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http://www.ncbi.nlm.nih.gov/gene/about-generif

A database and annotation tool that provides a simple mechanism to allow scientists to add to the functional annotation of genes described in Gene. To be processed, a valid Gene ID must exist for the specific gene, or the Gene staff must have assigned an overall Gene ID to the species. The latter case is implemented via records in Gene with the symbol NEWENTRY.

Proper citation: Gene Reference into Function (RRID:SCR_003436) Copy   

•   Source: SciCrunch Registry

https://github.com/immunogenomics/harmony

Software R package to project cells into shared embedding in which cells group by cell type rather than dataset specific conditions. Harmony simultaneously accounts for multiple experimental and biological factors. Used for integration of single cell data.

Proper citation: Harmony (RRID:SCR_022206) Copy   

•   Source: SciCrunch Registry

http://www.nihclinicalcollection.com

A plated array of approximately 450 small molecules that have a history of use in human clinical trials. The collection was assembled by the National Institutes of Health (NIH) through the Molecular Libraries Roadmap Initiative as part of its mission to enable the use of compound screens in biomedical research. Similar collections of FDA approved drugs have proven to be rich sources of undiscovered bioactivity and therapeutic potential. The clinically tested compounds in the NCC are highly drug-like with known safety profiles. These compounds can provide excellent starting points for medicinal chemistry optimization and, for high-affinity targets, may even be appropriate for direct human use in new disease areas.

Proper citation: NIH Clinical Collection (RRID:SCR_007349) Copy   

•   Source: SciCrunch Registry

http://www.project-redcap.org/

Web application that allows users to build and manage online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a "data dictionary" template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. REDCap has a quick and easy software installation process, so that you can get REDCap running and fully functional in a matter of minutes. Several language translations have already been compiled for REDCap (e.g. Chinese, French, German, Portuguese), and it is anticipated that other languages will be available in full versions of REDCap soon. The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions.

Proper citation: REDCap (RRID:SCR_003445) Copy   

•   Source: SciCrunch Registry

https://www.teamtat.org

Web based collaborative text annotation tool. Used for managing multi-user, multi-label document annotation. Project managers can specify annotation schema for entities and relations and select annotators and distribute documents anonymously to prevent bias. Document input format can be plain text, PDF or BioC (uploaded locally or automatically retrieved from PubMed/PMC), and output format is BioC with inline annotations. Displays figures from full text.

Proper citation: TeamTat (RRID:SCR_023439) Copy   

•   Source: SciCrunch Registry

https://ncats.nih.gov/grdr/rdhub

A database of biospecimens collected, stored, and distributed by biorepositories in the United States and around the globe. Its goals are: To help and assist interested parties and investigators search, locate, and identify desired biospecimens needed for their research; to facilitate collaboration and sharing of material and data among investigators across the globe; to accelerate research to facilitate the discovery of new treatments, therapeutics and eventually cures for rare diseases as well as common diseases; to identify, locate and increase the awareness of existing biorepositories across the globe; and to link the RD-HUB with the Global Rare Diseases Patient Registry and Data Repository (GRDR).

Proper citation: Biospecimens/Biorepositories: Rare Disease-HUB (RD-HUB) (RRID:SCR_004327) Copy   

•   Source: SciCrunch Registry

http://mind.loni.usc.edu

The MiND: Metadata in NIfTI for DWI framework enables data sharing and software interoperability for diffusion-weighted MRI. This site provides specification details, tools, and examples of the MiND mechanism for representing important metadata for DWI data sets at various stages of post-processing. MiND framework provides a practical solution to the problem of interoperability between DWI analysis tools, and it effectively expands the analysis options available to end users. To assist both users and developers in working with MiND-formatted files, we provide a number of software tools for download. * MiNDHeader A utility for inspecting MiND-extended files. * I/O Libraries Programming libraries to simplify writing and parsing MiND-formatted data. * Sample Files Example files for each MiND schema. * DIRAC LONI''s Diffusion Imaging Reconstruction and Analysis Collection is a DWI processing suite which utilizes the MiND framework.

Proper citation: LONI MiND (RRID:SCR_004820) Copy   

•   Source: SciCrunch Registry

http://ccr.coriell.org/Sections/Collections/USIDNET/?SsId=15

The USIDNET DNA and Cell Repository has been established as part of an NIH-funded program - the US Immunodeficiency Network - to provide a resource of DNA and functional lymphoid cells obtained from patients with various primary immunodeficiency diseases. These uncommon disorders include patients with defects in T cell, B cell and/or granulocyte function as well as patients with abnormalities in antibodies / immunoglobulins, complement and other host defense mechanisms. All samples in this Repository have been de-identified to protect the privacy of the individual donors. The USIDNET also operates a Patient Data Registry in addition to this Repository and certain clinical data relating to a specific sample may be available through the Registry for some of the patient samples in the Repository collection. Materials in the collection are being made available at modest cost to qualified investigators in academic and commercial organizations in an effort to stimulate research to increase understanding of these orphan diseases and to promote development of new treatments. Requestors are required to complete a Statement of Research Intent briefly describing their proposed use of materials obtained from the Repository and must sign an Assurance agreeing to conditions established by USIDNET for distribution of samples from its collection. Requestors wishing to obtain additional clinical data specific to individual samples in the Repository collection must make a separate application for that information to the Registry (see www.usidnet.org) Physicians or Patients wishing to submit cell samples for the Repository collection should first contact Coriell to arrange for the Repository to send them the correct sample collection tubes as well as prepaid mailers for returning the collected sample(s) to Coriell. Separate collection and shipping procedures may be involved depending on how many samples are to be shipped at one time and whether the shipment will involve freshly obtained blood or already established cell lines.

Proper citation: USIDNET DNA and Cell Repository (RRID:SCR_004661) Copy   

•   Source: SciCrunch Registry

http://ki.se/en/meb/twingene-and-genomeeutwin

In collaboration with GenomeEUtwin, the TwinGene project investigates the importance of quantitative trait loci and environmental factors for cardiovascular disease. It is well known that genetic factors are of considerable importance for some familial lipid syndromes and that Type A Behavior pattern and increased lipid levels infer increased risk for cardiovascular disease. It is furthermore known that genetic factors are of importance levels of blood lipid biomarkers. The interplay of genetic and environmental effects for these risk factors in a normal population is less well understood and virtually unknown for the elderly. In the TwinGene project twins born before 1958 are contacted to participate. Health and medication data are collected from self-reported questionnaires, and blood sampling material is mailed to the subject who then contacts a local health care center for blood sampling and a health check-up. In the simple health check-up, height, weight, circumference of waist and hip, and blood pressure are measured. Blood is sampled for DNA extraction, serum collection and clinical chemistry tests of C-reactive protein, total cholesterol, triglycerides, HDL and LDL cholesterol, apolipo��protein A1 and B, glucose and HbA1C. The TwinGene cohort contains more than 10000 of the expected final number of 16000 individuals. Molecular genetic techniques are being used to identify Quantitative Trait Loci (QTLs) for cardiovascular disease and biomarkers in the TwinGene participants. Genome-wide linkage and association studies are ongoing. DZ twins have been genome-scanned with 1000 STS markers and a subset of 300 MZ twins have been genome-scanned with Illumina 317K SNP platform. Association of positional candidate SNPs arising from these genomscans are planned. The TwinGene project is associated with the large European collaboration denoted GenomEUtwin (www.genomeutwin.org, see below) which since 2002 has aimed at gathering genetic data on twins in Europe and setting up the infrastructure needed to enable pooling of data and joint analyses. It has been the funding source for obtaining the genome scan data. Types of samples: * EDTA whole blood * DNA * Serum Number of sample donors: 12 044 (sample collection completed)

Proper citation: KI Biobank - TwinGene (RRID:SCR_006006) Copy   

•   Source: SciCrunch Registry

https://github.com/VH-Lab/vhlab-microscopyimageanalysis-matlab

Software Matlab app for analysis of high density imaging data like that from Array Tomography.

Proper citation: vhlab-microscopyimageanalysis-matlab (RRID:SCR_024450) Copy   

•   Source: SciCrunch Registry

http://www.biosyn.com/

A commercial supplier of custom synthetic molecules. They specialize in peptides, oligonucleotides, bioconjugation, molecular biology services, proteins and specialty chemistry.

Proper citation: Bio-Synthesis (RRID:SCR_000820) Copy   

•   Source: SciCrunch Registry

https://bioinformaticshome.com/tools/rna-seq/descriptions/LIGER.html

Software R package for integrating and analyzing multiple single-cell datasets. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors. Used for analysis of multiple scRNA-seq data sets.

Proper citation: LIGER (RRID:SCR_018100) Copy   

•   Source: SciCrunch Registry

http://drugcentral.org/

Database of drug information created and maintained by the Division of Translational Informatics at University of New Mexico. It provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic action.

Proper citation: DrugCentral (RRID:SCR_015663) Copy   

•   Source: SciCrunch Registry

http://www.gensat.org/

Gene expression data and maps of mouse central nervous system. Gene expression atlas of developing adult central nervous system in mouse, using in situ hybridization and transgenic mouse techniques. Collection of pictorial gene expression maps of brain and spinal cord of mouse. Provides tools to catalog, map, and electrophysiologically record individual cells. Application of Cre recombinase technologies allows for cell-specific gene manipulation. Transgenic mice created by this project are available to scientific community.

Proper citation: Gene Expression Nervous System Atlas (RRID:SCR_002721) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/glimmerhmm/

A gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).

Proper citation: GlimmerHMM (RRID:SCR_002654) Copy   

•   Source: SciCrunch Registry

http://neurospy.org

neurospy is a free software for functional imaging of fast neuronal activity. neurospy is a modular cross-platform application framework written in Java for the NetBeans Platform. At this time it runs on Windows XP-based LeCroy oscilloscopes and drives acousto-optic scanners via USB using the Analog Devices 9959 Direct Digital Synthesis chip. This combination makes one of the most powerful systems for scanning microscopy available today at any price. neurospy is very easy to port to other kinds of acquisition and scanning hardware.

Proper citation: neurospy (RRID:SCR_007016) Copy   

•   Source: SciCrunch Registry

http://ki-su-arc.se/dementia-in-swedish-twins-harmony/

A twin study characterizing the importance of genetic factors for dementia and using discordant twin pairs to study other putative risk factors which control for genetic propensity to develop the disease. Molecular genetic studies have identified a number of mutations and other markers associated with early age of onset Alzheimer''''s disease. However, most cases of late age of onset dementia are considered sporadic, that is, without a clear genetic basis. Twin studies provide a unique opportunity to characterize the importance of genetic factors for dementia. Discordant twin pairs additionally provide the opportunity to study other putative risk factors which controlling for genetic propensity to develop the disease. In the first wave of the Study of Dementia in Swedish Twins, all SATSA twins born before 1935 have been screened for dementia symptoms. Over 190 suspects have been identified. This pilot study has been expanded to the entire registry in the study known as HARMONY. All twins aged 65 and older were invited to participate in a computer assisted telephone screening interview. A total of 13,519 individuals completed the interview (response rate = 75.9%). Dementia screening was based on the TELE, which includes the 10-item MSQ, other cognitive items (counting backwards, recalling three words, and similarities), and questions about health and daily functioning; or on Blessed scores obtained from a proxy interview. Among those screened, 1565 were positive for suspicion of dementia and were referred for complete clinical evaluation by a physician and a nurse. Once the preliminary in-person evaluation suggested that the suspected case was demented, the twin partner was also invited for an identical clinical work-up. Response rate for clinical evaluations is 71.4%. Approximately half of those visited for evaluation have been diagnosed as demented according to DSM-IV criteria, of which two-thirds have Alzheimer''''s disease. An extensive assessment of probable risk exposure is also included. Longitudinal follow-up is yet another feature of the study. Association studies with candidate genes are also being performed. Types of samples * DNA Number of sample donors * 1154 (sample collection completed)

Proper citation: KI Biobank - HARMONY (RRID:SCR_008884) Copy   

•   Source: SciCrunch Registry

http://www.sb.fsu.edu/~rsref/Distribution/roadmap_distribution.htm

Software tool to display surface of macromolecule and its properties. Uses projections to map van der Waals or solvent accessible surface of macromolecule onto plane., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Roadmap (RRID:SCR_017207) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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