI. DCoE brings together six directorates and three centers. Their joint goal is to maximize opportunities for warriors and families to thrive through a collaborative global network to promote resilience, recovery and reintegration for PH and TBI.

Proper citation: Defense Centers of Excellence for Psychological Health and Traumatic Brain Injury (RRID:SCR_004696) Copy   

•   Source: SciCrunch Registry

http://www.the-scientist.com/

The Scientist is the magazine for life science professionalsa print and digital publication dedicated to covering a wide range of topics central to the study of cell and molecular biology, genetics, and other life-science fields. Through innovative print articles, online stories, and multimedia features, the magazine explores the latest scientific discoveries, trends in research, innovative techniques, new technology, business, and careers. It is read by leading researchers in industry and academia who value penetrating analyses and broad perspectives on life-science topics both within and beyond their areas of expertise. Written by prominent scientists and professional journalists, articles in The Scientist are concise, accurate, accessible, and entertaining.

Proper citation: The Scientist (RRID:SCR_004607) Copy   

•   Source: SciCrunch Registry

http://www.bioreclamationivt.com/

BioIVT, formerly BioreclamationIVT, is global provider of biological specimens and services. Provides biological and in vitro products specializing in control and disease state matrices manufactured from human and animal whole blood, plasma, serum, tissues and other fluids which are used in drug discovery, compound development, clinical and research diagnostics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bioreclamation (RRID:SCR_004728) Copy   

•   Source: SciCrunch Registry

https://tobiasrausch.com/delly/

Integrated structural variant prediction software that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout genome.

Proper citation: DELLY (RRID:SCR_004603) Copy   

•   Source: SciCrunch Registry

http://i.cs.hku.hk/~alse/MetaCluster/

A software for binning and annotating short paired-end reads.

Proper citation: MetaCluster-TA (RRID:SCR_004599) Copy   

•   Source: SciCrunch Registry

http://eyewiki.aao.org/Main_Page

EyeWiki is an ophthalmic wiki where ophthalmologists, other physicians, patients and the public can view an eye encyclopedia of content written by ophthalmologists covering the vast spectrum of eye disease, diagnosis and treatment. Any qualified ophthalmologist, or ophthalmologist in training, is invited to contribute content to the wiki and post it immediately. Categories: *Cataract / Anterior Segment *Cornea / External Disease *Glaucoma *Miscellaneous *Neuro-ophthalmology / Orbit *Oculoplastics / Orbit *Oncology / Pathology *Pediatric Ophthalmology / Strabismus *Refractive Management / Intervention *Retina / Vitreous *Uveitis

Proper citation: EyeWiki (RRID:SCR_004595) Copy   

•   Source: SciCrunch Registry

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

Nucleotide database as collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.

Proper citation: Nucleotide database (RRID:SCR_004630) Copy   

•   Source: SciCrunch Registry