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http://medicaldata.wikia.com/wiki/Main_Page

Portal serves as resource to understand the current state of medical data quality and the factors that affect it. The information is gathered from anecdotal and empirical examples from peer-reviewed journals, popular media and author contributions. Issues of importance include understanding and measuring medical data quality, contributing factors, best practices, and the effects of data quality on secondary uses of medical data.

Proper citation: Quality of Medical Data (RRID:SCR_000520) Copy   

•   Source: SciCrunch Registry

http://www.africacentre.ac.za/Biobank/tabid/460/Default.aspx

THIS RESOURCE IS NO LONGER IN SERVICE, documented November 30, 2015. Extensive collection of biological specimens of various kinds that are mostly collected from the population around the Africa Centre in northern KwaZulu-Natal, but there are also specimens collected from populations in and around Durban and elsewhere in KwaZulu-Natal. The results of tests carried out on these specimens are generally stored in the main databases of the various studies involved, and are linkable back to the demographic and other data collected from the individuals concerned. The Biobank is curated by staff of the Africa Centre's Virology Laboratory in Durban, where all the specimens are currently stored, mostly in -80C freezers. A particular strength of its holdings are the dried blood spot (DBS), specimens five drops of blood on a filter-paper card, obtained via a finger-prick - of which there are now nearly 115,000. The following is a list of its holdings (May 2011): * 67,700 DBS specimens collected since late 2002 primarily for HIV prevalence estimation of the population covered by the Africa Centre Demographic Surveillance population. All have at least been tested for HIV, and just over 21% give a Positive result. Specimens are collected annually, so for some individuals we might have a sequence of 8-10 specimens covering 2002-2011. * 36,601 DBS specimens collected by the Vertical Transmission Study (VTS) between Sep 2001 and Dec 2006. This study focussed on mother-child pairs and investigated the vertical transmission of HIV from mother to child. DBS specimens were collected from both the mothers (at initial screening, and then from their children at Birth, 6, 10, 14, 18, 22 weeks, and 7, 8, 9, 12, 15, 18, 21 and 24 months. * 6,585 DBS specimens collected as part of the KZN IMPACT study of PMTCT effectiveness in six districts of kwaZulu-Natal. The specimens were collected during 2004-2006 from infants aged 4-8 weeks when mothers brought them to clinics for immunisation. These DBS specimens are stored at room temperature, not in freezers. * 3,524 DBS specimens collected as part of the Kesho Bora study from Sep 2007 . They were collected from mothers at enrollment, and from the infants at delivery, 2 weeks, and at 4, 5, 7, 8 and 15 months. * 50,068 Plasma specimens * 28,775 breastmilk specimens * 11,277 breastmilk products (Pellets and lactoserum). These have all been extracted from the BM specimens in prev. item? * 11,188 RNA and DNA products extracted from DBS and plasma specimens from all our major studies. * 5,735 Serum specimens * 3,505 cell pellets * 1,778 whole blood specimens * 1,284 Peripheral Blood Mononuclear Cells from the Kesho Bora study mothers (665) and their children (619) * 179 skin tissue specimens from the KST study (Kaposi's Sarcoma) * 176 foreskins

Proper citation: Africa Centre Biobank (RRID:SCR_000638) Copy   

•   Source: SciCrunch Registry

http://www.isrec.isb-sib.ch/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Computational Cancer Genomics (CCG) group is dedicated to the development of analysis tools and databases relating molecular sequences and biological functions. Sponsors: This group is supported by the Swiss Institute of Bioinformatics (SIB).

Proper citation: Computational Cancer Genomics Group (RRID:SCR_000772) Copy   

•   Source: SciCrunch Registry

http://neuromorphometrics.org:8080/nvm/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Software tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis.

Proper citation: NVM (RRID:SCR_000600) Copy   

•   Source: SciCrunch Registry

http://www.measuredhs.com

A program that provides technical assistance for surveys that aim to advance global understanding of health and population trends in developing countries. The DHS program collects, analyzes, and disseminates accurate and representative data on population, health, HIV, and nutrition through more than 300 surveys in over 90 countries.

Proper citation: DHS Program (RRID:SCR_000905) Copy   

•   Source: SciCrunch Registry

https://dans.knaw.nl/en

Netherlands institute for permanent access to digital research resources. DANS encourages researchers to make their digital research data findable, accessible, interoperable and reusable. It does this by providing expert advice and certified services.

Proper citation: DANS (RRID:SCR_000904) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/rGADEM.html

R package with tools for de novo motif discovery in large-scale genomic sequence data.

Proper citation: rGADEM (RRID:SCR_001091) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/itk-snap/

Open source interactive software application for three dimentional medical images, manual delineation of anatomical regions of interest, and performing automatic image segmentation. Used for delineating anatomical structures and regions in MRI, CT and other 3D biomedical imaging data.WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons).

Proper citation: ITK-SNAP (RRID:SCR_002010) Copy   

•   Source: SciCrunch Registry

https://datashare.nida.nih.gov

Website which allows data from completed clinical trials to be distributed to investigators and public. Researchers can download de-identified data from completed NIDA clinical trial studies to conduct analyses that improve quality of drug abuse treatment. Incorporates data from Division of Therapeutics and Medical Consequences and Center for Clinical Trials Network.

Proper citation: NIDA Data Share (RRID:SCR_002002) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/resolver/SCR_002250

THIS RESOURCE IS NO LONGER IN SERVICE. Documented Jul 19, 2024. Metadatabase manually curated that provides web accessible tools related to genomics, transcriptomics, proteomics and metabolomics. Used as informative directory for multi-omic data analysis.

Proper citation: OMICtools (RRID:SCR_002250) Copy   

•   Source: SciCrunch Registry

http://www.incf.org/

Independent international facilitator catalyzing and coordinating global development of neuroinformatics aiming to advance data reuse and reproducibility in global brain research. Integrates and analyzes diverse data across scales, techniques, and species to understand brain function and positively impact the health and well being of society.

Proper citation: International Neuroinformatics Coordinating Facility (RRID:SCR_002282) Copy   

•   Source: SciCrunch Registry

http://www.ensembl.org/

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

Proper citation: Ensembl (RRID:SCR_002344) Copy   

•   Source: SciCrunch Registry

http://brainproducts.com/productdetails.php?id=17

Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more.

Proper citation: BrainVision Analyzer (RRID:SCR_002356) Copy   

•   Source: SciCrunch Registry

http://www.mayo.edu/research/departments-divisions/department-health-sciences-research/division-biomedical-statistics-informatics/software/bioinformatics-software-packages

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. A free bioinformatics software tool to help identify fusion transcripts from paired-end transcriptome sequencing data. The source codes of SnowShoes-FTD are provided in two formats: one configured to run on the Sun Grid Engine for parallelization with shorter run time, and the other formatted to run on a single LINUX node.

Proper citation: SnowsShoes-FTD (RRID:SCR_000076) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/SOAPfusion.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. An open source software tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by finding fusions directly and verifying them, differentiating it from all other existing tools by finding the candidate regions and searching for the fusions afterwards.

Proper citation: SOAPfusion (RRID:SCR_000079) Copy   

•   Source: SciCrunch Registry

http://www.iuphar.org/

Voluntary, non-governmental, non-profit pharmacologist association promoting international cooperation, sponsoring international and regional activities, encouraging free exchange of scientists and ideas, developing public awareness, establishing advisory committees. Has official relations with the World Health Organization (WHO). Helps pharmacologists to participate with other branches of science in international activities, either directly or under ICSU, WHO and UNESCO. Member of the International Council for Science (ICSU) and participates in the work of its scientific committees. Has its own publishing program. Pharmacology International, is published every June and December. Member Directory is maintained continually, as an online resource. Provides IUPHAR Receptor Database, major on-line repository of characterization data for receptors and drugs, and the IUPHAR Ion Channels Database. Official Reports from The IUPHAR Committee on Receptor Nomenclature and Drug Classification are published in Pharmacological Reviews. IUPHAR World Congresses of Pharmacology are held every few years.

Proper citation: International Union of Basic and Clinical Pharmacology (RRID:SCR_000135) Copy   

•   Source: SciCrunch Registry

http://cistrome.org

Web based integrative platform for transcriptional regulation studies.

Proper citation: Cistrome (RRID:SCR_000242) Copy   

•   Source: SciCrunch Registry

http://technelysium.com.au/?page_id=27

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31,2023. Software which is able to assemble data from 454 and Illumina next-generation sequencers, with up to 100,000 sequences if 2 Gb RAM is available.

Proper citation: ChromasPro (RRID:SCR_000229) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/

Sage Bionetworks, Mount Sinai School of Medicine (MSSM), University of Pennsylvania (Penn), the National Institute of Mental Health (NIMH), and Takeda Pharmaceuticals Company Limited (TAKEDA) have launched a Public-Private Pre-Competitive Consortium, the CommonMind Consortium, to generate and analyze large-scale genomic data from human subjects with neuropsychiatric disease and to make this data and the associated analytical results broadly available to the public. This collaboration brings together disease area expertise, large scale and well curated brain sample collections, and data management and analysis expertise from the respective institutions. As many as 450 million people worldwide are believed to be living with a mental or behavioral disorder: schizophrenia and bipolar disorder are two of the top six leading causes of years lived with disability according to the World Health Organization. The burden on the individual as well as on society is significant with estimates for the health care costs for these individuals as high as four percent GNP. This highlights a grave need for new therapies to alleviate this suffering. Researchers from MSSM including Dr. Pamela Sklar, Dr. Joseph Buxbaum and Dr. Eric Schadt will join with Dr. Raquel Gur and Dr. Chang-Gyu Hahn from Penn to combine their extensive brain bank collections for the generation of whole genome scale RNA and DNA sequence data. Dr.Pamela Sklar, Professor of Psychiatry and Neuroscience at MSSM commented this is an exciting opportunity for us to use the newest genomic methods to really expand our understanding of the molecular underpinnings of neuropsychiatric disease, while Dr Raquel Gur, Professor of Psychiatry from Penn observed this will be a great complement to some of the large-scale genetic analyses that have been carried out to date because it will give a more complete mechanistic picture. The CommonMind Consortium is committed to generating an open resource for the community and invites others with common goals to contact us at info (at) CommonMind.org.

Proper citation: CommonMind Consortium (RRID:SCR_000139) Copy   

•   Source: SciCrunch Registry

http://www.originlab.com/index.aspx?go=PRODUCTS/Origin

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 4, 2025.Software application for data analysis and graphing. Origin contains a variety of different graph types, including statistical plots, 2D and 3D vector graphs, and counter graphs. More advance version is OriginPro which offers advanced analysis tools and Apps for Peak Fitting, Surface Fitting, Statistics and Signal Processing.

Proper citation: Origin (RRID:SCR_014212) Copy   

•   Source: SciCrunch Registry