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http://automl.info/tpot/

Software Python package to automate building of ML pipelines by combining flexible expression tree representation of pipelines with stochastic search algorithms such as genetic programming.

Proper citation: Tree-Based Pipeline Optimization Tool (RRID:SCR_017531) Copy   

•   Source: SciCrunch Registry

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

Center that is a mouse cryoarchive and distribution center, which incorporates research goals that synergize with and extend the value of the resource. The goals of the UNC Chapel Hill center are to streamline and improve operating procedures, establish a comprehensive cryoarchive, develop and disseminate computational tools for mouse genotyping, and examine the effect of paternal age and epigenetics on mutation rate.

Proper citation: Mutant Mouse Resource and Research Center - University of North Carolina (RRID:SCR_016449) Copy   

•   Source: SciCrunch Registry

http://www.cdc.gov/genomics/hugenet/default.htm

Human Genome Epidemiology Network, or HuGENet, is a global collaboration of individuals and organizations committed to the assessment of the impact of human genome variation on population health and how genetic information can be used to improve health and prevent disease. Its goals include: establishing an information exchange that promotes global collaboration in developing peer-reviewed information on the relationship between human genomic variation and health and on the quality of genetic tests for screening and prevention; providing training and technical assistance to researchers and practitioners interested in assessing the role of human genomic variation on population health and how such information can be used in practice; developing an updated and accessible knowledge base on the World Wide Web; and promoting the use of this knowledge base by health care providers, researchers, industry, government, and the public for making decisions involving the use of genetic information for disease prevention and health promotion. HuGENet collaborators come from multiple disciplines such as epidemiology, genetics, clinical medicine, policy, public health, education, and biomedical sciences. Currently, there are 4 HuGENet Coordinating Centers for the implementation of HuGENet activities: CDC''s Office of Public Health Genomics, Atlanta, Georgia; HuGENet UK Coordinating Center, Cambridge, UK; University of Ioannina, Greece; University of Ottawa , Ottawa, Canada. HuGENet includes: HuGE e-Journal Club: The HuGE e-Journal Club is an electronic discussion forum where new human genome epidemiologic (HuGE) findings, published in the scientific literature in the CDC''s Office of Public Health Genomics Weekly Update, will be abstracted, summarized, presented, and discussed via a newly created HuGENet listserv. HuGE Reviews: A HuGE Review identifies human genetic variations at one or more loci, and describes what is known about the frequency of these variants in different populations, identifies diseases that these variants are associated with and summarizes the magnitude of risks and associated risk factors, and evaluates associated genetic tests. Reviews point to gaps in existing epidemiologic and clinical knowledge, thus stimulating further research in these areas. HuGE Fact Sheets: HuGE Fact Sheets summarize information about a particular gene, its variants, and associated diseases. HuGE Case Studies: An on-line presentation designed to sharpen your epidemiological skills and enhance your knowledge on genomic variation and human diseases. Its purpose is to train health professionals in the practical application of human genome epidemiology (HuGE), which translates gene discoveries to disease prevention by integrating population-based data on gene-disease relationships and interventions. Students will acquire conceptual and practical tools for critically evaluating the growing scientific literature in specific disease areas. HUGENet Publications: Articles related to the HuGENet movement written by our HuGENet collaborators. HuGE Navigator: An integrated, searchable knowledge base of genetic associations and human genome epidemiology, including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests. HuGE Workshops: HuGENet has sponsored meetings and workshops with national and international partners since 2001. Available are detailed summaries, agendas or the ability to download speaker slides. HuGE Book: Human Genome Epidemiology: A Scientific Foundation for Using Genetic Information to Improve Health and Prevent Disease. (The findings and conclusions in this book are those of the author(s) and do not necessarily represent the views of the funding agency.) HuGENet Collaborators: HuGENet is interested in establishing collaborations with individuals and organizations working on population based research involving genetic information. HuGE Funding: Funding opportunities for specific population-based genetic epidemiology research projects are available. Research initiatives whose aims include assessing the prevalence of human genetic variation, the association between genetic variants and human diseases, the measurement of gene-gene or gene-environment interaction, and the evaluation of genetic tests for screening and prevention are compiled to create a posted listing. Additional information and application details can be found by clicking on the respective links.

Proper citation: Human Genome Epidemiology Network (RRID:SCR_013117) Copy   

•   Source: SciCrunch Registry

https://www.drugabuse.gov

Portal provides list of genetic resources such as Brain Atlases and genomes for various species provided by National Institute of Drug Abuse.

Proper citation: Compilation of Genetics Resource Databases (RRID:SCR_017501) 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://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.anim.med.kyoto-u.ac.jp/nbr/default.aspx

NBRP-Rat was established to overcome limitations associated with properly utilizing existing rat resources. The collection of existing strains and genetic sub strains, phenotypic and genotypic characterization, cryopreservation of embryos, distribution of the collected rat strains, and a publicly accessible database of all assembled data are the major goals of this project. Once achieved, this unique database including the unique rat strains will become a powerful tool for biomedical research. A catalog of comparable, standardized and well characterized rat strains will lead to new and more precise research topics as well as it will facilitate biomedical sciences, drug discovery, advanced chemical research, and contributes to life sciences worldwide. As mentioned before, the major goals of NBRP-Rat are the collection, preservation and supply of rat strains. The repository includes strains from Japan and abroad, spontaneous mutants, congenic and recombinant strains as well as transgenic and mutagenized rats. Deposited rat strains are not only conserved as cryopreserved embryos and sperm. Many reference and frequently used rat strains are also maintained as living animals under SPF conditions. Furthermore, NBRP-rat provides a unique database on various rat strain phenotypes accompanied with basic genetic information. This allows scientists the selection of standardized and research specific strains. The animals themselves are provided free of charge to the research community (except for shipping costs). Sponsors: This project is one part of the National BioResource Projects (NBRP) in Japan for more than 20 species including animals, plants, microbes, tissues and DNAs. It is founded by the Japanese Ministry of Education, Culture, Sports, Science and Technology (Monkasho) and started in 2002.

Proper citation: National Bio Resource Project for the Rat. (RRID:SCR_012774) 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://www.tidebc.org/

A collaborative care and research initiative with a focus on prevention and treatment of Intellectual disability (ID) that is due to inborn errors of metabolism (IEM), which can be treated with diet or drugs. Health care policy and institutional culture is still operating under the old premise that all ID is incurable and thus, many children born with treatable ID are at risk of not being treated. To acknowledge the multidisciplinary scope and the ways in which health care professionals and researchers will collaborate, the goals of the TIDE BC project are demonstrated within a framework of 7 Work Packages: * Implementation of a new Protocol for diagnostic evaluation of ID, focusing of treatable conditions; * Development of infrastructure to facilitate implementation, evaluation and sustainability of the Protocol; * Investments into next generation genomic technologies; * Improving evidence of and access to treatments; * Evaluation and health economy; * Knowledge dissemination; * Education and Mentoring. The objectives addressed in all Work Packages reflect a highly integrated cluster combining clinical care, research, evaluation, and knowledge dissemination.

Proper citation: TIDE BC (RRID:SCR_003924) Copy   

•   Source: SciCrunch Registry

http://www.zfatlas.psu.edu/

Atlas containing 2- and 3-dimensional, anatomical reference slides of the lifespan of the zebrafish to support research and education worldwide. Hematoxylin and eosin histological slides, at various points in the lifespan of the zebrafish, have been scanned at 40x resolution and are available through a virtual slide viewer. 3D models of the organs are reconstructed from plastic tissue sections of embryo and larvae. The size of the zebrafish, which allows sections to fall conveniently within the dimensions of the common 1 x 3 glass slide, makes it possible for this anatomical atlas to become as high resolution as for any vertebrate. That resolution, together with the integration of histology and organ anatomy, will create unique opportunities for comparisons with both smaller and larger model systems that each have their own strengths in research and educational value. The atlas team is working to allow the site to function as a scaffold for collaborative research and educational activity across disciplines and model organisms. The Zebrafish Atlas was created to answer a community call for a comprehensive, web-based, anatomical and pathological atlas of the zebrafish, which has become one of the most widely used vertebrate animal models globally. The experimental strengths of zebrafish as a model system have made it useful for a wide range of investigations addressing the missions of the NIH and NSF. The Zebrafish Atlas provides reference slides for virtual microscopic viewing of the zebrafish using an Internet browser. Virtual slide technology allows the user to choose their own field of view and magnification, and to consult labeled histological sections of zebrafish. We are planning to include a complete set of embryos, larvae, juveniles, and adults from approximately 25 different ages. Future work will also include a variety of comparisons (e.g. normal vs. mutant, normal vs. diseased, multiple stages of development, zebrafish with other organisms, and different types of cancer)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Zebrafish Atlas (RRID:SCR_006722) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/LDheatmap/index.html

Software application that plots measures of pairwise linkage disequilibria for SNPs (entry from Genetic Analysis Software)

Proper citation: LDHEATMAP (RRID:SCR_006312) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/hclust/hclust.htm

Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: HCLUST (RRID:SCR_009154) Copy   

•   Source: SciCrunch Registry

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://software.broadinstitute.org/software/discovar/blog/

Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes.

Proper citation: Discovar assembler (RRID:SCR_016755) 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

https://www.beast2.org/

Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager.

Proper citation: BEAST2 (RRID:SCR_017307) Copy   

•   Source: SciCrunch Registry

https://depmap.org/portal/

Portal for identifying genetic and pharmacologic dependencies and biomarkers that predicts them by providing access to datasets, visualizations, and analysis tools that are being used by Cancer Dependency Map Project at Broad Institute. Project to systematically identify genes and small molecule dependencies and to determine markers that predict sensitivity. All data generated by DepMap Project are available to public under CC BY 4.0 license on quarterly basis and pre-publication.

Proper citation: Cancer Dependency Map Portal (RRID:SCR_017655) Copy   

•   Source: SciCrunch Registry

https://deepblue.mpi-inf.mpg.de/

Central data access hub for large collections of epigenomic data. It organizes data from different sources using controlled vocabularies and ontologies. Data Server for storing, organizing, searching, and retrieving genomic and epigenomic data, handling associated metadata, and to perform different types of analysis.

Proper citation: Deep Blue Epigenomic Data Server (RRID:SCR_017490) Copy   

•   Source: SciCrunch Registry

http://taylor0.biology.ucla.edu/structureHarvester/

Web based program for collating results generated by program STRUCTURE. Provides assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of number of genetic groups that best fit data. Reformats data for use in downstream programs, such as CLUMPP.It is complement for using software Structure in genetics population. Website and program for visualizing STRUCTURE output and implementing Evanno method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Structure Harvester (RRID:SCR_017636) Copy   

•   Source: SciCrunch Registry