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

A native Java-based imaging processing environment similar to the ITK/VTK paradigm. Initially developed as an extension to MIPAV (CIT, NIH, Bethesda, MD), the JIST processing infrastructure provides automated GUI generation for application plug-ins, graphical layout tools, and command line interfaces. This repository maintains the current multi-institutional JIST development tree and is recommended for public use and extension. JIST was originally developed at IACL and MedIC (Johns Hopkins University) and is now also supported by MASI (Vanderbilt University).

Proper citation: JIST: Java Image Science Toolkit (RRID:SCR_008887) Copy   

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http://www.swanrepository.com/

The SWAN Repository is the biologic specimen bank of the Study of Women''s Health Across the Nation (SWAN). SWAN is a National Institutes of Health funded, multi-site, longitudinal study of the natural history of the midlife including the menopausal transition. The overall goal of SWAN is to describe the chronology of the biological and psychosocial characteristics that occur during midlife and the menopausal transition. In addition, SWAN is describing the effect of the transition and its associated characteristics on subsequent health and risk factors for age related chronic diseases. SWAN was designed to collect and analyze information on demographics, health and social characteristics, reproductive history, pre-existing illness, physical activity, and health practices of mid-life women in multi-ethnic, community-based samples; elucidate factors that differentiate symptomatic from asymptomatic women during the menopausal transition; identify and utilize appropriate markers of the aging of the ovarian-hypothalamo-pituitary axis and relate these markers to alterations in menstrual cycle characteristics as women approach and traverse the menopause; and explain factors that differentiate women most susceptible to long-term pathophysiological consequences of ovarian hormone deficiency from those who are protected. The biological specimen bank can also be linked by identification number (not by participant name) to data collected in the Core SWAN protocol. The specimen bank can also be linked with data from the Daily Hormone Study as well as menstrual calendars. Types of data include: epidemiological data, psychosocial data, physical measures, as well as data from assays (endocrine and cardiovascular information). SWAN has seven clinical study sites located in six states, two in California, and one each in Chicago, Boston, Detroit area, northern New Jersey and Pittsburgh. The SWAN cohort was recruited in 1996/7 and consists of 3302 African American, Caucasian, Chinese American, Hispanic and Japanese American women. Cohort members complete an annual clinic visit. The Core Repository includes over 1.8 million samples from the first 11 years of specimen collection. This includes samples from annual visits and samples from the Daily Hormone Sub-study (DHS). During an Annual visit, participants provide materials for up to 24-28 aliquots to be incorporated into the Repository. During a DHS visit, a participant provides 6 serum samples and between ~30-50 urine samples depending upon the length of her menstrual cycle. DHS participants (887) provide urine samples collected throughout one menstrual cycle each year. A typical DHS collection consists of a blood draw plus collection of 10 ml of urine daily throughout the month-long menstrual cycle, up to 50 days. DHS Repository samples consist of 6 serum samples and 30 5 ml urine samples. Specimen collection occurs from the time of menstrual bleed to the subsequent menstrual bleed or up to 50 days, whichever come first. The current DHS collection consists of more than 200,000 specimens stored in 5 ml vials. The SWAN DNA Repository currently contains extracted diluted DNA from 1538 SWAN participants. B-lymphocytes were transformed with Epstein Barr virus, and the resulting transformed b-cells aliquoted. Information about using these transformed cells for genomic or proteomic studies is available. DNA has been extracted from one aliquot (per woman) of the immortalized cells using the Puregene system. There was an average DNA yield of 217.0 mg/mL and a A260/A280 average ratio of 1.86. This DNA, in turn, has been aliquoted into 20ng/1 ml units for release by the DNA Repository. Samples are free of personal identifiers and collected under consents that allow a broad range of activities related to women''s health. All of these samples are available to researchers who wish to study the midlife and menopausal transition. Scientists who use these specimens can also request data collected during a participant''s annual visit including medical and health history, psychosocial measures, biological measures and anthropometry.

Proper citation: Study of Womens Health Across the Nation (SWAN) Repository (RRID:SCR_008810) Copy   

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http://www.mouse-genome.bcm.tmc.edu/ENU/MutagenesisProj.asp

THIS RESOURCE IS NO LONGER IN SERVICE. For updated mutant information, please visit MMRRC or The Jackson Laboratory. Produces, characterizes, and distributes mutant mouse strains with defects in embryonic and postembryonic development. The goal of the ENU Mutagenesis project III is to determine the function of genes on mouse Chromosome 11 by saturating the chromosome with recessive mutations. The distal 40 cM of mouse Chr 11 exhibits linkage conservation with human Chromosome 17. We are using the chemical N-ethyl-N-nitrosourea (ENU) to saturate wild type chromosomes with point mutations. By determining the function of genes on a mouse chromosome, we can extrapolate to predict function on a human chromosome. We expect many of the new mutants to represent models of human diseases such as birth defects, patterning defects, growth and endocrine defects, neurological anomalies, and blood defects. Because many of the mutations we expect to isolate may be lethal or detrimental to the mice, we are using a unique approach to isolate mutations. This approach uses a balancer chromosome that is homozygous lethal and carries a dominant coat color marker to suppress recombination over a reasonable interval.

Proper citation: Mouse Mutagenesis Center for Developmental Defects (RRID:SCR_007321) Copy   

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https://www.archrproject.com/

Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing.

Proper citation: ArchR (RRID:SCR_020982) Copy   

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https://alzped.nia.nih.gov

Publicly available, searchable, data resource that aims to increase transparency, reproducibility and translatability of preclinical efficacy studies of candidate therapeutics for Alzheimer’s disease. Knowledge platform for dissemination of data and analysis to scientists, from academic centers, industry, disease focused foundations. Provides quick access and visibility to integrated preclinical efficacy data from published and unpublished studies.

Proper citation: Alzheimer Disease Preclinical Efficacy Database (RRID:SCR_021230) Copy   

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http://hms-dbmi.github.io/scde/index.html

Software package that implements a set of statistical methods for analyzing single-cell RNA-seq data, including differential expression analysis (Kharchenko et al.) and pathway and geneset overdispersion analysis (Fan et al.)

Proper citation: SCDE (RRID:SCR_015952) Copy   

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http://www.grc.nia.nih.gov/

A research program of the NIA which focuses on neuroscience, aging biology, and translational gerontology. The central focus of the program's research is understanding age-related changes in physiology and the ability to adapt to environmental stress, and using that understanding to develop insight about the pathophysiology of age-related diseases. The IRP webpage provides access to other NIH resources such as the Biological Biochemical Image Database, the Bioinformatics Portal, and the Baltimore Longitudinal Study of Aging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Intramural Research Program (RRID:SCR_012734) Copy   

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http://mrtools.mgh.harvard.edu/index.php/TBR

A tool for functional connectivity analysis of fcMRI data that maps functional data from individual sessions onto a priori spatial components from group level parcellations.

Proper citation: Template Based Rotation (RRID:SCR_012157) Copy   

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http://cbl.uh.edu/ORION/

Project to develop tools that explore single neuron function via sophisticated image analysis. ORION software bridges advanced optical imaging and compartmental modeling of neuronal function by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function.

Proper citation: ORION (RRID:SCR_010621) Copy   

•   Source: SciCrunch Registry

https://github.com/nskvir/RepEnrich

Software tool to profile enrichment of next generation sequencing reads at transposable elements. Method to estimate repetitive element enrichment using high throughput sequencing data. Used to study genome wide transcriptional regulation of repetitive elements.RepEnrich2 is updated method to estimate repetitive element enrichment using high-throughput sequencing data.

Proper citation: RepEnrich (RRID:SCR_021733) Copy   

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https://github.com/evarol/HYDRA

Software tool as novel non-linear learning algorithm for simultaneous binary classification and subtype identification. Can handle imaging and non-imaging data and can find applications in exploratory analyses other than clustering of brain images.Software performs clustering of heterogenous disease patterns within patient group.

Proper citation: Heterogeneity through Discriminative Analysis (RRID:SCR_021958) Copy   

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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   

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http://senselab.med.yale.edu/cellpropdb

A repository for data regarding membrane channels, receptor and neurotransmitters that are expressed in specific types of cells. The database is presently focused on neurons but will eventually include other cell types, such as glia, muscle, and gland cells. This resource is intended to: * Serve as a repository for data on gene products expressed in different brain regions * Support research on cellular properties in the nervous system * Provide a gateway for entering data into the cannonical neuron forms in NeuronDB * Identify receptors across neuron types to aid in drug development * Serve as a first step toward a functional genomics of nerve cells * Serve as a teaching aid

Proper citation: Cell Properties Database (RRID:SCR_007285) Copy   

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

Atlas of segmented and normalized high-resolution postmortem MRI of the human hippocampus. Additional data (raw images) is available through the SCM link. It requires knowing how to use CVS.

Proper citation: Penn Hippocampus Atlas (RRID:SCR_000421) Copy   

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https://masst.gnps2.org/microbemasst/

Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns.

Proper citation: microbeMASST (RRID:SCR_024713) Copy   

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https://imputationserver.sph.umich.edu/index.html#!pages/home

Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4.

Proper citation: Michigan Imputation Server (RRID:SCR_023554) Copy   

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https://www.rdocumentation.org/packages/DGCA/versions/1.0.2

Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix.

Proper citation: Differential Gene Correlation Analysis (RRID:SCR_020964) Copy   

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https://github.com/denisecailab/minian

Software miniscope analysis pipeline that requires low memory and computational demand so it can be run without specialized hardware. Offers interactive visualization that allows users to see how parameters in each step of pipeline affect output.

Proper citation: Minian (RRID:SCR_022601) Copy   

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http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/03255

Data set that looked at religion, self-rated health, depression, and psychological well-being in a sample of older Blacks and older Whites (aged 65 and over) within the United States. Questions were asked regarding religious status, activities, and beliefs among those who currently practice the Christian faith, those who used to be Christian but are not now, and those who have never been associated with any religion during their lifetimes. Demographic variables include age, race, sex, education, and income. Wave II was collected in 2004 and reinterviewed 1,024 respondents. There were 75 respondents who refused to participate, 112 who could not be located, 70 that were too ill for participation, 11 who had moved to nursing homes and 208 were deceased. * Dates of Study: 2001- 2004 * Study Features: Longitudinal, Minority Oversample * Sample Size: 1,500

Proper citation: Religion Aging and Health Survey (RRID:SCR_003625) Copy   

•   Source: SciCrunch Registry

http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00158

Data set from an ongoing, longitudinal-sequential study of adult-cognitive development, which began in 1956, that focuses on individual differences in age-related changes and differences across cohorts. The general purpose of the study is to examine the changes in intelligence and various abilities throughout adulthood. The data provide a normative base to determine the ages of detectable decrements in ability and the magnitudes of the decrements. The study also seeks to examine patterns of generational differences and age-related differences and to determine the effects of educational intervention on intellectual decline. This study is a mixed cross-sectional, longitudinal, and time-lag design. Included are family studies of cognitive similarity, prospective studies of early signs of dementia via psychological and genetic markers, as well as the investigation of personality and demographic variables that affect cognitive change in adults from young adulthood to advanced old age. Questionnaire topics include health behavior, behavioral rigidity, family environment, Life Complexity Inventory, CES-D Depression, and cognitive and neuropsychology batteries. Group Health Cooperative of Puget Sound Medical Records and Pharmacy Records. * Dates of Study: 1956-Present * Study Features: Longitudinal * Sample Size: 6,000+

Proper citation: Seattle Longitudinal Study (RRID:SCR_003654) Copy   

•   Source: SciCrunch Registry