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https://atgu.mgh.harvard.edu/plinkseq/

An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software)

Proper citation: PLINK/SEQ (RRID:SCR_013193) Copy   

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https://www.broadinstitute.org/scientific-community/software/cancer-therapeutics-response-portal

Cancer Therapeutics Response Portal (CTRP) links genetic, lineage, and other cellular features of cancer cell lines to small-molecule sensitivity with the goal of accelerating discovery of patient-matched cancer therapeutics. CTRP can be mined to develop insights into small-molecule mechanisms of action and novel therapeutic hypotheses, and to support future discovery of drugs matched to patients based on predictive biomarkers.

Proper citation: Cancer Therapeutics Response Portal (CTRP) (RRID:SCR_026293) Copy   

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https://github.com/transmart

tranSMART is a knowledge management platform that enables scientists to develop and refine research hypotheses by investigating correlations between genetic and phenotypic data, and assessing their analytical results in the context of published literature and other work. tranSMART is licensed through GPL 3. The integration, normalization, and alignment of data in tranSMART permits users to explore data very efficiently to formulate new research strategies. Some of tranSMART''s specific applications include: * Revalidating previous hypotheses * Testing and refining novel hypotheses * Conducting cross-study meta-analysis * Searching across multiple data sources to find associations of concepts, such as a gene''s involvement in biological processes or experimental results * Comparing biological processes and pathways among multiple data sets from related diseases or even across multiple therapeutic areas Data Repository The tranSMART Data Repository combines a data warehouse with access to federated sources of open and commercial databases. tranSMART accommodates: * Phenotypic data, such as demographics, clinical observations, clinical trial outcomes, and adverse events * High content biomarker data, such as gene expression, genotyping, pharmacokinetic and pharmaco-dynamics markers, metabolomics data, and proteomics data * Unstructured text-data, such as published journal articles, conference abstracts and proceedings, and internal studies and white papers * Reference data from sources such as MeSH, UMLS, Entrez, GeneGo, Ingenuity, etc. * Metadata providing context about datasets, allowing users to assess the relevance of results delivered by tranSMART Data in tranSMART is aligned to allow identification and analysis of associations between phenotypic and biomarker data, and it is normalized to conform with CDISC and other standards to facilitate search and analysis across different data sources. tranSMART also enables investigators to search published literature and other text sources to evaluate their analysis in the context of the broader universe of reported research. External data can also be integrated into the tranSMART data repository, either from open data projects like GEO, EBI Array Express, GCOD, or GO, or from commercially available data sources. Making data accessible in tranSMART enables organizations to leverage investments in manual curation, development costs of automated ETL tools, or commercial subscription fees across multiple research groups. Dataset Explorer tranSMART''s Dataset Explorer provides flexible, powerful search and analysis capabilities. The core of the Dataset Explorer integrates and extends the open source i2b2 application, Lucene text indexing, and GenePattern analytical tools. Connections to other open source and commercial analytical tools such as Galaxy, Integrative Genomics Viewer, Plink, Pathway Studio, GeneGo, Spotfire, R, and SAS can be established to expand tranSMART''s capabilities. tranSMART''s design allows organizations flexibility in selecting analytical tools accessible through the Dataset Explorer, and provides file export capabilities to enable researchers to use tools not accessible in the tranSMART portal.

Proper citation: tranSMART (RRID:SCR_005586) Copy   

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http://www2.le.ac.uk/

Public research university based in Leicester, England. Famous for the discovery of genetic fingerprinting and contributing to the discovery and identification of the remains of King Richard III.

Proper citation: University of Leicester; Leicester; United Kingdom (RRID:SCR_004900) Copy   

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http://www.gene.com/

A biotechnology corporation that uses human genetic information to discover, develop, manufacture and commercialize medicines to treat patients with serious or life-threatening medical conditions.

Proper citation: Genentech (RRID:SCR_003997) Copy   

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http://www.cephb.fr/

The Centre d''Etude du Polymorphisme Humain (CEPH) is a research laboratory, the main activities of which are the setting up, storage, processing and distribution of DNA collections for the identification of genetic factors conferring susceptibility to complex disorders. These collections are established in partnership and full collaboration with external French or international research groups. The Foundation currently hosts the CEPH reference panel, the HGDP panel (Human genome Diversity Cell Line Panel) and several collections amounting mid-2008 to more than 250 000 samples. The goal of CEPH is to understand complex multifactorial disorders necessitates the establishment of structures facilitating access to large and integrated collection of individuals, characterized by a large number of variables emanating from different technologies and platforms. To achieve this goal, CEPH facilitates the setting up of integrated analyses combining clinical, genetic and environmental data, for the identification of susceptibility factors to complex multifactorial disorders Additionally, CEHP allows the reception, storage, processing and distribution of biological sample collections. At the same time, it promotes and participates in the design and setting up of genetic studies: - in partnership and full collaboration with external research groups - giving access to a large number of variables - in a sufficient number of subjects - allowing large scale integrated analyses

Proper citation: Centre dEtude du Polymorphisme Humain (RRID:SCR_008026) Copy   

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http://www.acpfg.com.au/

At the Australian Centre for Plant Functional Genomics (ACPFG), scientists are improving wheat and barley''s tolerance to environmental stresses such as drought, heat, salinity and nutrient toxicities. These stresses known as abiotic stresses, are a major cause of yield and quality loss throughout the world and cause significant problems for cereal growers. These scientists are developing the technologies and resources needed to produce new cereal varieties that allow sustainable farming to generate economic, social and environmental benefits to Australia. ACPFG research is helping to ensure Australia maintains its competitive position in cereal production. - Identify the genetic mechanisms that control tolerance to specific stresses and compare these with those controlling broad range tolerance to abiotic stresses - Use genome-wide analyses to define key cellular processes that enable adapted plants to withstand abiotic stress, and to apply that understanding to the genetic improvement of crops such as wheat and barley - Unravel regulatory networks that control plant growth under abiotic stress - Identify ways of manipulating these networks, through existing genetic diversity or through functional genomics technologies, to deliver tangible industry outcomes, namely cereal varieties better tailored to hostile environments

Proper citation: Australian Center For Plant Functional Genomics PTY LTD (RRID:SCR_008383) Copy   

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http://www.cshl.edu/

Non profit, private research and education institution that performs molecular and genetic research used to generate methods for better diagnostics and treatments for cancer and neurological diseases. Research of cancer causing genes and their respective signaling pathways, mutations and structural variations of the human genome that could cause neurodevelopmental and neurodegenerative illnesses such as autism, schizophrenia, and Alzheimer's and Parkinson's diseases and also research in plant genetics and quantitative biology.

Proper citation: Cold Spring Harbor Laboratory (RRID:SCR_008326) Copy   

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http://www.ohsu.edu/xd/research/centers-institutes/onprc/

Center that aims to develop biomedical technologies using nonhuman primate (NHP) models. Its goal is to uncover the root causes of various disease and disorders, unlock secrets of the brain, and unleash new methods of diagnostics and treatment.

Proper citation: Oregon National Primate Research Center (RRID:SCR_008291) Copy   

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http://www.illumina.com/

American company incorporated that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Provides a line of products and services that serve the sequencing, genotyping and gene expression and proteomics markets. Its headquarters are located in San Diego, California.

Proper citation: Illumina (RRID:SCR_010233) Copy   

•   Source: SciCrunch Registry

http://csbio.unc.edu/CCstatus/index.py?run=Geneseek

MUGA genotypes for 458 samples from the developing CC lines described in the February 2012 issue of Genetics. Genotypes for 168 reference strains that include biological and technical replicates for the the 8 CC founder strains and their F1 crosses are also provided. Genotype calls are those reported by Illumina. All results are provided as comma separated files with one row per marker. Each marker is identified by a probe name and its genomic position in NCBI Build 37.

Proper citation: MUGA (RRID:SCR_014072) Copy   

•   Source: SciCrunch Registry

http://fcon_1000.projects.nitrc.org/indi/enhanced/

Dataset of 1000 characterized community-ascertained participants using state-of-the-art multiband imaging-based resting state fMRI (R-fMRI) and diffusion tensor imaging (DTI), genetics, and a deep phenotyping protocol from a large cross-sectional sample of brain development, maturation and aging (ages 6 - 85 yrs). The Center for Magnetic Resonance Research (CMRR), University of Minnesota, provided the NKI-RS effort with the latest version of the Multiband EPI sequence (Xu et al. 2012) and associated image reconstruction algorithms, enabling the acquisition of state-of-the-art imaging datasets for this large-scale imaging effort. The enhanced NKI-RS expands upon the phenotypic protocol of the original NKI-RS and captures a broad range of behavioral and cognitive phenomenology relevant to psychiatric health and illness. The validity and value of assessments were evaluated by consulting leaders in the field of psychiatric phenotyping.

Proper citation: NKI-RS Enhanced Sample (RRID:SCR_010461) Copy   

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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

http://www.mirecc.va.gov/visn6/

The VISN 6 MIRECC is organized as a translational medicine multi-site center focused on post deployment mental health issues. The overarching goals are improving clinical assessment and treatment and development of novel interventions through basic and clinical research. This MIRECC aims: (1) To determine whether early intervention in post-deployment mental health is effective in forestalling the development or decreasing the severity of post-deployment mental illness, (2) To determine what neuroimaging, genetic, neurocognitive, or other characteristics predict the development of post-deployment mental illness, and (3) To assess the longitudinal course of post-deployment mental illness.

Proper citation: Mid-Atlantic (VISN 6) Mental Illness Research, Education and Clinical Center (RRID:SCR_008077) Copy   

•   Source: SciCrunch Registry

http://www.emory.edu/LIVING_LINKS/

The primary mission of the Living Links Center is to study human evolution by investigating our close genetic, anatomical, cognitive, and behavioral similarities with great apes. The Living Links Center was established for primate studies that shed light on human behavioral evolution. It is an integrated part of the Yerkes National Primate Research Center, which is the nation's oldest and largest primate center. The Living Links Center is home to two socially housed groups of chimpanzees and two socially housed groups of capuchin monkeys. The research conducted in this center is broken down into four categories: - Chimpanzees: Chimpanzee research at the Living Links Center is conducted at the Yerkes Field Station, which is home to two socially housed chimpanzee groups known as FS1 and FS2. Each mixed gender group of 12 individuals lives in a large outdoor enclosure with wooden climbing structures and play objects attached to an indoor sleeping area. FS1 and FS2 can hear, but not see each other because their enclosures are ~200m apart and separated by a small hill. Chimpanzee research is conducted on a volunteer basis with members of each group. - Elephants: This newly found presence of mirror self-recognition in elephants, previously predicted due to their well-known social complexity, is thought to relate to empathetic tendencies and the ability to distinguish oneself from others. As a result of this study, the elephant now joins a cognitive elite among animals commensurate with its well-known complex social life and high level of intelligence. Although elephants are far more distantly related to us than the great apes, they seem to have evolved similar social and cognitive capacities making complex social systems and intelligence part of this picture. These parallels between humans and elephants suggest a convergent cognitive evolution possibly related to complex sociality and cooperation. - Capuchin Monkeys: Though there are several different species of capuchin monkey, the one most widely studied in captivity by Living Links, is the brown, or tufted, capuchin (Cebus apella). - Collaborative Projects: projects with collaborators around the world. Sponsors: This center is supported by the Yerkes National Primate Research Center.

Proper citation: Living Links: Center for the Advanced Study of Ape and Human Evolution (RRID:SCR_001776) Copy   

•   Source: SciCrunch Registry

https://monarchinitiative.org/

Repository of information about model organisms, in vitro models, genes, pathways, gene expression, protein and genetic interactions, orthology, disease, phenotypes, publications, and authors, and ability to navigate multi-scale spatial and temporal phenotypes across in vivo and in vitro model systems in context of genetic and genomic data, using semantics and statistics. Discovery system provides basic and clinical science researchers, informaticists, and medical professionals with integrated interface and set of discovery tools to reveal genetic basis of disease, facilitate hypothesis generation, and identify novel candidate drug targets. Database that indexes authoritative information on experimental models of disease from MGI, RGD and ZFIN.

Proper citation: MONARCH Initiative (RRID:SCR_000824) Copy   

•   Source: SciCrunch Registry

http://www.gramene.org

Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site.

Proper citation: Gramene (RRID:SCR_002829) Copy   

•   Source: SciCrunch Registry

http://wwwn.cdc.gov/dls/genetics/rmmaterials/default.aspx

The goal of the Genetic Testing Reference Materials Coordination Program (GeT-RM) is to coordinate a self-sustaining community process to improve the availability of appropriate and characterized reference materials for: Quality control (QC), Proficiency testing (PT), Test development & validation, Research. The purpose of this program is: - To help the genetic testing community obtain appropriate and characterized reference materials - To facilitate and coordinate information exchange between users and providers of QC and reference materials - To coordinate efforts for contribution, development, characterization and distribution of reference materials for genetic testing Get-RM provides information about cell lines, DNA, and other kinds of materials that could be used as reference materials for molecular genetic testing. Some of these materials have been characterized by the GeT-RM program and can be divided into three categories: - Genetic Inherited Disease & Pharmacogenetics This section includes information about cell lines, DNA, and other samples that can be used as reference materials for various inherited diseases (including cystic fibrosis, fragile X, Huntington disease, and Ashkenazi Jewish-related diseases), pharmacogenetic loci, and biochemical genetics. The GeT-RM program has confirmed the genotype of many of the genomic DNA samples through testing in multiple clinical genetic laboratories. - Molecular Oncology This section includes information about commercially available cell lines, DNA, and other kinds of materials that could be used as reference materials for various types of cancers, including leukemia/lymphoma and solid tumors. - Infectious Disease This section includes information about commercially available cell lines, DNA, and other kinds of materials that could be used as reference materials for various infectious disease pathogens including viruses, bacteria, and protozoa.

Proper citation: Center for Disease Control and Prevention: Genetic Testing Reference Materials Coordination Program (RRID:SCR_013029) 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

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