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http://marrvel.org/

Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.

Proper citation: MARRVEL (RRID:SCR_016871) Copy   

•   Source: SciCrunch Registry

https://www.iigm.it/site/index.php?l=ENG

Private research institute in Turin, Italy. Research programs in immunogenetics, functional genomics, genomic epidemiology, tumour diagnostic and prognostic biomarker research, epigenetic modifications in disease, quantitative biology and computational neuroscience.

Proper citation: Italian Institute for Genomic Medicine; Turin; Italy (RRID:SCR_017062) Copy   

•   Source: SciCrunch Registry

https://cmmt.ubc.ca/

Center is part of University of British Columbia Faculty of Medicine, located at British Columbia Children Hospital Research Institute (BCCHR) in Vancouver, British Columbia, Canada. Research at CMMT is focused on discovering genetic susceptibility to illnesses such as Huntington Disease, Type 2 diabetes and bipolar disorder.

Proper citation: University of British Columbia Centre for Molecular Medicine and Therapeutics (RRID:SCR_017241) Copy   

•   Source: SciCrunch Registry

http://rgd.mcw.edu

Database for genetic, genomic, phenotype, and disease data generated from rat research. Centralized database that collects, manages, and distributes data generated from rat genetic and genomic research and makes these data available to scientific community. Curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data is provided. Facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Strain reports include description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources.

Proper citation: Rat Genome Database (RGD) (RRID:SCR_006444) Copy   

•   Source: SciCrunch Registry

http://www.progenygenetics.com/

Fully customizable, comprehensive genetic pedigree and clinical data management software including a multi-user relational database with an integrated pedigree drawing component to manage genetic and pedigree data in one database. Manage Pedigrees, Individuals, SNPs, STRs, Samples, Plates, Genotypes and exports to multiple analysis platforms. (entry from Genetic Analysis Software) * LIMS software, providing advanced sample tracking and management (including functionality to generate and record barcodes) and configurable workflows for your specific environment. * Full genotype management gives users the ability to track not only family-based studies, but Whole Genome Association studies containing 1000''s of samples with large arrays.

Proper citation: PROGENY (RRID:SCR_006647) Copy   

•   Source: SciCrunch Registry

http://research.nhgri.nih.gov/dog_genome/

The Dog Genome Project at the National Human Genome Research Institute is working to develop resources necessary to map and clone canine genes in an effort to utilize dogs as a model system for genetics and cancer research. The US National Human Genome Research Institute (NHGRI) agreed to fund a project to sequence the entire genome of a boxer dog named Tasha, because it recognized the value of the dog as an unrivaled model for the study of human disease. The National Human Genome Research Institute (NHGRI) led the National Institutes of Health's (NIH) contribution to the International Human Genome Project, which had as its primary goal the sequencing of the human genome. This project was successfully completed in April 2003. Now, the NHGRI's mission has expanded to encompass a broad range of studies aimed at understanding the structure and function of the human genome and its role in health and disease. To that end NHGRI supports the development of resources and technology that will accelerate genome research and its application to human health. A critical part of the NHGRI mission continues to be the study of the ethical, legal and social implications (ELSI) of genome research. NHGRI also supports the training of investigators and the dissemination of genome information to the public and to health professionals.

Proper citation: NHGRI Dog Genome Project (RRID:SCR_002256) Copy   

•   Source: SciCrunch Registry

http://bmerc.bu.edu/projects/wdrepeat/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. This website contains a library of WD-repeat containing proteins in which the repeats appear as multi-aligned sets. WD-repeat-containing proteins are those that contain 4 or more copies of the WD-repeat (tryptophan-aspartate repeat), a sequence motif approximately 31 amino acids long, that encodes a structural repeat. This repeat is described by the following profile, where x is ANY amino acid. By clicking on each high-lighted character you will obtain the distribution of amino acids found at that position of the repeat among an aligned set of WD-repeat containing proteins. The tertiary structure of only one member of this family has been determined, that of the G protein beta subunit, which contains 7 WD-repeats. Each of the 7 repeats folds into a small antiparallel beta-sheet. The over-lines above indicate the position of these strands, with a being the strand closest to the central pore and d at the external surface of the folded protein. These sheets are arranged around a central pseudosymmetry axis into a beta propeller. The WD-repeat-containing proteins form a very large family that is diverse in both its function and domain structure. Within all these proteins the WD-repeat domains are thought to have two common features: the domain folds into a beta propeller; and the domains form a platform without any catalytic activity on which multiple protein complexes assemble reversibly. The fact that these proteins play such key roles in the formation of protein-protein complexes in nearly all the major pathways and organelles unique to eukaryotic cells has two important implications. It supports both their ancient and proto eukaryotic origins and supports a likely association with many genetic diseases.

Proper citation: WD repeat Family of Proteins (RRID:SCR_002160) Copy   

•   Source: SciCrunch Registry

http://lincscloud.org/

A catalog of gene-expression data collected from human cells treated with chemical compounds and genetic reagents. Computational methods to reduce the number of necessary genomic measurements along with streamlined methodologies enable the current effort to significantly increase the size of the CMap database and along with it, our potential to connect human diseases with the genes that underlie them and the drugs that treat them. The NIH has funded a large expansion of the Connectivity Map dataset through the Library of Integrated Network-based Cellular Signatures (LINCS). The Broad Institute's LINCS center aims to create a first installment of data generation and analysis for the LINCS program. Through these data LINCS intends to accelerate the discovery process by systematically revealing connections between genes/compounds discovered in screens and molecular pathways that underlie disease states.

Proper citation: LINCS Connectivity Map (RRID:SCR_002639) Copy   

•   Source: SciCrunch Registry

http://genecards.org

Database of human genes that provides concise genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes. Information featured in GeneCards includes orthologies, disease relationships, mutations and SNPs, gene expression, gene function, pathways, protein-protein interactions, related drugs and compounds and direct links to cutting edge research reagents and tools such as antibodies, recombinant proteins, clones, expression assays and RNAi reagents.

Proper citation: GeneCards (RRID:SCR_002773) Copy   

•   Source: SciCrunch Registry

https://www.hsph.harvard.edu/alkes-price/software/

Software application that uses genotyping data from SNP arrays for accurately inferring chromosomal segments of distinct continental ancestry in admixed populations, using dense genetic data. (entry from Genetic Analysis Software)

Proper citation: Hapmix (RRID:SCR_004203) Copy   

•   Source: SciCrunch Registry

http://www.mknt.hu/sites/default/files/NEPSYBANK_0.doc

The Hungarian Society of Clinical Neurgenetics established a nationwide collaboration for prospective collection of human biological materials and databases from patient with neurological and psychiatric diseases. The basic triangle of the NEPSYBANK is the sample, the information and the study management. The present participants of the NEPSYBANK are the Department of Neurology and Psychiatry of the four Medical Universities (in Budapest, Debrecen, Pecs, Szeged) and the National Institute of Psychiatry and Neurology in Budapest. The NEPSYBANK is a disease based biobank collecting both phenotypical and environmental data and biological materials such as DNA/RNA, whole blood, plasma, cerebral spinal fluid, muscle / nerve / skin biopsy, brain, and fibroblast. The target of the diseases is presently (Phase I): stroke syndromes, dementias, movement disorders, motoneuron diseases, epilepsy, multiple sclerosis, schizophrenia, alcohol addiction. In the near future (Phase II.) it is planned to enlarge the scale with headaches, disorders of the peripheral nerves, disorders of neuromuscular transmission, disorders of skeletal muscle, depression, anxiety. DNA/RNA is usually extracted from whole blood, but occasionally different tissues such as muscle, brain etc. can be used as well. The extracting procedures differ among the institutes, but in all cases the concentration and the quality of the DNA/RNA must be registered in the database. Participating institutional biobanks have committed themselves to follow common quality standards, which provide access to samples after prioritization on scientific grounds only. In every case the following data are registered. 1. General data: main bank categories, age, sex, ethnicity, body height, body weight, economic stats, education, type of place of living, marital status, birth complications, alcohol, drugs, smoking. 2. Sample properties (sample ID, type of sample, date of extraction, concentration, and level of purity). General patient data as blood pressure, heart rate, internal medical status, ECG, additional diseases. Disease specific question e.g. in schizophrenia the diagnosis after DSMIV and ICD 10, detailed diagnostic questions after both classification, detailed psychiatric and neurological status, laboratory findings, rating scales, data of neuroimaging, genetic tests, applied medication (with generic name, dose, duration), adverse drug effects and other treatments. The Biobank Information Management System (BIMS) is responsible for linkage of databases containing information on the individual sample donors. If you want to have samples from the NEPSYBANK an application must be submitted containing the following information: short research plan including aims and study design, ethic application with a positive decision, specific demands regarding the right of disposition, agreements with grant organizations which regulate immaterial property, information about financing (academic grants, support from industry). All participants have the right to withdraw their samples through a simple order.

Proper citation: Hungarian Neurological-Psychiatric Biobank (RRID:SCR_003715) Copy   

•   Source: SciCrunch Registry

http://coot.embl.de/g2d/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases.

Proper citation: Candidate Genes to Inherited Diseases (RRID:SCR_008190) Copy   

•   Source: SciCrunch Registry

http://www.seattle.eric.research.va.gov/VETR/Home.asp

The Vietnam Era Twin (VET) Registry is a closed cohort composed of approximately 7,000 middle-aged male-male twin pairs both of whom served in the military during the time of the Vietnam conflict (1964-1975). The Registry is a United States Department of Veterans Affairs (VA) resource that was originally constructed from military records; the Registry has been in existence for almost 20 years. It is one of the largest national twin registries in the US and currently has members living in all 50 states. Initially formed to address questions about the long-term health effects of service in Vietnam, the Registry has evolved into a resource for genetic epidemiological studies of mental and physical health conditions. Several waves of mail and telephone surveys have collected a wealth of health-related information on Registry twins, referred to as members. In addition to twins, selected adult offspring of twins and the mothers of those offspring are also VET Registry members. More recent data collection efforts have focused on specific sets of twin pairs and have conducted detailed clinical or laboratory testing. Selected Vietnam Era Registry Research Studies: * Veteran Health Study * VETSA 2: A Longitudinal Study of Cognitive Aging * Alcoholism Course thought Midlife: A Twin Family Study and Offspring of Twins: G, E and GxE Risk for Alcoholism * GE: Offspring of Twins with Substance Use Disorder * Mechanisms Linking Depression to Cardiovascular Risk (Twins Heart Study 2) * Post-traumatic Stress Disorder and Cardiovascular Disease * Biological Markers for Post-traumatic Stress Disorder (T3) * Memory and the Hippocampus in Vietnam-era Twins with PTSD (Time 3)

Proper citation: Vietnam Era Twin Registry (RRID:SCR_008807) Copy   

•   Source: SciCrunch Registry

http://gene64.dna.affrc.go.jp/RPD/main_en.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 22, 2016.

A database on the proteome of rice that contains reference maps based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of proteins from rice tissues and subcellular compartments.

Proper citation: Rice Proteome Database (RRID:SCR_000743) Copy   

•   Source: SciCrunch Registry

http://www.dsmz.de/

The DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganisms and Cell Cultures) is the most comprehensive biological resource center in Europe. With more than 18.000 microorganisms, 1.200 plant viruses, 600 human and animal cell lines, 770 plant cell cultures and more than 7.100 cultures deposited for the purposes of patenting, DSMZ has demonstrated their obligation to serve science for decades. Main functions of DSMZ are: - to collect, maintain and store microorganisms and cell lines, as well as other biological material of relevance for applied biology, biotechnology, microbiology, teaching and other areas of research and general application; - to keep the scientific and industrial community informed on the contents of the collections by the means of catalogs, special lists, databases or electronic media; - to supply scientists and institutions with DSMZ cultures, in accordance with national and international laws such as the Infektionsschutzgesetz (Act dealing with protection against infection), the Genetic Engineering Act, the Foreign Trade Laws, the Convention on Biological Diversity as well as the DSMZ terms of supply; - to function as an internationally recognized collection center for the deposit of microorganisms, cell lines, and other biological material which have been cited in scientific literature or which are used in national or international test procedures (e.g. type strains, reference strains for national and international quality control regulations or susceptibility tests, strains with special properties, such as the production of enzymes, degradation of pollutants, host strains for plasmids, etc.); - to act as an International Depositary Authority (IDA) for the deposit of biological material for patent purposes according to the Budapest Treaty; - to act, in a confidential manner, as a center for the safe deposit of biological material; - to act as an advisory center for the scientific community and to offer teaching and service facilities. The DSMZ collections contain over 26 000 cultures (including 6500 patent deposits) representing more than 16 000 cultures of microorganisms (Archaea, Bacteria, plasmids, phages, yeasts, fungi), 750 plant cell cultures, 600 plant viruses, 700 antisera and 580 human and animal cell lines. Unique subcollections are held in the prokaryotes groups of acidophiles, alkaliphiles, halophiles, methanogens, phototrophs, thermophiles, and sulfate reducers. The research is focused on collection related fields which include: - Taxonomy - Evolution - Phylogeny - Microbial diversity and molecular assessment of diversity - Molecular systematics - Research on pathobiological aspects of leukemia-lymphoma cell lines applying classical and molecular genetics, immunological and cell biological methods * Development of cultivation and preservation methods for biological material * Characterization and identification of biological material

Proper citation: German Collection of Microorganisms and Cell Cultures (RRID:SCR_001711) Copy   

•   Source: SciCrunch Registry

http://irefindex.org

An index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index includes multiple interaction types including physical and genetic (mapped to their corresponding protein products) as determined by a multitude of methods. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once. iRefIndex project has three long term objectives: # to facilitate exchange of interaction data between interaction databases. # to consolidate interaction data from multiple sources. # to provide feedback to source interaction databases. iRefIndex is made available in a number of formats: MITAB tab-delimited text files, iRefWeb interface, iRefScape plugin for Cytoscape, PSICQUIC Web services, and an interface for the R programming language environment.

Proper citation: Interaction Reference Index (RRID:SCR_002085) Copy   

•   Source: SciCrunch Registry

http://www.type2diabetesgenetics.org/

Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease.

Proper citation: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) (RRID:SCR_003743) Copy   

•   Source: SciCrunch Registry

http://www.semel.ucla.edu/creativity/

The purpose of this center is to study the molecular, cellular, systems and cognitive mechanisms that result in cognitive enhancements and explain unusual levels of performance in gifted individuals, including extraordinary creativity. Additionally, by understating the mechanisms responsible for enhancements in performance we may be better suited to intervene and reverse disease states that result in cognitive deficits. One of the key topics addressed by the Center is the biological basis of cognitive enhancements, a topic that can be studied in human subjects and animal models. In the past much of the focus in the brain sciences has been on the study of brain mechanisms that degrade cognitive performance (for example, on mutations or other lesions that cause cognitive deficits). The Tennenbaum Center for the Biology of Creativity at UCLA enables an interdisciplinary team of leading scientists to advance knowledge about the biological bases of creativity. Starting with a pilot project program, a series of investigations was launched, spanning disciplines from basic molecular biology to cognitive neuroscience. Because the concept of creativity is multifaceted, initial efforts targeted refinement of the component processes necessary to generate novel, useful cognitive products. The identified core cognitive processes: 1.) Novelty Generation the ability to flexibly and adaptively generate products that are unique; 2.) Working Memory and Declarative Memory the ability to maintain, and then use relevant information to guide goal-directed performance, along with the capacity to store and retrieve this information; and 3.) Response Inhibition the ability to suppress habitual plans and substitute alternate actions in line with changing problem-solving demands. To study the basic mechanisms underlying these complex brain functions we use translational strategies. Starting from foundational studies in basic neuroscience, we forged an interdisciplinary strategy that permits the most advanced techniques for genetic manipulation and basic neurobiological research to be applied in close collaboration with human studies that converge on the same core cognitive processes. Our integrated research program aims to reveal the genetic architecture and fundamental brain mechanisms underlying creative cognition. The work holds enormous promise for both enhancing healthy cognitive performance and designing new treatments for diverse cognitive disorders. Sponsors: The Tennenbaum Center for the Biology of Creativity was inspired by the vision and generosity of Michael Tennenbaum.

Proper citation: Tennenbaum Center for the Biology of Creativity (RRID:SCR_000668) Copy   

•   Source: SciCrunch Registry

http://ccb.loni.usc.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Center focused on the development of computational biological atlases of different populations, subjects, modalities, and spatio-temporal scales with 3 types of resources: (1) Stand-alone computational software tools (image and volume processing, analysis, visualization, graphical workflow environments). (2) Infrastructure Resources (Databases, computational Grid, services). (3) Web-services (web-accessible resources for processing, validation and exploration of multimodal/multichannel data including clinical data, imaging data, genetics data and phenotypic data). The CCB develops novel mathematical, computational, and engineering approaches to map biological form and function in health and disease. CCB computational tools integrate neuroimaging, genetic, clinical, and other relevant data to enable the detailed exploration of distinct spatial and temporal biological characteristics. Generalizable mathematical approaches are developed and deployed using Grid computing to create practical biological atlases that describe spatiotemporal change in biological systems. The efforts of CCB make possible discovery-oriented science and the accumulation of new biological knowledge. The Center has been divided into cores organized as follows: - Core 1 is focused on mathematical and computational research. Core 2 is involved in the development of tools to be used by Core 3. Core 3 is composed of the driving biological projects; Mapping Genomic Function, Mapping Biological Structure, and Mapping Brain Phenotype. - Cores 4 - 7 provide the infrastructure for joint structure within the Center as well as the development of new approaches and procedures to augment the research and development of Cores 1-3. These cores are: (4)Infrastructure and Resources, (5) Education and Training, (6) Dissemination, and (7) Administration and Management. The main focus of the CCB is on the brain, and specifically on neuroimaging. This area has a long tradition of sophisticated mathematical and computational techniques. Nevertheless, new developments in related areas of mathematics and computational science have emerged in recent years, some from related application areas such as Computer Graphics, Computer Vision, and Image Processing, as well as from Computational Mathematics and the Computational Sciences. We are confident that many of these ideas can be applied beneficially to neuroimaging.

Proper citation: Center for Computational Biology at UCLA (RRID:SCR_000334) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/

Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAP (RRID:SCR_000689) Copy   

•   Source: SciCrunch Registry