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http://www.mssm.edu/research/programs/manhattan-hiv-brain-bank/
Biorepository of tissues and fluids relevant for the neurologic, neuropsychologic, psychiatric and neuropathologic manifestations of HIV infection, linked to medical records and an on-going clinical trial for research use by the scientific community. The MHBB conducts a longitudinal, observational study that follows a group of HIV-infected individuals who have agreed to be fluid and organ donors for the purposes of AIDS research. They are currently the largest, multidisciplinary neuroAIDS cohort in New York City, the epicenter of the US HIV epidemic. Research participants undergo regular neurologic, neuropsychologic, and psychiatric evaluations, and provide body fluid samples that are linked to clinical information. Upon their demise, study participants become organ donors. This program has supplied clinical information, tissue, and fluid samples to over 70 qualified AIDS researchers across America, Europe and Australia. In fulfilling its resource mission, the MHBB functions as part of the National NeuroAIDS Tissue Consortium (NNTC). MHBB provides a means by which people living with HIV can be engaged in the struggle to improve our knowledge about HIV infection and the damage it causes to the body.
Proper citation: Manhattan HIV Brain Bank (RRID:SCR_010520) Copy
http://brainandsociety.org/the-brain-observatory
Formerly a topical portal studying the brain which collected and imaged 1000 human brains, the Brain Observatory has partnered with the Institute for Brain and Society to build virtual laboratories that will feed directly into the database of images and knowledge created in the context of the Human Brain Library. The Brain Observatory will also host exhibits, conferences, and events aimed at promoting a heightened awareness of brain research and how its results can benefit personal brain fitness and mental health.
Proper citation: Brain Observatory (RRID:SCR_010641) Copy
http://www.biobanks.se/medicalbiobank.htm
A biobank created from a cross-sectional population of a town in Sweden. The Medical Biobank is mainly based on three cohorts: The V��sterbotten intervention cohort, the MONICA-cohort, and the Mammary screening cohort. These sub-cohorts together are named Northern Sweden Health and Disease Study Cohort (North Health). These sub-cohorts together is named Northern Sweden Health and Disease Study Cohort (North Health). Originally, the V��sterbotten Intervention program (VIP) is a long-term project intended for health promotion of the population of V��sterbotten. All individuals 40, 50 and 60 years of age in the population of the county are invited for screening (approx. 254.000 inhabitants). They are asked to complete a questionnaire concerning various lifestyle factors including diet. They are also asked to donate a separate blood sample to the Medical Biobank for freeze storage for later research purposes. The project started in 1985 and the cohort covered in December 2002, 74,000 individuals, of whom 67,000 had donated blood samples. The material is supplemented with population based samples from a local mammary screening (44,000 sampling occasions, 25,700 unique individuals) and from the Northern Sweden MONICA Project (11,500 sampling occasions, 7,500 unique individuals). The total cohort contains at the moment 85.000 unique individuals with 130.000 sampling occasions. The VIP and MONICA cohorts are population based and the mammary screening cohort are nearly population based. Follow-up: * For the VIP-cohort a second sample (and questionnaire) is collected with a 10-year interval of the individuals within the cohort. * Repeated sampling was performed in the MONICA project in 1999 on individuals participating in 1986, 1990, and 1994. * From 1997 repeated screening has started within the mammary screening program with sampling every second year, in the age group 50-69 years within the county. Biobank content: * Life-Style Questionnaire: Every attending subject is asked to answer a questionnaire, which in the VIP and MONICA-projects includes questions about education, occupation/working conditions, daily habits including smoking, diet, etc and in the mammary screening cohort on reproductive conditions. The dietary questionnaire has been validated twice. The data from the questionnaires, as well as from results from the biobank, are kept in a database for future research purposes. The questionnaires in the VIP and the MONICA project are optically read. * Measurements: Blood Pressure, Anthropometry, Glucose Tolerance Test, Blood Lipids * Blood Samples: The attendants are asked for their willingness to donate a sample of 20-ml whole blood for future analyses. The sample is taken after 4 hours of fasting or in the morning after an over night fasting (most samples) in the VIP and MONICA cohorts. The 20-ml sample is divided into 10 subsamples consisting of 6 plasma, 2 leukocyte (buffy coat) and 2 erythrocyte samples. All material is frozen at -80 degrees C. The organization of the bank is elaborated with specially trained staff and an organization of transport-, storage- and security facilities. For DNA handling a specialized laboratory has been built up. * End-points: Mortality, Cancer events, Cardiovascular events, Other morbidity, Other registry-based follow-up * Registries: At regular intervals the cohort is scanned for incident myocardial infarctions (MI) and stroke utilizing the Northern Sweden MONICA registry and for cancer using the regional cancer registry. In the future the same procedure will be applied also on other registries e.g. diabetes, osteoporosis, dementia.
Proper citation: Medical Biobank (RRID:SCR_010748) Copy
Project aims to promote data sharing, archiving, and reuse among researchers who study human development. Focuses on creating tools for scientists to store, manage, preserve, analyze and share video and related data.
Proper citation: Databrary (RRID:SCR_010471) Copy
A genome browser that includes mappings between genomic features and Affymetrix microarrays. Associated with annmap is: * a Bioconductor package, annmap that provides programmatic access to the underlying MySQL database tables (which are freely available for download on this site) * xmapbridge, a Bioconductor package that outputs numeric data in a form suitable for presentation in the browser. This is supported by XMapBridge, a Java client that sits on the local desktop and performs the graph rendering for the browser.
Proper citation: Annmap (RRID:SCR_011783) Copy
http://mirtar.mbc.nctu.edu.tw/human/
An integrated web server for identifying miRNA-target interactions in human. The tool enables biologists easily to identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. It also provides perspective of information on the miRNA targets on alternatively spliced transcripts.
Proper citation: miRTar (RRID:SCR_010851) Copy
A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences.
Proper citation: oPOSSUM (RRID:SCR_010884) Copy
http://tfclass.bioinf.med.uni-goettingen.de/tfclass
Database that classifies human transcription factors based on the characteristics of their DNA-binding domains. It comprises six levels (superclasses, classes, families, subfamilies, genera and factor species), two of which are optional (subfamilies and factor species). The full classification can also be obtained as html document and as ontology in obo-format., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: TFClass (RRID:SCR_012018) Copy
Community of scientists focused on the study of epithelial cell function and mucosal biology including inflammation and host defense of the gastrointestinal tract. It focuses on the intestinal and inflammatory bowel diseases; gut microbiology; and stem cell and developmental biology of the intestine and liver in organ physiology, regenerative medicine, and metabolism.
Proper citation: Harvard Digestive Disease Center (RRID:SCR_015587) Copy
http://csb.pitt.edu/erc_analysis/Methods.php
Web-based statistical application that measures correlated rates across a phylogeny, allowing for extraction of genes with similar evolutionary histories. It can identify new functional connections between genes.
Proper citation: Evolutionary Rate Covariation (RRID:SCR_015669) Copy
https://portals.broadinstitute.org/cmap/
Collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms. camp aims to enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Connectivity Map 02 (RRID:SCR_015674) Copy
http://ccb.jhu.edu/software/hisat2/index.shtml
Graph-based alignment of next generation sequencing reads to a population of genomes.
Proper citation: HISAT2 (RRID:SCR_015530) Copy
Project portal for a cooperative research program sponsored by the National Institute of Allergy and Infectious Diseases (NIAID). CTOT-C is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for pediatric heart, lung, or kidney transplant recipients.
Proper citation: Clinical Trials in Organ Transplantation in Children (CTOT-C) (RRID:SCR_015860) Copy
Web server implemented in JAVA and PHP for annotating genetic variants by m6A function. It predicts and annotates N6-methyladenosine (m6A) alterations from genetic variants data such as germline SNPs or cancer somatic mutations. It employs two accurate prediction models for human and mouse using Random Forest algorithm. It conducts a statistical analysis for all the predicted m6A alterations. Provides statistical diagrams and a genome browser to visualize the topology characteristics of predicted m6A alterations.
Proper citation: m6ASNP: Annotation of genetic variants by m6A function (RRID:SCR_016048) Copy
https://plusconsortium.umn.edu
Research consortium from many different fields to plan, perform and analyze the studies that are needed to help researchers conduct future prevention and intervention for Lower Urinary Tract Symptoms (LUTS) in women.
Proper citation: Prevention of Lower Urinary Tract Symptoms (RRID:SCR_016923) Copy
https://commonfund.nih.gov/hubmap
Project to facilitate research on single cells within tissues by supporting data generation and technology development to explore the relationship between cellular organization and function, as well as variability in normal tissue organization at the level of individual cells. Framework for functional mapping the human body with cellular resolution.Designed to support diverse spatial and non-spatial omics and imaging data types and to integrate with a wide range of analysis workflows.
Proper citation: The Human BioMolecular Atlas Program (RRID:SCR_016922) Copy
Project to ethically obtain and evaluate human kidney biopsies from participants with Acute Kidney Injury (AKI) or Chronic Kidney Disease (CKD), create a kidney tissue atlas, define disease subgroups, and identify critical cells, pathways, and targets for novel therapies. Used to develop the next generation of software tools to visualize and understand the various components of kidney diseases and to optimize data collection. Multi site collaboration comprised of patients, clinicians, and investigators from across the United States.
Proper citation: Kidney Precision Medicine Project (RRID:SCR_016920) Copy
https://github.com/Frederik-D-Weber/cosleep
Software Python tool for sleep EEG analysis. Used for Closed and Open loop in Slow Ocillations, Sleep Stimulation in Auditory or Recording in full PSG using OpenBCI Cyton.
Proper citation: COsleep (RRID:SCR_017053) Copy
International non-profit organization for patients, relatives, and physicians with pituitary tumors and disorders.
Proper citation: Pituitary Network Association (RRID:SCR_015006) Copy
https://sites.google.com/ucsd.edu/drc/home
Research center across five institutions for clinical research in diabetes. Collaborators include UC San Diego's School of Medicine, Salk Institute, Cedars-Sinai Medical Center, UC Los Angeles' School of Medicine, and LA Biomedical Research Center.
Proper citation: University of California San Diego - University of California Los Angeles Diabetes Research Center (RRID:SCR_015100) Copy
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