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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)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Phelan-McDermid Syndrome FoundationResource, disease-related portal, topical portal, portal, community building portal, funding resource, data or information resourceThe Phelan-McDermid Syndrome Foundation, established in 2002, is a 501(c)3 nonprofit group that provides support services for those who have family members affected by 22q13 Deletion Syndrome / Phelan-McDermid Syndrome. It also raises money to further awareness of the syndrome through research and sponsoring an international conference every two years that brings together families, researchers and therapists. The Foundation facilitates connections between families through networking, communications and support services. We also build alliances with other rare diseases groups to expand our reach and exposure. The syndrome, which affects families worldwide, is a rare genetic occurrence and is the result of a damaged or missing protein on the 22nd chromosome. Our Foundation works with researchers who are looking into the cause and possible cure for the syndrome. PMSF's grants and fellowships program is intended to encourage research projects that will advance the development of treatments and cures for PMS. Our mission is to bring together everyone affected by 22q13 Deletion Syndrome/Phelan-McDermid Syndrome to help them through the challenges they face every day and to raise awareness in the medical and research communities.22q13 deletion syndrome, phelan-mcdermid syndrome, rare disease, genetic, meeting, child, chromosome 22, treatment, therapy, research, grant, fellowshipSCR_001707(Phelan-McDermid Syndrome Foundation, RRID:SCR_001707)Phelan-McDermid SyndromeLast checked upnif-0000-10203
BrainNavigatorResource, atlas, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented December 31, 2013. An interactive atlas and 3D brain software for research, structure analysis, and education, it offers six atlases representing four species: the mouse, rat, monkey and human. The stereotaxic coordinates atlases are available for all four species and the rodent models have additional chemoarchitectonic atlases. BrainNavigator helps locate specific areas of the brain, making visualizing and experimental planning in the brain easier. *Plan: Browse 6 Atlases, Visualize with 3D models, Search Literature, Analyze gene expression, Identify connections *Publish: Access reference tools, Use and print images for publication, Search literature *Propose: Use and print images for proposals, Search literature, Locate gene expression in 2D and 3D, Identify connections *Produce: Simulate injections, Customize new coordinates, virtually slice sections, overlay atlas maps on your own images, create personal atlas maps With BrainNavigator, you''ll gain 24/7 access to their powerful 3D brain interactive software tool that helps further research in the neurosciences. In addition, their vast library of widely respected and referenced brain publications will provide a plethora of information on the most current brain research available. As publisher of the gold standard in brain atlas publications authored by the team around the leading brain cartographers George Paxinos and Charles Watson, they are pleased to bring an advanced tool to today''s neuroscientists and educators. Combining atlas content and 3D capabilities based on technologies from the Allen Institute for Brain Science, this online workflow solution brings brain research, analysis and education tools to your fingertips.3d, 2d, acetylcholinesterase, anatomy, brain, coronal, reconstruction, sagittal, sterotaxic, visualization, molecular neuroanatomy resource, training resource, connection, literature, gene expression, imageSCR_008289(BrainNavigator, RRID:SCR_008289)Last checked downnif-0000-24037
Research Collaboratory for Structural Bioinformatics Protein Data BankResource, service resource, data or information resource, databaseCollection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.3-dimensional, annotation, molecule, nucleic acid, protein, visualization, sequence, function, macromolecule, ligand, model, dna, x-ray crystallography, ribosome, structure, oncogene, nucleic acids, molecular structure, cryomicroscopy, gold standardSCR_012820(Research Collaboratory for Structural Bioinformatics Protein Data Bank, RRID:SCR_012820) Rutgers University; New Jersey; USA , University of California at San Diego; California; USA DOE, NIH, NSFrelated to: pdb-data, PDB2MultiGif, GlyProt, pdb-care, pdb2linucs, GlyVicinity, GlyTorsion, GlySeq, AffinDB, StatAlign, Community Structure-Activity Resource, Binding MOAD, ConSurf Database, glycosciences.de, DOMINE: Database of Protein Interactions, Jenalib: Jena Library of Biological Macromolecules, SynSysNet, EMDataBank.org: Unified Data Resource for Cryo Electron Microscopy, PDBe - Protein Data Bank in Europe, TFinDIT, HOLLOW, ccPDB - Compilation and Creation of datasets from PDB, DOMMINO - Database Of MacroMolecular INteractiOns, InterEvol database, Polbase, PoSSuM, ProtChemSI, RNA CoSSMos, PDBsum, Worldwide Protein Data Bank , canSAR, CAPS Database, Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING, Combinatorial Extension (CE), Metalloprotein Site Database, PDBj - Protein Data Bank Japan, Statistical Torsional Angles Potentials of NMR Refinement Database, Metalloprotein Ligand Interaction Database, CARP, PDBTM, RNA FRABASE - RNA FRAgments search engine and dataBASE, AmiGO, ConsensusPathDB, Biological Magnetic Resonance Data Bank, DDBJ - DNA Data Bank of Japan, FlyMine, NCBI Protein, NCBI Nucleotide, FunTree, IndelFR - Indel Flanking Region Database, NMR Restraints Grid, Enzyme Structures Database, Electron Microscopy Data Bank at PDBe, Worldwide Protein Data Bank , DDBJ - DNA Data Bank of Japan, PDBe - Protein Data Bank in Europe, MINAS - Metal Ions in Nucleic AcidS, RCSB PDB, PDBj - Protein Data Bank Japan, used by: SGC, Ligand Expo , DARC - Database for Aligned Ribosomal Complexes, FireDB, Protein Data Bank Bind Database, Protein Data Bank Site, NIF Data Federation, ChannelPedia, MobiDB, Protein Database, listed by: re3data.org, affiliated with: EMDataBank.org: Unified Data Resource for Cryo Electron Microscopy, ConSurf-DB, works_with: CellPhoneDBPMID:12037327Last checked upnif-0000-00135, SCR_017379http://www.rcsb.org, http://www.pdb.org
Internet Brain Segmentation RepositoryResource, data set, data or information resourceData set of manually-guided expert segmentation results along with magnetic resonance brain image data. Its purpose is to encourage the development and evaluation of segmentation methods by providing raw test and image data, human expert segmentation results, and methods for comparing segmentation results. Please see the MediaWiki for more information. This repository is meant to contain standard test image data sets which will permit a standardized mechanism for evaluation of the sensitivity of a given analysis method to signal to noise ratio, contrast to noise ratio, shape complexity, degree of partial volume effect, etc. This capability is felt to be essential to further development in the field since many published algorithms tend to only operate successfully under a narrow range of conditions which may not extend to those experienced under the typical clinical imaging setting. This repository is also meant to describe and discuss methods for the comparison of results.3d model, anatomy, brainstem, cerebellum, cortex, gray matter, imaging, morphology, mri, segmentation, volume, white matter, adult human, male, child, image collection, application, magnetic resonance, os independent, php, quality metrics, segmentation, test data, web serviceSCR_001994(Internet Brain Segmentation Repository, RRID:SCR_001994)Harvard Medical School; Massachusetts; USA Normal, TumorNINDSlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked upnif-0000-00032http://www.cma.mgh.harvard.edu/ibsr/
brainmap.orgResource, software resource, software application, data or information resource, databaseA community database of published functional and structural neuroimaging experiments with both metadata descriptions of experimental design and activation locations in the form of stereotactic coordinates (x,y,z) in Talairach or MNI space. BrainMap provides not only data for meta-analyses and data mining, but also distributes software and concepts for quantitative integration of neuroimaging data. The goal of BrainMap is to develop software and tools to share neuroimaging results and enable meta-analysis of studies of human brain function and structure in healthy and diseased subjects. It is a tool to rapidly retrieve and understand studies in specific research domains, such as language, memory, attention, reasoning, emotion, and perception, and to perform meta-analyses of like studies. Brainmap contains the following software: # Sleuth: database searches and Talairach coordinate plotting (this application requires a username and password) # GingerALE: performs meta-analyses via the activation likelihood estimation (ALE) method; also converts coordinates between MNI and Talairach spaces using icbm2tal # Scribe: database entry of published functional neuroimaging papers with coordinate results3d model, atlas, data management, imaging, map, neuroinformatics, warping, neuroimaging, brain, talairach, mni, java, modeling, magnetic resonance, nifti-1, ontology, os independent, pet, spect, visualization, functional neuroimaging, fmriSCR_003069(brainmap.org, RRID:SCR_003069)University of Texas Health Science Center at San Antonio; Texas; USA Healthy, DiseasedNIMHrelated to: Brede Database, uses: Scribe, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)References (3)Last checked upnif-0000-00049http://www.nitrc.org/projects/brainmap
3DBarResource, production service resource, analysis service resource, reference atlas, software resource, service resource, atlas, data or information resourceSoftware package for reconstructing three-dimensional models of brain structures from 2-D delineations using a customizable and reproducible workflow. 3dBAR also works as an on-line service (http://service.3dbar.org) offering a variety of functions for the hosted datasets: * downloading reconstructions of desired brain structures in predefined quality levels in various supported formats as well as created using customizable settings, * previewing models as bitmap thumbnails and (for webGL enabled browsers) interactive manipulation (zooming, rotating, etc.) of the structures, * downloading slides from available datasets as SVG drawings. 3dBAR service can also be used by other websites or applications to enhance their functionality. * Operating System: Linux * Programming Language: Python * Supported Data Format: NIfTI-1, Other Format, VRML3d, reconstruction, brain structure, brain, algorithm or reusable library, web service, atlas application, three dimensional display, spinal cord, sensory system, waxholm spaceSCR_008896(3DBar, RRID:SCR_008896)Nencki Institute of Experimental Biology; Warsaw; Poland related to: Scalable Brain Atlas, Allen Mouse Brain Atlas, Waxholm Space Atlas, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)PMID:22227717Last checked upnlx_151380http://www.nitrc.org/projects/bar3d, http://service.3dbar.org, http://www.3dbar.org:8080/, http://3dbar.org
NeuroSynthResource, software resource, source code, data or information resource, databasePlatform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data extracted from published articles. It''s a website wrapped around a set of open-source Python and JavaScript packages. Neurosynth lets you run crude but useful analyses of fMRI data on a very large scale. You can: * Interactively visualize the results of over 3,000 term-based meta-analyses * Select specific locations in the human brain and view associated terms * Browse through the nearly 10,000 studies in the database Their ultimate goal is to enable dynamic real-time analysis, so that you''ll be able to select foci, tables, or entire studies for analysis and run a full-blown meta-analysis without leaving your browser. You''ll also be able to do things like upload entirely new images and obtain probabilistic estimates of the cognitive states most likely to be associated with the image.activation foci, magnetic resonance imaging assay, brain, human, fmri, neuroimaging, python, image, functional neuroimagingSCR_006798(NeuroSynth, RRID:SCR_006798)University of Texas at Austin; Texas; USA NIMHrelated to: Brainspell, used by: NeuroVault, NIF Data Federation, listed by: GitHub, NeuroImaging Tools and Resources Collaboratory (NITRC)PMID:21706013Last checked upnlx_55906http://www.nitrc.org/projects/neurosynth, https://github.com/tyarkoni/neurosynth
UAB-UCSD Core Center for Acute Kidney Injury Research Clinical Studies of AKI Resource, service resource, resource, core facility, access service resourceCore facility which provides investigators access to patients with AKI through an established international network of collaborating investigators. It also provides core resources to support the design and conduct of clinical research in AKI and genomics resources to perform systematic genomic analyses and allow correlation with clinical phenotypic information.acute kidney injury, patient data, patient data access, kidney clinical researchSCR_015287( UAB-UCSD Core Center for Acute Kidney Injury Research Clinical Studies of AKI , RRID:SCR_015287)University of Alabama at Birmingham School of Medicine; Alabama; USA , University of California San Diego School of Medicine; California; USA , UAB-UCSD Core Center for Acute Kidney Injury Research NIDDKlisted by: NIDDK Information NetworkLast checked up
UAB-UCSD Core Center for Acute Kidney Injury Research Resource, disease-related portal, topical portal, resource, service resource, portal, access service resource, data or information resourceResearch center for kidney research, specifically acute kidney injury. It supports shared core facilities, encourages collaboration between investigators from different backgrounds and disciplines whose shared interest is in kidney research, and provides intellectual resources and infrastructure.acute kidney injury research, kidney research center, kidney core facilitiesSCR_015282( UAB-UCSD Core Center for Acute Kidney Injury Research , RRID:SCR_015282)University of Alabama at Birmingham School of Medicine; Alabama; USA , University of California San Diego School of Medicine; California; USA NIDDKlisted by: NIDDK Information NetworkLast checked up
Adenylate Uridylate-rich-Rich Element-Containing mRNA DatabaseResource, data or information resource, databaseDatabase that contains the complete entries of human ARE-containing full-length mRNAs.
ARED is further clustered into five groups depending on the number of motifs in the ARE stretch. Groups 1-4 contain five, four, three and two pentameric (AUUUA) repeats, respectively, while Group 5 contains only one repeat within the 13-bp pattern. Clustering was performed in such a way that, for example, Group 1 included not only exact five or more continuous ARE pentamers but also those with 10% ambiguity, so that a stretch of NUUUAUUUAUUUAUUUAUUUN would fall in this category. This process was verified by a phylogenic tree relationship using Clustal-W alignment of ARE stretches and their variations. As could be expected, this analysis showed that the lower the number of ARE motifs in a group, the higher the number of sequences that were included, and apparently the more functionally diverse the corresponding ARE-genes.
adenylate uridylate-rich element-mrna, are-gene, mrna, rna sequence databaseSCR_013107(Adenylate Uridylate-rich-Rich Element-Containing mRNA Database, RRID:SCR_013107)Last checked upnif-0000-02566http://rc.kfshrc.edu.sa/ared/
Mid-Atlantic Nutrition Obesity Research Center Biological Mechanisms and Functional Genomics Core Resource, service resource, resource, core facility, access service resourceCore that provides investigators with access to adipose tissue samples from well-characterized subjects. It also assists investigators with analysis of adipose tissue morphology and metabolism, specialized cell and organ culture methods, and analysis of gene and protein expression.adipose tissue, adipose tissue morphology, adipose specimenSCR_015432( Mid-Atlantic Nutrition Obesity Research Center Biological Mechanisms and Functional Genomics Core , RRID:SCR_015432)University of Maryland School of Medicine; Maryland; USA , Mid-Atlantic Nutrition Obesity Research Center ObesityNIDDKlisted by: NIDDK Information NetworkLast checked down
Boston Nutrition and Obesity Research Centers Adipose Biology and Nutrient Metabolism Core Resource, service resource, resource, core facility, access service resourceCore that facilitates and fosters research on mechanisms regulating white, brite or beige and brown adipose tissue mass, distribution, nutrient signaling and depot-specific metabolic and endocrine functions in health and disease.adipose tissue, nutrient signaling, endocrine functionSCR_015419( Boston Nutrition and Obesity Research Centers Adipose Biology and Nutrient Metabolism Core , RRID:SCR_015419) Boston Nutrition and Obesity Research Centers ObesityNIDDKlisted by: NIDDK Information NetworkLast checked up
University of Chicago Digestive Diseases Research Core Center Administrative CoreResource, service resource, core facility, access service resourceCore that has oversight of the other four cores of University of Chicago's Digestive Disease Research Core Center and determines the center's overall direction.administrative, digestive disease researchSCR_015602(University of Chicago Digestive Diseases Research Core Center Administrative Core, RRID:SCR_015602)University of Chicago Digestive Diseases Research Core Center digestive diseaseNIDDKlisted by: NIDDK Information NetworkLast checked up
University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Administrative Core Resource, service resource, resource, core facility, access service resourceCore facility that is responsible for managing and organizing the activities of the internal governance committee and the external advisory board, promoting the techniques, methodologies, instrumentation, and resources offered by the core facilities, and supporting the integration of bioinformatics, biostatistics, clinical research, and metabolomics into clinical and translational research.admnistration, management core, administrative servicesSCR_015439( University of North Carolina at Chapel Hill Nutrition and Obesity Research Center Administrative Core , RRID:SCR_015439)University of North Carolina at Chapel Hill; North Carolina; USA , University of North Carolina at Chapel Hill Nutrition and Obesity Research Center ObesityNIDDKlisted by: NIDDK Information NetworkLast checked up
Kutcher Adolescent Depression ScaleResource, material resource, assessment test providerA psychological self-rating scale developed by Dalhousie University professor of psychiatry Stan Kutcher, to assess the level of depression in adolescents. While there are some variations, the 11-item version of the KADS is the most commonly used and most thoroughly verified for efficacy in monitoring outcomes in adolescents who are receiving treatment for major depressive disorder. Its items are worded using standard and colloquial terminology, and responses are scored on a simple 4 choice scale. There are ten questions about depression symptom frequency that the patient rates on a straight 4 point scale according to the following choices: hardly ever, much of the time, most of the time, all the time, and one question relating to the severity of suicidal ideation. Scores on the test range from 0 to 33. Unlike some rating scales, there is no threshold for sub-clinical presentation, or ranges for mild, moderate, and severe symptoms. Higher scores simply indicate more severe current depression symptoms. (Adapted from Wikipedia)adolescentSCR_003687(Kutcher Adolescent Depression Scale, RRID:SCR_003687)Depressive Disorder, Major Depressive DisorderLast checked downnlx_157842
Eating Attitudes TestResource, material resource, assessment test providerA widely used standardized self-report measure of symptoms and concerns characteristic of eating disorders. The original 40-item version was developed for a study to examine socio-cultural factors in the development and maintenance of eating disorders. A 26-item refinement of the original test has been made and it has been translated into many different languages and used in hundreds of studies. The EAT-26 has been useful as a screening tool to assess eating disorder risk in high school, college and other special risk samples such as athletes. It can be used in a non-clinical as well as a clinical setting not specifically focused on eating disorders. It can be administered in group or individual settings and is designed to be administered by mental health professionals, school counselors, coaches, camp counselors, and others with interest in gathering information to determine if an individual should be referred to a specialist for evaluation for an eating disorder. It is intended primarily for adolescents and adults. The EAT-26 should be used as the first step in a two-stage screening process. According to this methodology, individuals who score 20 or more on the test should be interviewed by a qualified professional to determine if they meet the diagnostic criteria for an eating disorder. The tests are rated on a six-point scale in response to how often the individual engages in specific behaviors. (adapted from Wikipedia)adolescent, adult humanSCR_003695(Eating Attitudes Test, RRID:SCR_003695)Eating disorderLast checked upnlx_157848
Eating Disorder InventoryResource, material resource, assessment test providerA self-report questionnaire used to assess the presence of eating disorders, anorexia nervosa, bulimia nervosa, and eating disorder not otherwise specified including Binge Eating Disorder (BED). The original questionnaire consisted of 64 questions, divided into eight subscales. There have been two subsequent revisions by Garner; Eating disorder inventory-two (EDI-2) and Eating disorder inventory-three (EDI-3). (Adapted from Wikipedia) The EDI-3 consists of 91 items organized into 12 primary scales: Drive for Thinness, Bulimia, Body Dissatisfaction, Low Self-Esteem, Personal Alienation, Interpersonal Insecurity, Interpersonal Alienation, Interoceptive Deficits, Emotional Dysregulation, Perfectionism, Asceticism, and Maturity Fears.adolescent, adult human, body dissatisfaction, low self-esteem, personal alienation, interpersonal insecurity, interpersonal alienation, interoceptive deficit, emotional dysregulation, perfectionism, asceticism, maturity fear, spanishSCR_003696(Eating Disorder Inventory, RRID:SCR_003696)Eating disorder, Bulimia nervosa, Anorexia nervosa, Binge eatingLast checked upnlx_157849
Treatment Options for type 2 Diabetes in Adolescents and Youth Resource, narrative resource, training material, resource, clinical trial, data or information resourceRandomized, double blind, nationwide clinical trial to compare the efficacy and safety of three interventions to treat adolescents and youth with type 2 diabetes (T2D): (1) metformin alone, (2) metformin plus rosiglitazone, and (3) metformin plus an intensive lifestyle intervention called the TODAY Lifestyle Program (TLP). The secondary aims are to: compare and evaluate the safety of the three treatment arms; compare the effects of the three treatments on the pathophysiology of type 2 diabetes (T2D) with regards to beta cell function and insulin resistance, body composition, nutrition, physical activity and aerobic fitness, cardiovascular risk factors, microvascular complications, quality of life, and psychological outcomes; evaluate the influence of individual and family behaviors on treatment response; and compare the relative cost effectiveness of the three treatment arms. The study recruits patients over a three-year period and follows patients for a minimum of two years. Patients are randomized within two years of the diagnosis of T2D. Materials that were used for the study are made publicly available: * The TODAY Standard Diabetes Education (TSDE) program, developed especially for youth with type 2 diabetes. (All participants received the TSDE program) * The TODAY Lifestyle Program (TLP) that was among the treatments tested.adolescent, child, young human, glycemic control, metformin, drug, rosiglitazone behavior, lifestyle program, lifestyle change, intervention, treatment, safety, efficacy, male, female, experimental protocol, bibliographySCR_001547( Treatment Options for type 2 Diabetes in Adolescents and Youth , RRID:SCR_001547)George Washington University; Washington D.C.; USA Type 2 diabetes, ObesityNIDDKlisted by: ClinicalTrials.gov, NIDDK Research Resources, NIDDK Information Network, submitted by: NIDDK Information NetworkReferences (3)Last checked upnlx_152858
Mexican Adolescent Mental Health SurveyResource, data set, clinical trial, data or information resourceA face-to-face household survey of assessing the prevalence of mental health disorders in a probability sample of 3005 adolescents aged 12-17 years residing in the Mexico City metropolitan area during 2005. The prevalence of mental health disorders and the use of services were assessed with the computer-assisted adolescent version of the World Mental Health Composite International Diagnostic Interview.adolescent, depressive disorder, mental disorder, mental illness, dsm-ivSCR_009654(Mexican Adolescent Mental Health Survey, RRID:SCR_009654)Mental disease, Depressive Disorder, AgingMexican Ministry of Education, National Council on Science and Technology - Mexico, National Institute of Psychiatry Ramon de la Fuente MuñizReferences (8)Last checked upnlx_156052
Teen-Longitudinal Assessment of Bariatric Surgery Resource, disease-related portal, topical portal, resource, research forum portal, portal, data or information resourceConsortium made up of five clinical centers and a data coordinating center facilitating coordinated clinical, epidemiological, and behavioral research in the field of adolescent bariatric surgery, through an observational study protocol for uniform data collection pre-operative, at surgery, and through 2 years post-operative at participating centers performing bariatric surgery on teenagers. The use of standardized definitions and data-collection instruments for sequential patients scheduled for surgery at each site will yield meaningful evidence-based recommendations for patient evaluation, selection, and follow-up care. In addition to investigating surgical outcomes, another broader goal of Teen-LABS is to better understand the etiology, pathophysiology, and behavioral aspects of severe obesity in youth and how this condition affects human beings over time. The Teen-LABS consortium members include: Cincinnati Children's Hospital Medical Center, Texas Children's Hospital, Children's Hospital of Alabama, University of Pittsburgh, Nationwide Children's Hospitaladolescent human, bariatrics, pre-operative, at surgery, post-operative, clinical, epidemiology, behavior, surgical outcome, metadata standard, observational study, clinical, experimental protocol, evidence-based recommendation, patient evaluation, follow-up careSCR_001492( Teen-Longitudinal Assessment of Bariatric Surgery , RRID:SCR_001492)Bariatric surgery, ObesityNIDDKlisted by: NIDDK Information Network, submitted by: NIDDK Information NetworkLast checked downnlx_152747
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