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http://www.nitrc.org/projects/brainlife_io/

Platform for publishing reproducible code and datasets and providing access to national supercomputers, private clouds, and institutional high-performance computer systems to promote open software and data sharing to advance understanding of the human brain.

Proper citation: brainlife.io (RRID:SCR_016513) Copy   

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https://www.popmednet.org/

Software as an open source informatics platform to facilitate the implementation and operation of distributed health data networks. Consists of a web-based portal for distributing requests and administering the network, and the DataMart Client. Designed by the Therapeutics Research and Infectious Disease Epidemiology (TIDE) group at the Department of Population Medicine (DPM) of the Harvard Pilgrim Health Care Institute (HPHCI) to enable creation, operation, and governance of distributed health data networks.

Proper citation: PopMedNet (RRID:SCR_016456) 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

https://www.jax.org/research-and-faculty/resources/optogenetics-resource

Mouse lines expressing proteins that activate, inhibit or detect neuronal activity are available from The Jackson Laboratory Repository. Many of these strains have been generated by HHMI Janelia Farm GENIE Project or by Allen Institute for Brain Science.

Proper citation: Optogenetics Resource at JAX (RRID:SCR_017508) Copy   

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http://snpselector.duhs.duke.edu/hqsnp36.html

This is the HQSNP DB (high-quality SNP database) developed by CHG bioinformatics group. The high-quality SNP is defined as a SNP having allele frequency or genotyping data. The majority of the HQSNPs come from HapMap, others come from JSNP (Japanese SNP database), TSC (The SNP Consortium), Affymetrix 120K SNP, and Perlegen SNP. There are four kinds of SNP search you can do: * Get SNPs by dbSNP rs#: Choose this search if you have already selected a list of SNPs and you just want to get the SNP information. The program will generate a Excel file containing the SNP flanking sequence, variation, quality, function, etc. In the Excel file, there are 10 highlighted fields. You can send only those highlighted information to Illumina to get SNP pre-score. (The same fields are presented in other types of searches as well.) * Get gene SNPs by gene names: Choose this search if you have a list of gene names and you want to get the SNP information in these genes. The gene name can be official gene symbol, Ensembl gene ID, RefSeq accession ID, LocusLink number, etc. * Get gene SNPs by genome regions: Choose this search if you have a list of genome regions and you want to get all gene SNP information in these regions. The software will find all the Ensembl genes in the regions and find SNPs associated to each Ensembl gene. * Get genome scan SNPs by genome regions: Choose this search if you have a list of genome regions and you want to get evenly spaced SNPs in these regions. A SNP selection tool (SNPselector) was built upon HQSNP. It took snp ID list, gene name list, or genome region list as input and searched SNPs for genome scan or gene assoctiation study. It could take an optional ABI SNP file (exported from ABI SNP search web page) as input for checking whether the candidate SNP is available from ABI. It could also take an optional Illumina SNP pre-score file as input to select SNP for Illumina SNP assay. It generated results sorted by tag SNP in LD block, SNP quality, SNP function, SNP regulatory potential, and SNP mutation risk. SNPselector is now retired from public use (as of September 30, 2010).

Proper citation: High Quality SNP Database (RRID:SCR_007230) Copy   

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http://cmckb.cellmigration.org

It is a database of keys facts about proteins, families, and complexes involved in cell migration. This ongoing project provides a large amount of automated and curated data, collected from numerous online resources that are updated monthly. These data include names, synonyms, sequence information, summaries, CMC research data, reagents, structures, as well as protein family and complex details. CMKB''s ultimate goal is to create a database that will enable the cell migration community to conveniently access significant information about molecules of interest. This will also serve as a stepping stone to pathway analysis and demonstrate how these molecules coordinate with one another during cell adhesion and movement. Sponsors: This resource is supported by the Cell Migration Consortium.

Proper citation: CMKB (RRID:SCR_007229) Copy   

•   Source: SciCrunch Registry

http://www.oreganno.org/oregano/

Open source, open access database and literature curation system for community based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. Automatically cross referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, eVOC: Cell type ontology, and Taxonomy database. Community driven resource for curated regulatory annotation.

Proper citation: Open Regulatory Annotation Database (RRID:SCR_007835) Copy   

•   Source: SciCrunch Registry

https://leger2.helmholtz-hzi.de/cgi-bin/expLeger.pl

Knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species.Provides information on gene functions (as annotated or supposed by literature from homologous organisms) , protein expression levels under defined experimental conditions ,subcellular localization of proteins (expected and/or experimentally validated) , biological meaning of genes and proteins based on KEGG, InterPro and Gene Ontology.

Proper citation: LEGER: the post-genome Database for Listeria Research (RRID:SCR_007760) Copy   

•   Source: SciCrunch Registry

http://pmap.burnham.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A database of proteolytic pathways. Its goal is to contribute to the scientific community and the understanding of proteolysis by providing better tools and data to researchers and medical researchers.

Proper citation: PMAP (RRID:SCR_000740) Copy   

•   Source: SciCrunch Registry

https://wiki.nci.nih.gov/display/cageneindex/Cancer+Gene+Index+End+User+Documentation

THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 17, 2016. A database of genes that have been experimentally associated with human cancer diseases and/or pharmacological compounds, the evidence of these associations, and relevant annotations on the data.

Proper citation: Cancer Gene Index (RRID:SCR_001117) Copy   

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https://github.com/zhenzonglei/abat

Software stores mutiple MATLAB functions to read, analyze, and visualize various kinds of data from Allen Brain Atlas.

Proper citation: Allen Brain Atlas Tools (RRID:SCR_023855) Copy   

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https://www.cernerenviza.com/syndicated-insights-and-reports-for-life-sciences/cancermpact

American healthcare company that provides data, analytics, and research to the life sciences industry, with particular focus on oncology and rare diseases.

Proper citation: Cerner Enviza (RRID:SCR_024435) Copy   

•   Source: SciCrunch Registry

http://rulai.cshl.edu/tred

Collects mammalian cis- and trans-regulatory elements together with experimental evidence. Regulatory elements were mapped on to assembled genomes. Resource for gene regulation and function studies. Users can retrieve primers, search TF target genes, retrieve TF motifs, search Gene Regulatory Networks and orthologs, and make use of sequence analysis tools. Uses databases such as Genbank, EPD and DBTSS, and employ promoter finding program FirstEF combined with mRNA/EST information and cross-species comparisons. Manually curated.

Proper citation: Transcriptional Regulatory Element Database (RRID:SCR_005661) Copy   

•   Source: SciCrunch Registry

http://www.genepath.org/

GenePath is a web-enabled intelligent assistant for the analysis of genetic data and for discovery of genetic networks. GenePath uses abductive inference to elucidate network constraints and logic to derive consistent networks. Typically, it starts with a set of genetic experiments, uses a set of embedded rules (patterns) to infer relations between genes and outcome, and based on these relations constructs a genetic network.

Proper citation: GenePath (RRID:SCR_007974) Copy   

•   Source: SciCrunch Registry

http://genomics.senescence.info/genes/

Collection of annotated and manually curated data of genes related to aging divided into genes related to longevity and/or aging in model organisms (yeast, worms, flies, mice, etc.) and aging related human genes.

Proper citation: GenAge (RRID:SCR_010223) Copy   

•   Source: SciCrunch Registry

https://www.acu.ac.uk/research-information-network/

A network resource that aims to enhance and broaden understanding of how researchers in the UK create and use information resources. The network provides services of all kinds to support the development of effective policies and practices for researchers, institutions, funders, information professionals and everyone who is involved in the information landscape.

Proper citation: Research Information Network (RRID:SCR_000931) Copy   

•   Source: SciCrunch Registry

http://www.alzforum.org/res/com/ant/

The Alzheimer Research Forum is the web''s most dynamic scientific community dedicated to understanding Alzheimer''s disease and related disorders. It also contains a database of providers of antibodies directed against several hundred molecules and proteins of relevant to research on Alzheimer and other neurodegenerative diseases. The web site reports on the latest scientific findings, from basic research to clinical trials; creates and maintains public databases of essential research data and reagents, and produces discussion forums to promote debate, speed the dissemination of new ideas, and break down barriers across the numerous disciplines that can contribute to the global effort to cure Alzheimer''s disease. The ARF team of professional science writers and editors, information technology experts, web developers and producers all work closely with our distinguished and diverse Advisory Board to ensure a high-quality of information and services. We very much welcome our readers'' participation in all aspects of the web site. Sponsors: The Alzheimer Research Forum is an independent nonprofit organization. It is supported by grants and individual donations.

Proper citation: Alzforum Antibody Directory for Neuroscience Research (RRID:SCR_013601) Copy   

•   Source: SciCrunch Registry

http://web.stanford.edu/group/barres_lab/brain_rnaseq.html

Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain.

Proper citation: Brain RNA-Seq (RRID:SCR_013736) Copy   

•   Source: SciCrunch Registry

https://phenodb.org/

Database for phenotype genotype associations for humans. Used by clinical researchers to store standardized phenotypic information, diagnosis, and pedigree data and then run analyses on VCF files from individuals, families or cohorts with suspected Mendelian disease.

Proper citation: PhenoDB (RRID:SCR_016551) Copy   

•   Source: SciCrunch Registry

https://www.sdu.dk/da/Om_SDU/Institutter_centre/Ist_sundhedstjenesteforsk/Centre/DTR.aspx?sideid=index&sprog=eng

Twin registry to studying causes of cancer, gene inheritance and environment. Contains information on twins born in Denmark. Comprises twins born through more than 125 years.

Proper citation: Danish Twin Registry (RRID:SCR_017482) Copy   

•   Source: SciCrunch Registry