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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Oct 12, 2019)

Physical Resource or Software Tool Software

16,890 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
ImageQuantResource, software resource, image analysis software, data processing software, software applicationSoftware for automatic general image analysis. It provides fully automatic analysis of 1-D gels including lane creation, background subtraction, band detection, molecular weight calibration, quantity calibration, and normalization. Editing tools are provided for cropping, rotating, and filtering images.automatic image analysis, general image analysis, image analysis softwareSCR_014246(ImageQuant, RRID:SCR_014246)GE Healthcare Last checked down
Unified Human InteractomeResource, data or information resource, databaseA database of human molecular interaction networks that integrates human protein-protein and transcriptional regulatory interactions from 15 distinct resources and aims to give direct and easy access to the integrated data set and to enable users to perform network-based investigations. The database includes tools (i) to search for molecular interaction partners of query genes or proteins in the integrated dataset, (ii) to inspect the origin, evidence and functional annotation of retrieved proteins and interactions, (iii) to visualize and adjust the resulting interaction network, (iv) to filter interactions based on method of derivation, evidence and type of experiment as well as based on gene expression data or gene lists and (v) to analyze the functional composition of interaction networks.molecular interaction network, interactome, protein, protein interaction network, protein interaction, pathway, function, visualization, protein-protein interaction, transcriptional regulatory interaction, networkSCR_005805(Unified Human Interactome, RRID:SCR_005805)University of Algarve; Faro; Portugal listed by: OMICtoolsReferences (4)Last checked upnif-0000-03609, OMICS_01911http://www.mdc-berlin.de/unihi
University of Pittsburgh Brain Tissue Donation ProgramResource, biomaterial supply resource, tissue bank, service resource, brain bank, storage service resource, material resource, material storage repositoryBrain tissue donation is a valuable contribution to mental health research. It enables scientists to investigate how the normal brain works, and how the brain is disturbed when it is affected by schizophrenia, depression, bipolar (manic depressive) disease or other related disorders. The Department of Psychiatry at the University of Pittsburgh has established a brain tissue bank to which brain tissue can be donated at no expense. The gift of brain tissue enables scientists to conduct research designed to understand causes, to develop new treatments, and ultimately to find cures for diseases that affect the brain. Brain tissue donation is a gift that makes it possible for researchers to study various types of mental disorders. Donations of brain tissue from individuals without these disorders are also needed to establish comparisons with brain samples from individuals who have these disorders. Any legally competent adult or guardian may indicate during life their interest in donating brain tissue after death. Next-of-kin either of healthy individuals or of those with psychiatric disorders may give consent to donate brain tissue following the death of a loved one. Brain tissue is removed during autopsy at a morgue or hospital and is transported to the University of Pittsburgh Medical Center for examination and study.brain tissue, brain, tissue, mental disease, normal control, schizophrenia, depressive disorder, bipolar disorder, post mortem, early adult, middle adultSCR_005028(University of Pittsburgh Brain Tissue Donation Program, RRID:SCR_005028)University of Pittsburgh Conte Center for the Neuroscience of Mental Disorders Mental disease, Normal control, Schizophrenia, Depressive Disorder, Bipolar Disorderlisted by: One Mind Biospecimen Bank ListingLast checked downnlx_144013
Ludwig Boltzman Tumour BankResource, biomaterial supply resource, material resource, tissue bank, data or information resourceAs a basis for the experimental cluster projects, and for further future projects a collection of various biological specimens of cancer patients shall be established. All participating Ludwig Boltzmann Institutes (LBIs) are supplying biological specimens from tumor patients and clinical documentation. At the LBI for Gynecology and Gynecologic Oncology a tumor bank for biological specimens from gynecologic cancer patients already exists. All the procedures for sample processing and storage are well established. Existing equipment for storing tissue specimens at -196 degrees C can be used. Materials from the following malignant diseases are collected: Breast cancer Colorectal cancer Neuroendocrine tumors (NET) (Small cell lung cancer (SCLC) and Carcinoid tumors) Types of biological materials: Tissue (fresh frozen) Bone marrow Blood (serum/plasma/cell fractions) Pleural effusions Ascitic fluids Sputum Bronchial lavage Stool The biological specimens are initially processed at the respective LBIs or at their connected lab facilities. Enrichment of blood samples for disseminated tumor cells is done at the LBI for Gynecology and Gynecologic oncology. Long time storage of all materials is done at appropriate temperatures at the same institution. This LBI also coordinates the logistics. All relevant sample-specific and clinical data are surveyed at the respective LBIs and stored centralized in an on-line data bank in anonymized form, respecting all relevant regulations on data protection and security.tissue, bone marrow, blood, serum, plasma, cell fraction, pleural effusion, ascitic fluid, sputum, bronchial lavage, stool, tumor cell, fresh frozen, frozen, tumor, cancer, breast cancer, colorectal cancer, neuroendocrine tumor, small cell lung cancer, carcinoid tumor, gynecologic cancer, clinical data, bodily fluidSCR_004322(Ludwig Boltzman Tumour Bank, RRID:SCR_004322)Ludwig Boltzmann Cluster Translationale Onkologie Tumor, Cancer, Breast cancer, Colorectal cancer, Neuroendocrine tumor, Small cell lung cancer, Carcinoid tumor, Gynecologic cancerlisted by: One Mind Biospecimen Bank ListingLast checked upnlx_33431
MSDF Drug Development PipelineResource, database, data or information resourceA database providing information about compounds under investigation for therapeutic use. There are currently 44 compounds on record with 100 compounds in the process of being uploaded to the database.database, drug development, pipeline, therapeutic useSCR_013825(MSDF Drug Development Pipeline, RRID:SCR_013825)Multiple Sclerosis Discovery Forum related to: Multiple Sclerosis Discovery Forum, listed by: Multiple Sclerosis Discovery ForumLast checked up
Mammalian Mitochondrial Genomics DatabaseResource, data or information resource, databaseDatabase developed to assist the phylogeneticist user in retrieving individual gene sequence alignments for genes in complete mammalian mitochondrial genomes. Data retrieval in MamMiBase requires three stages. At the first stage, the user must select the mammalian species or group that (s)he wishes to study. In the second stage, the user will select the outgroup from a list that included all species selected in the first stage plus Xenopus laevis and Gallus gallus. Finally, at the third stage, the user will select individual mitochondrial gene alignments or a phylogenetic tree that (s)he wishes to download.phylogeny, mitochondrial, genome, gene, sequenceSCR_003084(Mammalian Mitochondrial Genomics Database, RRID:SCR_003084)Brazilian National Laboratory of Scientific Computation Brazilian Ministry of Science Technology and Innovation, FAPERJ, National Research Council, Rio de Janeiro Science FoundationPMID:15713730Last checked downnif-0000-03099
PELICANResource, software resource, software applicationSoftware utility for graphically editing the pedigree data files used by programs such as FASTLINK, VITESSE, GENEHUNTER and MERLIN. It can read in and write out pedigree files, saving changes that have been made to the structure of the pedigree. Changes are made to the pedigree via a graphical display interface. The resulting display can be saved as a pedigree file and as a graphical image file.gene, genetic, genomic, java, pedigree, linkage analysis, editorSCR_001695(PELICAN, RRID:SCR_001695)Google Sites listed by: OMICtools, Genetic Analysis SoftwarePMID:15059819Last checked downnlx_154035, OMICS_00215http://www.mrc-bsu.cam.ac.uk/personal/frank/software/pelican/, http://www.rfcgr.mrc.ac.uk/Software/PELICAN/
dbNSFPResource, data or information resource, databaseA database for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Version 2.0 is based on the Gencode release 9 / Ensembl version 64 and includes a total of 87,347,043 nsSNVs and 2,270,742 essential splice site SNVs. It compiles prediction scores from six prediction algorithms (SIFT, Polyphen2, LRT, MutationTaster, MutationAssessor and FATHMM), three conservation scores (PhyloP, GERP++ and SiPhy) and other related information including allele frequencies observed in the 1000 Genomes Project phase 1 data and the NHLBI Exome Sequencing Project, various gene IDs from different databases, functional descriptions of genes, gene expression and gene interaction information, etc. Some dbNSFP contents (may not be up-to-date though) can also be accessed through variant tools, ANNOVAR, KGGSeq, UCSC Genome Browser''s Variant Annotation Integrator, Ensembl Variant Effect Predictor and HGMD.non-synonymous single-nucleotide variant, function, annotation, functional prediction, non-synonymous mutation, splice site mutationSCR_005178(dbNSFP, RRID:SCR_005178) Google Sites , University of Texas Health Science Center at Houston; Texas; USA used by: Exomiser, listed by: OMICtoolsReferences (2)Last checked upOMICS_00172
Endogenous GPCR ListResource, data or information resource, databaseThis database lists the G protein coupled receptors expressed endogenously in various cell lines. In so far as possible, we have tried to follow the receptor nomenclature recommended by IUPHAR. Please refer to the following web sites for additional information on receptor nomenclature: Official database of the IUPHAR committee on receptor nomenclature :http://www.iuphar-db.org/index.jsp British Journal of Pharmacology Volume 150 Issue S1 (February 2007) Guide to Receptors and channels. :http://www.nature.com/bjp/journal/vgrac/ncurrent/index.html The Endogenous GPCR List has been available in various forms since 1994 and seems to have enduring utility. We intend to continue to maintain, and when possible, improve this list. Suggestions for future enhancements are welcome. Information to be added to the database (e.g. additional endogenous receptors) is extremely welcome!SCR_013205(Endogenous GPCR List, RRID:SCR_013205)IUPHAR Last checked upnif-0000-02798
NC-IUPHARResource, international standard specification, narrative resource, standard specification, data or information resourceNC-IUPHAR is the International Union of Basic and Clinical Pharmacology Committee on Receptor Nomenclature and Drug Classification. NC-IUPHAR has the mission of: * Issuing guidelines for receptor and ion channel classification, and * addressing the main issues in pharmacology today, * Classifying the major receptor and ion channel systems, * Facilitating the interface between the discovery of new sequences from the Human Genome Project and the designation of the derived proteins as functional receptors and ion channels also designating the receptor polymorphisms which are functionally important, * Setting up a website ( http://www.iuphar-db.org ) with access to data on all known receptor systems, freely available to all scientists, anywhere in the world. NC-IUPHAR has established close links with the HUGO Gene Nomenclature Committee (HGNC), which attributes human gene names; the International Union of Pure and Applied Chemistry (IUPAC), to standardize correct use of drug names; and the International Union of Biochemistry and Molecular Biology (IUBMB) to collaborate on receptor-related enzyme nomenclature. NC-IUPHAR publishes official reports in Pharmacological Reviews and maintains an online database giving peer-reviewed pharmacological, chemical, genetic, functional and anatomical information on the 354 nonsensory G protein-coupled receptors (GPCRs), 71 ligand-gated ion channel subunits and 141 voltage-gated-like ion channel subunits encoded by the human, rat and mouse genomes.human, mouse, rat, g protein-coupled receptors, voltage-gated ion channels, ligand-gated ion channels, nuclear hormone receptors, receptor subtype, gold standardSCR_006901(NC-IUPHAR, RRID:SCR_006901)IUPHAR Last checked downnlx_54120
UTMB Mass Spectrometry CoreResource, service resource, core facility, access service resourceThe Mass Spectrometry Core is dedicated to providing a wide range of mass spectral analyses. As an integral component of the BRF Proteomics Section, it is a vital proteomics resource, providing high quality data in a timely manner and engaging investigators in the interpretation of the results.SCR_011041(UTMB Mass Spectrometry Core, RRID:SCR_011041)University of Texas Medical Branch at Galveston related to: University of Texas Medical Branch at Galveston Labs and Facilities, listed by: Science ExchangeLast checked downSciEx_9686
University of Texas Medical Branch at Galveston Labs and FacilitiesResource, service resource, portal, core facility, access service resource, data or information resourceAn Portal, Core facilitySCR_012463(University of Texas Medical Branch at Galveston Labs and Facilities, RRID:SCR_012463)University of Texas Medical Branch at Galveston related to: UTMB Mass Spectrometry Core, listed by: Science ExchangeLast checked upSciEx_1911
University of Texas Tumor BankResource, biomaterial supply resource, material resource, tissue bankTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016.tissue, tumor tissue, dna, rna, frozen, paraffin, fresh, cancer, tumorSCR_005048(University of Texas Tumor Bank, RRID:SCR_005048)University of Texas Medical Branch at Galveston Cancer, Tumorlisted by: One Mind Biospecimen Bank ListingLast checked downnlx_99346
Mexican Health and Aging StudyResource, data set, biomaterial supply resource, material resource, data or information resourceA dataset of a prospective panel study of health and aging in Mexico. The study was designed to ensure comparability with the U.S. Health and Retirement Study in many domains, and the NHANES III. The baseline survey in 2001 is nationally representative of the 13 million Mexicans born prior to 1951. The six Mexican states which are home to 40% of all migrants to the U.S. were over-sampled at a rate of 1.7:1. Spouse/partners of eligible respondents were interviewed also, even if the spouse was born after 1950. Completed interviews were obtained in 9,862 households, for a total of 15,186 individual interviews. All interviews were face-to-face, with average duration of 82 minutes. A direct interview (on the Basic questionnaire) was sought, and Proxy interviews were obtained when poor health or temporary absence precluded a direct interview. Questionnaire topics included the following: * HEALTH MEASURES: self-reports of conditions, symptoms, functional status, hygienic behaviors (e.g., smoking & drinking history), use/source/costs of health care services, depression, pain, reading and cognitive performance; * BACKGROUND: Childhood health and living conditions, education, ability to read/write and count, migration history, marital history; * FAMILY: rosters of all children (including deceased children); for each, demographic attributes, summary indicators of childhood and current health, education, current work status, migration. Parent and sibling migration experiences; * TRANSFERS: financial and time help given to and received by respondent from children, indexed to specific child; time and financial help to parent; * ECONOMIC: sources and amounts of income, including wages, pensions, and government subsidies; type and value of assets. All amount variables are bracketed in case of non-response. * HOUSING ENVIRONMENT: type, location, building materials, other indicators of quality, and ownership of consumer durables; * ANTHROPOMETRIC: for a 20% sub-sample, measured weight, height; waist, hip, and calf circumference; knee height, and timed one-leg stands. Current plans are to conduct another two follow-up surveys in 2012 and 2014 and will field the 3rd and 4th waves of survey data collection in Mexico. For the 2012 wave, interviews will be sought for: every person who was part of the panel in 2003 and their new spouse / partner, if applicable, and a new sample of persons born between 1952 and 1962. For the 2014 wave, we will follow-up the whole sample from 2012. Interviews will be conducted person-to-person. Direct interviews will be sought with all informants, but proxy interviews are allowed for those unable to complete their own interview for health or cognitive reasons. A next-of-kin interview will be completed with a knowledgeable respondent for those who were part of the panel but have died since the last interview. A sub-sample will be selected to obtain objective markers such as blood sample and anthropometric measures. Data Availability: The 2001 baseline data, 2003 follow-up data, and documentation can be downloaded. * Dates of Study: 2001-2003 * Study Features: Longitudinal, International, Anthropometric Measures * Sample Size: 2001: 15,186 (Baseline) Link: * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00142health, mexican, adult human, mexico, longitudinal, international, anthropometric measure, middle adult human, late adult human, interview, survey, spouse, health behavior, health status, childhood, family background, migration, income, housing environment, family life, behavior, housing, living arrangement, mental health, quality of life, questionnaire, disease, disability, economic, family, urban, rural, blood, self-report, chronic condition, symptom report, functionality, cognition, socioeconomic, work history, health insurance, health expenditure, parent, child, household resident, asset, pension, smoking, alcohol use, depressive disorder, pain, reading, education, demographics, employmentSCR_000818(Mexican Health and Aging Study, RRID:SCR_000818)University of Texas Medical Branch at Galveston AgingNIAlisted by: One Mind Biospecimen Bank Listing, Inter-university Consortium for Political and Social Research (ICPSR)Last checked upnlx_151859http://www.mhas.pop.upenn.edu/english/home.htm
Longitudinal Study of Elderly Mexican American HealthResource, data set, data or information resourceA dataset of a longitudinal study of over 3,000 Mexican-Americans aged 65 or over living in five southwestern states. The objective is to describe the physical and mental health of the study group and link them to key social variables (e.g., social support, health behavior, acculturation, migration). To the extent possible, the study was modeled after the existing EPESE studies, especially the Duke EPESE, which included a large sample if African-Americans. Unlike the other EPESE studies that were restricted to small geographic areas, the Hispanic EPESE aimed at obtaining a representative sample of community-dwelling Mexican-American elderly residing in Texas, New Mexico, Arizona, Colorado, and California. Approximately 85% of Mexican-American elderly reside in these states and data were obtained that are generalizable to roughly 500,000 older people. The final sample of 3,050 subjects at baseline is comparable to those of the other EPESE studies. Data Availability: Waves I to IV are available through the National Archive of Computerized Data on Aging (NACDA), ICPSR. Also available through NACDA is the ??????Resource Book of the Hispanic Established Populations for the Epidemiologic Studies of the Elderly?????? which offers a thorough review of the data and its applications. All subjects aged 75 or older were interviewed for Wave V and 902 new subjects were added. Hemoglobin A1c test kits were provided to subjects who self-reported diabetes. Approximately 270 of the kits were returned for analyses. Wave V data are being validated and reviewed. A tentative timeline for the archiving of Wave V data is November 2006. Wave VI interviewing and data collection is scheduled to begin in Fall 2006. * Dates of Study: 1993-2006 * Study Features: Longitudinal, Minority oversamples, Anthropometric Measures * Sample Size: ** 1993-4: 3,050 (Wave I) ** 1995-6: 2,438 (Wave II) ** 1998-9: 1,980 (Wave III) ** 2000-1: 1,682 (Wave IV) ** 2004-5: 2,073 (Wave V) ** 2006-7: (Wave VI) Links: * ICPSR Wave 1: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/2851 * ICPSR Wave 2: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/3385 * ICPSR Wave 3: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/4102 * ICPSR Wave 4: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/4314 * ICPSR Wave 5: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/25041 * ICPSR Wave 6: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/29654longitudinal, minority, anthropometric measure, mexican-american, questionnaire, physical health, mental health, functional impairment, risk factor, mortality, morbidity, late adult human, southwestern united states, arizona, california, colorado, new mexico, texas, iadl, adl, living arrangement, blood pressure, social support, family, stress, life event, employment, health, acculturation, religion, social involvement, global health rating, self-esteem, medical condition, performance-oriented mobility assessment, ces-d, height, weight, cognition, health care services utilization, behavior, income, financial strain, medication, insurance coverage, migration, interview, hemoglobin a1c test, demographics, ethnicity, health behavior, health problem, health status, hispanic, latino american, life expectancy, quality of lifeSCR_008941(Longitudinal Study of Elderly Mexican American Health, RRID:SCR_008941)University of Texas Medical Branch at Galveston , National Archive of Computerized Data on Aging (NACDA) Aging, DiabetesNIArelated to: Established Populations for Epidemiologic Studies of the Elderly, listed by: Inter-university Consortium for Political and Social Research (ICPSR)Last checked downnlx_151848http://www.utmb.edu/pmch/hepese/, http://pmch.utmb.edu/sponsoredprograms/sp_populationhealth.aspxhttp://www.utexas.edu/cola/centers/prc/research/profiles/angellongitudinal/
UF Molecular Pathology CoreResource, service resource, portal, core facility, access service resource, data or information resourceA core facility that provides services in histology, sample processing, and immunohistochemistry. These include cryosectioning, whole slide imaging, hematoxylin and eosin staining, immunfluorescence, and tissue microarrays.histology, immunohistochemistry, sample processing, clinical research, cryosectioning, imaging, staining, immunfluorescence, microarrays, core facilitySCR_001055(UF Molecular Pathology Core, RRID:SCR_001055)University of Florida; Florida; USA related to: University of Florida Labs and Facilities, listed by: Science ExchangeLast checked upSciEx_8810http://www.scienceexchange.com/facilities/molecular-pathology-core-ufl
Mouse Brain Image Visualizer (MBIV)Resource, data processing software, software application, data visualization software, atlas, software resource, data or information resourceThe Mouse Brain Image/Atlas Visualizer (MBIV) is a Java-based 2D visualization tool, available both as a web-based applet or downloadable application, for browsing high resolution 3D MRI mouse brain images and their associated atlases. A user can dynamically access images and atlases in our mouse brain database through the interface provided by MBIV and then select from the database the datasets they wish to upload and browse on their local machine.SCR_013358(Mouse Brain Image Visualizer (MBIV), RRID:SCR_013358)University of Florida; Florida; USA related to: MRM NeAt (Neurological Atlas) Mouse Brain DatabaseLast checked upnlx_61725
Intrinsic Unscented Kalman Filter (IUKF) Tractography Software v1.0Resource, data visualization software, 3d visualization software, data processing software, software resource, software applicationA tractography algorithm for HARDI which provides a relatively accurate and efficient fiber tracking mechanism by reconstructing a bi-tensor model for underlying signals and exploiting intrinsic operations on the space of diffusion tensors. Given HARDI data sets, IUKF is capable of tracking in the presence of complex local geometries, such as crossing and kissing fibers. Reconstruction is only performed at the voxels along estimated fibers.filter, data visualization software, 3d visualization, tractography, algorithm, fiber tracking, HARDISCR_014127(Intrinsic Unscented Kalman Filter (IUKF) Tractography Software v1.0, RRID:SCR_014127)University of Florida; Florida; USA NINDSlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked uphttp://www.cise.ufl.edu/~salehian/Softwares.html
University of Florida College of Medicine; Florida; USAResource, degree granting program, medical school program resource, training resourceA medical school which offers degrees in medicine, in addition to medical science, biomedical engineering, physician assistant studies and an interdisciplinary program in biomedical sciences.florida, university, medical school, biomedical science, physician assistantSCR_000152(University of Florida College of Medicine; Florida; USA, RRID:SCR_000152)University of Florida; Florida; USA uses: FluoroFinderLast checked upnlx_80125
International Affective Picture SystemResource, data or information resource, databaseCollection of pictures designed to provide a standardized set of pictures for studying emotion and attention. Provides normative ratings of emotion (pleasure, arousal, dominance) for a set of color photographs that provide a set of normative emotional stimuli for experimental investigations of emotion and attention. Used in psychological research.collection, normative, rating, emotion, color, photograph, stimuli, attentionSCR_016869(International Affective Picture System, RRID:SCR_016869)University of Florida; Florida; USA submitted by: Resource Identification PortalLast checked down
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