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

A software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions.

Proper citation: ngs.plot (RRID:SCR_011795) Copy   

•   Source: SciCrunch Registry

http://www.insdc.org/

International collaboration of the International Nucleotide Sequence Databases (INSD), DDBJ, ENA, and GenBank, maintained for over 18 years. Individuals submitting data to the international sequence databases should be aware of INSDC policy.

Proper citation: INSDC (RRID:SCR_011967) Copy   

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http://SchistoDB.net

SchistoDB is a genomic database for the parasitic organism Schistosoma mansoni, one of the major causative agents of schistosomiasis worldwide. It currently incorporates sequences and annotation for S. mansoni in a single user-friendly database. Several genomic scale analyses are available as well as ESTs, oligonucleotides, metabolic pathways and drugs. Make your data available: If you''d like to have your updates and/or datasets integrated in SchistoDB, drop us an email.

Proper citation: Schistosoma mansoni Database (RRID:SCR_004341) Copy   

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http://nematode.lab.nig.ac.jp/

Expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from their expression pattern project and to make the data available to the scientific community. Information available in the current version is as follows: * Map: Visual expression of the relationships among the cosmids, predicted genes and the cDNA clones. * Image: In situ hybridization images that are arranged by their developmental stages. * Sequence: Tag sequences of the cDNA clones are available. * Homology: Results of BLASTX search are available. Users of the data presented on our web pages should not publish the information without our permission and appropriate acknowledgment. Methods are available for: * In situ hybridization on whole mount embryos of C.elegans * Protocols for large scale in situ hybridization on C.elegans larvae

Proper citation: NEXTDB (RRID:SCR_004480) Copy   

•   Source: SciCrunch Registry

http://www.who.int/ictrp/en/

Public database of information about all clinical trials involving humans, this global initiative provides a single point of access to information about ongoing and completed clinical trials. It contains the trial registration data sets made available by data providers around the world meeting criteria for content and quality control. It also aims to: * To improve the comprehensiveness, completeness and accuracy of registered clinical trial data * To communicate and raise awareness of the need to register clinical trials * To ensure the accessibility of registered data * To build capacity for clinical trial registration * To encourage the utilization of registered data * To ensure the sustainability of the ICTRP The mission of the WHO International Clinical Trials Registry Platform is to ensure that a complete view of research is accessible to all those involved in health care decision making. This will improve research transparency and will ultimately strengthen the validity and value of the scientific evidence base. The registration of all interventional trials is a scientific, ethical and moral responsibility. The ICTRP: * Publishes the ICTRP Search Portal * Supports the WHO Registry Network * Supports countries and regions wanting to establish WHO-compliant clinical trial registries or policies on trial registration.

Proper citation: WHO International Clinical Trials Registry Platform (RRID:SCR_004475) Copy   

•   Source: SciCrunch Registry

http://www.digimorph.org/

A dynamic archive of information on digital morphology and high-resolution X-ray computed tomography of biological specimens serving imagery for more than 750 specimens contributed by almost 150 collaborating researchers from the world''s premiere natural history museums and universities. Browse through the site and see spectacular imagery and animations and details on the morphology of many representatives of the Earth''s biota. Digital Morphology, part of the National Science Foundation Digital Libraries Initiative, develops and serves unique 2D and 3D visualizations of the internal and external structure of living and extinct vertebrates, and a growing number of ''invertebrates.'' The Digital Morphology library contains nearly a terabyte of imagery of natural history specimens that are important to education and central to ongoing cutting-edge research efforts. Digital Morphology visualizations are now in use in classrooms and research labs around the world and can be seen in a growing number of museum exhibition halls. The Digital Morphology site currently presents: * QuickTime animations of complete stacks of serial CT sections * Animated 3D volumetric movies of complete specimens * Stereolithography (STL) files of 3D objects that can be viewed interactively and rapidly prototyped into scalable physical 3D objects that can be handled and studied as if they were the original specimens * Informative introductions to the scanned organisms, often written by world authorities * Pertinent bibliographic information on each specimen * Useful links * A course resource for our ''Digital Methods for Paleontology'' course, in which students learn how to generate all of the types of imagery displayed on the Digital Morphology site

Proper citation: DigiMorph (RRID:SCR_004416) Copy   

•   Source: SciCrunch Registry

https://www.med.unc.edu/pgc/

Consortium conducting meta-analyses of genome-wide genetic data for psychiatric disease. Focused on autism, attention-deficit hyperactivity disorder, bipolar disorder, major depressive disorder, schizophrenia, anorexia nervosa (AN), Tourette syndrome (TS), and obsessive-compulsive disorder (OCD). Used to investigate common single nucleotide polymorphisms (SNPs) genotyped on commercial arrays, structural variation (copy number variation) and uncommon or rare genetic variation. To participate you are asked to upload data from your study to central computer used by this consortium. Genetic Cluster Computer serves as data warehouse and analytical platform for this study . When data from your study have been incorporated, account will be provided on central server and access to all GWAS genotypes, phenotypes, and meta-analytic results relevant to deposited data and participation aims. NHGRI GWAS Catalog contains updated information about all GWAS in biomedicine, and is usually excellent starting point to find comprehensive list of studies. Files can be obtained by any PGC member for any disease to which they contributed data. These files can also be obtained by application to NIMH Genetics Repository. Individual-level genotype and phenotype data requires application, material transfer agreement, and informed consent consideration. Some datasets are also in controlled-access dbGaP and Wellcome Trust Case-Control Consortium repositories. PGC members can also receive back cleaned and imputed data and results for samples they contributed to PGC analyses.

Proper citation: Psychiatric Genomics Consortium (RRID:SCR_004495) Copy   

•   Source: SciCrunch Registry

http://www.fishbase.org/home.htm

A global species database and encyclopedia of over 32,800 species and subspecies of fishes that is searchable by common name, genus, species, geography, family, ecosystem, references literature, tools, etc. It links to other, related databases such as the Catalog of Fishes, GenBack, and LarvalBase. It is associated with a partner journal, Acta Ichthyologica et Piscatoria. It is available in English, Greek, Spanish, Portuguese, French, Dutch, Italian, and German. Photo and video submissions are welcome. FishBase 2004 is also available on DVD or CD-ROMs with full information on 28,500 species. It comes together with the FishBase 2000 book and can be ordered for 95 US$ including air-mail.

Proper citation: FishBase (RRID:SCR_004376) Copy   

•   Source: SciCrunch Registry

https://www.bannerhealth.com/research/locations/sun-health-institute/programs/body-donation

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. An autopsy-based, research-devoted brain bank, biobank and biospecimen bank that derives its human donors from the Arizona Study of Aging and Neurodegenerative Disease (AZSAND), a longitudinal clinicopathological study of the health and diseases of elderly volunteers living in Maricopa county and metropolitan Phoenix, Arizona. Their function is studied during life and their organs and tissue after death. To date, they have concentrated their studies on Alzheimer's disease, Parkinson's disease, heart disease and cancer. They share the banked tissue, biomaterials and biospecimens with qualified researchers worldwide. Registrants with suitable scientific credentials will be allowed access to a database of available tissue linked to relevant clinical information, and will allow tissue requests to be initiated., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Brain and Body Donation Program (RRID:SCR_004822) Copy   

•   Source: SciCrunch Registry

http://www.smpdb.ca/

An interactive, visual database containing more than 350 small molecule pathways found in humans. More than 2/3 of these pathways (>280) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing exquisitely detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the HMDB or DrugBank and each protein or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. The database is easily browsed and supports full text, sequence and chemical structure searching. Users may query SMPDB with lists of metabolite names, drug names, genes / protein names, SwissProt IDs, GenBank IDs, Affymetrix IDs or Agilent microarray IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams. Gene, metabolite and protein concentration data can also be visualized through SMPDB''s mapping interface. All of SMPDB''s images, image maps, descriptions and tables are downloadable.

Proper citation: Small Molecule Pathway Database (RRID:SCR_004844) Copy   

•   Source: SciCrunch Registry

http://optn.transplant.hrsa.gov/

The only national patient waiting list and an online database system, called UNet, that links all of the professionals involved in the donation and transplantation system for the collection, storage, analysis, and publication of all OPTN data pertaining to the patient waiting list, organ matching, and transplants. The system contains data regarding every organ donation and transplant event occurring in the U.S. since October 1, 1987. UNet is a fail-safe, 24/7, secure Internet-based transplant information database created to enable the nation''''s organ transplant institutions to: * register patients for transplants * match donated organs to waiting patients * manage the time-sensitive, life-critical data of all patients, before and after their transplants Data reports are available by type: National Data, Regional Data, State Data, Center Data, Build Advanced Report, and Annual Report Data. UNet is being used right now by all of the nation''''s organ transplant programs, organ procurement organizations, and histocompatibility (tissue typing) laboratories working cooperatively to efficiently share a limited number of donated organs among thousands of patients.

Proper citation: Organ Procurement and Transplantation Network (RRID:SCR_004883) Copy   

•   Source: SciCrunch Registry

http://www.hmpdacc.org/

Common repository for diverse human microbiome datsets and minimum reporting standards for Common Fund Human Microbiome Project.

Proper citation: HMP Data Analysis and Coordination Center (RRID:SCR_004919) Copy   

•   Source: SciCrunch Registry

http://www.ikaros-project.org/

Ikaros is an open infrastructure for system level modeling of the brain including databases of experimental data, computational models and functional brain data. The system makes heavy use of the emerging standards for Internet based information and makes all information accessible through an open web-based interface. In addition, Ikaros can be used as a control architecture for robots which in the extension will lead to the development of a brain inspired robot architecture. The main components of the Ikaros systems are: a platform independent simulation kernel; a set of computational brain models; a set of I/O modules for interfacing with data files and peripheral such as robots or video cameras; tools for building systems of interconnected models; a plug-in architecture that allows new models to be easily added to the system; and a database with data from learning experiments that can be used for validation of the computational models.

Proper citation: Ikaros Project (RRID:SCR_007391) Copy   

•   Source: SciCrunch Registry

http://www.thebiogrid.org/

Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts.

Proper citation: Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) Copy   

•   Source: SciCrunch Registry

https://ida.loni.usc.edu/login.jsp

Archive used for archiving, searching, sharing, tracking and disseminating neuroimaging and related clinical data. IDA is utilized for dozens of neuroimaging research projects across North America and Europe and accommodates MRI, PET, MRA, DTI and other imaging modalities.

Proper citation: LONI Image and Data Archive (RRID:SCR_007283) Copy   

•   Source: SciCrunch Registry

http://sbml.org

A computer-readable format for representing models of biochemical reaction networks in software. It''s applicable to models of metabolism, cell-signaling, and many others. This website is the portal for the global SBML development effort; you can find information about all aspects of SBML.

Proper citation: SBML (RRID:SCR_007422) Copy   

•   Source: SciCrunch Registry

https://gpcrdb.org/

The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). :The GPCRDB contains data on sequences, ligand binding constants and mutations. In addition, t he system provides computationally derived data such as multiple sequence alignments, homology models, and a series of query and visualization tools. :The GPCRDB is designed to be a data storage medium, as well as a tool to aid biomedical scientists with answering questions by offering a single point of access to many types of data that are integrated and visualized in a user-friendly way. Although most parts of the GPCRDB are self-explanatory, if you have not used this resource before it is adviced that you to take a look at the usage page. Sponsors: This resource is supported by Organon and Unilever, and the NIH. Keywords: G protein, Coupled, receptor, Molecular, Heterogenous, Data, Sequence, Ligand, Mutation, Computational, Software, Alignment, Homology, Model, Visualization, Tool, Biomedical, Scientist, Integration,

Proper citation: G Protein-Coupled Receptor Data Base (RRID:SCR_007419) Copy   

•   Source: SciCrunch Registry

http://enhancer.lbl.gov/

Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth.

Proper citation: VISTA Enhancer Browser (RRID:SCR_007973) Copy   

•   Source: SciCrunch Registry

http://vega.sanger.ac.uk/

Central repository for high quality frequently updated manual annotation of vertebrate finished genome sequence. Human, mouse and zebrafish are in the process of being completely annotated, whereas for other species the annotation is only of specific genomic regions of particular biological interest. The majority of the annotation is from the HAVANA group at the Welcome Trust Sanger Institute. Users can BLAST, search for specific text, export, and download data. Genomes and details of the projects for each species are available through the homepages for human mouse and zebrafish. The website is built upon code from the EnsEMBL (http://www.ensembl.org) project. Some Ensembl features are not available in Vega. From the users point of view perhaps the most significant of these is MartView. However due to their inclusion in Ensembl, Vega human and mouse data can be queried using Ensembl MartView. Vega contains annotation of the human MHC region in eight haplotypes, and the LRC region in three haplotypes. Vega also contains annotation on the Insulin Dependent Diabetes (IDD) regions on non-reference assemblies for mouse.

Proper citation: VEGA (RRID:SCR_007907) Copy   

•   Source: SciCrunch Registry

http://fmf.igh.cnrs.fr/ISSAID/infevers

Registry for Familial Mediterranean Fever (FMF) and hereditary inflammatory disorders mutations. As of 2014, it includes twenty genes including: MEFV, MVK, TNFRSF1A, NLRP3, NOD2, PSTPIP1, LPIN2 and NLRP7, and contains over 1338 sequence variants. Confidential data, simple and complex alleles are accepted. For each gene, a menu offers: 1) a tabular list of the variants that can be sorted by several parameters; 2) a gene graph providing a schematic representation of the variants along the gene; 3) statistical analysis of the data according to the phenotype, alteration type, and location of the mutation in the gene; 4) the cDNA and gDNA sequences of each gene, showing the nucleotide changes along the sequence, with a color-based code highlighting the gene domains, the first ATG, and the termination codon; and 5) a download menu making all tables and figures available for the users, which, except for the gene graphs, are all automatically generated and updated upon submission of the variants. The entire database was curated to comply with the HUGO Gene Nomenclature Committee (HGNC) and HGVS nomenclature guidelines, and wherever necessary, an informative note was provided.

Proper citation: INFEVERS (RRID:SCR_007738) Copy   

•   Source: SciCrunch Registry