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http://www.geisha.arizona.edu/geisha/

Online repository for chicken in situ hybridization information. This site presents whole mount in situ hybridization images and corresponding probe and genomic information for genes expressed in chicken embryos in Hamburger Hamilton stages 1-25 (0.5-5 days). The GEISHA project began in 1998 to investigate using high throughput whole mount in situ hybridization to identify novel, differentially expressed genes in chicken embryos. An initial expression screen of approximately 900 genes demonstrated feasibility of the approach, and also highlighted the need for a centralized repository of in situ hybridization expression data. Objectives: The goals of the GEISHA project are to obtain whole mount in situ hybridization expression information for all differentially expressed genes in the chicken embryo between HH stages 1-25, to integrate expression data with the chicken genome browsers, and to offer this information through a user-friendly graphical user interface. In situ hybridization images are obtained from three sources: 1. In house high throughput in situ hybridization screening: cDNAs obtained from several embryonic cDNA libraries or from EST repositories are screened for expression using high throughput in situ hybridization approaches. 2. Literature curation: Agreements with journals permit posting of published in situ hybridization images and related information on the GEISHA site. 3. Unpublished in situ hybridization information from other laboratories: laboratories generally publish only a small fraction of their in situ hybridization data. High quality images for which probe identity can be verified are welcome additions to GEISHA.

Proper citation: GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database (RRID:SCR_007440) Copy   

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http://gene3d.biochem.ucl.ac.uk/Gene3D/

A large database of CATH protein domain assignments for ENSEMBL genomes and Uniprot sequences. Gene3D is a resource of form studying proteins and the component domains. Gene3D takes CATH domains from Protein Databank (PDB) structures and assigns them to the millions of protein sequences with no PDB structures using Hidden Markov models. Assigning a CATH superfamily to a region of a protein sequence gives information on the gross 3D structure of that region of the protein. CATH superfamilies have a limited set of functions and so the domain assignment provides some functional insights. Furthermore most proteins have several different domains in a specific order, so looking for proteins with a similar domain organization provides further functional insights. Strict confidence cut-offs are used to ensure the reliability of the domain assignments. Gene3D imports functional information from sources such as UNIPROT, and KEGG. They also import experimental datasets on request to help researchers integrate there data with the corpus of the literature. The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes. Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins. The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Gene3D (RRID:SCR_007672) Copy   

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http://www.jobs.nih.gov/

A listing of all current openings across the NIH. You may search for NIH Jobs, browse job descriptions, view all descriptions or use the quick links.

Proper citation: Jobs(at)NIH (RRID:SCR_006471) Copy   

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http://code.google.com/p/google-refine/

Software tool that stores definitions of views of data, along with the ontology concepts they represent. This is a part of the Neuroscience Information Framework (NIF) code stack.

Proper citation: ConceptMapper (RRID:SCR_006548) Copy   

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http://www.informatics.jax.org/searches/AMA_form.shtml

Ontology that organizes anatomical structures for the adult mouse (Theiler stage 28) spatially and functionally, using ''is a'' and ''part of'' relationships. The ontology is used to describe expression data for the adult mouse and phenotype data pertinent to anatomy in standardized ways. The browser can be used to view anatomical terms and their relationships in a hierarchical display.

Proper citation: Adult Mouse Anatomy Ontology (RRID:SCR_006568) Copy   

•   Source: SciCrunch Registry

http://i2b2.cchmc.org/

A data warehouse that integrates information on patients from multiple sources and consists of patient information from all the visits to Cincinnati Children''''s between 2003 and 2007. This information includes demographics (age, gender, race), diagnoses (ICD-9), procedures, medications and lab results. They have included extracts from Epic, DocSite, and the new Cerner laboratory system and will eventually load public data sources, data from the different divisions or research cores (such as images or genetic data), as well as the research databases from individual groups or investigators. This information is aggregated, cleaned and de-identified. Once this process is complete, it is presented to the user, who will then be able to query the data. The warehouse is best suited for tasks like cohort identification, hypothesis generation and retrospective data analysis. Automated software tools will facilitate some of these functions, while others will require more of a manual process. The initial software tools will be focused around cohort identification. They have developed a set of web-based tools that allow the user to query the warehouse after logging in. The only people able to see your data are those to whom you grant authorization. If the information can be provided to the general research community, they will add it to the warehouse. If it cannot, they will mark it so that only you (or others in your group with proper approval) can access it.

Proper citation: i2b2 Research Data Warehouse (RRID:SCR_013276) Copy   

•   Source: SciCrunch Registry

http://www.geworkbench.org

geWorkbench (genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available plug-ins supporting the visualization and analysis of gene expression and sequence data. Example use cases include: * loading data from local or remote data sources. * visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways. * providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory networks reconstruction, BLAST searches, pattern/motif discovery, etc. * validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis. geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale Analysis of Genomic and Cellular Networks (one of the 7 National Centers for Biomedial Computing funded through the NIH Roadmap). Additionally, geWorkbench is supported by caBIG, NCI''s cancer Biomedical Informatics Grid initiative.

Proper citation: genomics Workbench (RRID:SCR_013599) Copy   

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http://www.metabolomicsworkbench.org

Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops.

Proper citation: Metabolomics Workbench (RRID:SCR_013794) Copy   

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http://chavi-id.org

A consortium whose goal is to further HIV research and accelerate the development of a preventative HIV vaccine. Its main research target is to define immunogens and immunization regimens that induce sustained HIV cross-protective B cell and CD4+ T cell responses.

Proper citation: CHAVI-ID (RRID:SCR_014047) Copy   

•   Source: SciCrunch Registry

https://www.pathology.umn.edu/research/liver-tissue-cell-distribution-system

Tissue bank that provides human liver tissue from regional centers for distribution to scientific investigators throughout the United States. These USA regional centers have active liver transplant programs with human subjects approval to provide portions of the resected pathologic liver for which the transplant is performed.

Proper citation: Minnesota Liver Tissue Cell Distribution System (RRID:SCR_004840) Copy   

•   Source: SciCrunch Registry

http://udn.nichd.nih.gov/brainatlas_home.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 1, 2019. The first brain atlas for the common marmoset to be made available since a printed atlas by Stephan, Baron and Schwerdtfeger published in 1980. It is a combined histological and magnetic resonance imaging (MRI) atlas constructed from the brains of two adult female marmosets. Histological sections were processed from Nissl staining and digitized to produce an atlas in a large format that facilitates visualization of structures with significant detail. Naming of identifiable brain structures was performed utilizing current terminology. For the present atlas, an adult female was perfused through the heart with PBS followed by 10% formalin. The brain was then sent to Neuroscience Associates of Knoxville, TN, who prepared the brain for histological analysis. The brain was cut in the coronal (frontal) plane at 40 microns, every sixth section stained for Nissl granules with thionine and every seventh section stained for myelinated fibers with the Weil technique. The mounted sections were photographed at the NIH (Medical Arts and Photography Branch). The equipment used was a Nikon Multiphot optical bench with Zeiss Luminar 100 mm lens, and scanned with a Better Light 6100 scan back driven by Better Light Viewfinder 5.3 software. The final images were saved as arrays of 6000x8000 pixels in Adobe Photoshop 6.0. A scale in mm provided with these images permitted construction of the final Nissl atlas files with a horizontal and vertical scale. Some additional re-touching (brightness and contrast) was done with Adobe Photoshop Elements 2.0. The schematic (labeled) atlas plates were created from the Nissl images. The nomenclature came almost exclusively from brainmaps.org, where a rhesus monkey brain with structures labeled can be found. The labels for the MRI images were placed by M. R. Zametkin, under supervision from Dr. Newman.

Proper citation: Brain atlas of the common marmoset (RRID:SCR_005135) Copy   

•   Source: SciCrunch Registry

http://frederick.cancer.gov/

A federally funded research and development center dedicated to biomedical research. NCI-Frederick partners with university, government, and corporate scientists to speed the translation of laboratory research into new diagnostic tests and treatments for cancer and HIV/AIDS. NCI-Frederick is comprised of more than 2,800 government- and contractor-employed biomedical researchers, laboratory technicians, and support staff and several cancer research centers. The FNLCR provides quick response capabilities and meets special long-term research and development needs for NCI that cannot be met as effectively by existing in-house or contractor resources.

Proper citation: NCI-Frederick (RRID:SCR_004880) Copy   

•   Source: SciCrunch Registry

http://science.education.nih.gov/SciEdBlog

A blog put out by the NIH Office of Science Education.

Proper citation: NIH SciEd Blog (RRID:SCR_005499) Copy   

•   Source: SciCrunch Registry

http://www.neuroepigenomics.org/methylomedb/

A database containing genome-wide brain DNA methylation profiles for human and mouse brains. The DNA methylation profiles were generated by Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS) method and analyzed by Methyl-Analyzer software package. The methylation profiles cover over 80% CpG dinucleotides in human and mouse brains in single-CpG resolution. The integrated genome browser (modified from UCSC Genome Browser allows users to browse DNA methylation profiles in specific genomic loci, to search specific methylation patterns, and to compare methylation patterns between individual samples. Two species were included in the Brain Methylome Database: human and mouse. Human postmortem brain samples were obtained from three distinct cortical regions, i.e., dorsal lateral prefrontal cortex (dlPFC), ventral prefrontal cortex (vPFC), and auditory cortex (AC). Human samples were selected from our postmortem brain collection with extensive neuropathological and psychopathological data, as well as brain toxicology reports. The Department of Psychiatry of Columbia University and the New York State Psychiatric Institute have assembled this brain collection, where a validated psychological autopsy method is used to generate Axis I and II DSM IV diagnoses and data are obtained on developmental history, history of psychiatric illness and treatment, and family history for each subject. The mouse sample (strain 129S6/SvEv) DNA was collected from the entire left cerebral hemisphere. The three human brain regions were selected because they have been implicated in the neuropathology of depression and schizophrenia. Within each cortical region, both disease and non-psychiatric samples have been profiled (matching subjects by age and sex in each group). Such careful matching of subjects allows one to perform a wide range of queries with the ability to characterize methylation features in non-psychiatric controls, as well as detect differentially methylated domains or features between disease and non-psychiatric samples. A total of 14 non-psychiatric, 9 schizophrenic, and 6 depression methylation profiles are included in the database.

Proper citation: MethylomeDB (RRID:SCR_005583) Copy   

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http://llama.mshri.on.ca/funcassociate/

A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool

Proper citation: FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) Copy   

•   Source: SciCrunch Registry

http://bard.nih.gov/

Database that allows scientists without specialized training to effectively utilize Molecular Libraries Program (MLP) data. It allows the research community to utilize and develop new chemical probes to explore biological functions by building a central, permanently accessible link to all aspects of chemical biology data and analyses. The project is split into two basic segments, the first segment delivering functionality for a data dictionary, as well as assay protocol and data entry tools. The second builds a data warehouse for analysis and visualization, accessible through a public RESTful API. They will initially deploy two clients that will use this API - a web-based interface and a desktop application. Advanced access to data and the platforms will also be available to support plug-in development and the repackaging of data by others. Initially the project will focus on small molecule assays. Features: * allow scientists to annotate assay data using a common, shared language * provide facile access to data, integrating existing chemical biology and computational resources * enable meaningful analysis and interpretation of discovery data by the research community * support hypothesis generation for iterative probe- and drug-discovery projects * inform the entire small molecule discovery and development process, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BARD (RRID:SCR_006283) Copy   

•   Source: SciCrunch Registry

http://crcview.hegroup.org/

Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in.

Proper citation: CRCView (RRID:SCR_007092) Copy   

•   Source: SciCrunch Registry

http://www.cpc.unc.edu/projects/addhealth

Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database.

Proper citation: Add Health (National Longitudinal Study of Adolescent Health) (RRID:SCR_007434) Copy   

•   Source: SciCrunch Registry

http://compbio.soe.ucsc.edu/yeast_introns.html

Database of information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. Listed are known spliceosomal introns in the yeast genome and the splice sites actually used are documented. Through the use of microarrays designed to monitor splicing, they are beginning to identify and analyze splice site context in terms of the nature and activities of the trans-acting factors that mediate splice site recognition. In version 3.0, expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors is included. These data are displayed on each intron page for browsing and can be downloaded for other types of analysis.

Proper citation: Yeast Intron Database (RRID:SCR_007144) Copy   

•   Source: SciCrunch Registry

https://imagej.net/

Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.

Proper citation: ImageJ (RRID:SCR_003070) Copy   

•   Source: SciCrunch Registry