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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 5, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
AceViewResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER SUPPORTED, documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions.est, exon, expression, function, gene, alignment, arabidopsis, cdna, co-alignment, coding, disease, genome, genomic, human, intron, localization, mammal, mouse, mrna, nematode, pathway, phenotype, plant, polyadenylation, promoter, rat, sequence, signal, tissue, transcript, transcriptome, worm, blast, gold standardSCR_002277(AceView, RRID:SCR_002277)NCBI Last checked downnif-0000-21007
Evolutionary Lineage Inferred from Structural AnalysisResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. ELISA is an online database that combines functional annotation with structure and sequence homology modeling to place proteins into sequence-structure-function neighborhoods. The atomic unit of the database is a set of sequences and structural templates that those sequences encode. A graph that is built from the structural comparison of these templates is called PDUG (protein domain universe graph). It introduces a method of functional inference through a probabilistic calculation done on an arbitrary set of PDUG nodes. Further, all PDUG structures are mapped onto all fully sequenced proteomes allowing an easy interface for evolutionary analysis and research into comparative proteomics. ELISA is the first database with applicability to evolutionary structural genomics explicitly in mind.evolutionary, function, functional, analysis, annotation, atomic unit, calculation, comparative, domain, genomic, homology, modeling, place, probabilistic, protein, protein domain and protein classification databases, proteome, proteomic, sequence, structural, structure, templateSCR_002343(Evolutionary Lineage Inferred from Structural Analysis, RRID:SCR_002343)Boston University; Massachusetts; USA Last checked downnif-0000-21141
Familial Hypertrophic Cardiomyopathy DNA Mutation DatabaseResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The aim of this locus-specific mutation database was to provide an online resource that contains summarized and updated information on familial hypertrophic cardiomyopathy (FHC)-associated mutations and related data, for researchers and clinicians. It also serves as a means of publishing previously unpublished data, which could be of value in understanding genotype/phenotype correlations. This database contains mutations in various genes known to cause familial hypertrophic cardiomyopathy, a genetic disorder associated with defects in the sarcomere [1]. Only gene symbols approved by HUGO are used and mutations are reported in accordance with guidelines recommended by the Mutation Database Initiative of HUGO and EBI.familial, gene, gene-, genetic, cardiomyopathy, clinic, correlation, defect, disorder, genotype, hypertrophic, locus, mutation, or disease- specific databases, phenotype, research, sarcomere, system-SCR_002346(Familial Hypertrophic Cardiomyopathy DNA Mutation Database, RRID:SCR_002346)Last checked downnif-0000-21151
BiobehavioralResource, blog, narrative resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. Biobehavioral blog on research and medicine as a continuum from biological mechanisms to behavioural phenomena.SCR_008710(Biobehavioral, RRID:SCR_008710)Last checked downnlx_11905
OBD-PKB InterfaceResource, ontology, data or information resource, controlled vocabularyTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This interface is for exploring data collected as part of the NIF Neurodegenerative Disease Ontology project. Not generally intended for public consumption yet, but people are welcome to look - large caveat emptor applies. Sponsors: This resource is part of the NIF, disease, neurodegenerative, softwareSCR_002882(OBD-PKB Interface, RRID:SCR_002882)University of California; Berkeley; USA Last checked downnif-0000-25570
Movement Disorder Virtual University (MDVU): Resource LibraryResource, assessment test provider, training resource, narrative resource, slide, report, material resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented April 15, 2016. The Movement Disorder Virtual University (MDVU) Resource Library contains detailed movement disorder information and resources including rating scales, scoring sheets, patient fact sheets, teaching slide sets, research news, meeting reports, anatomical illustrations, movement disorder treatment and rehabilitation directory, a glossary, support organizations, drug package information, and a library of links.drug information, dystonia, essential tremor, fact sheets, botulinum toxin, definitions, directory, glossary, human, huntington's disease, illustrations, information, links, movement disorders, myoclonus, news, parkinson's disease, patient advocacy, pediatric, progressive supranuclear palsy, rating scales, rehabilitation, restless legs syndrome, scoring sheets, spasticity, support organizations, tic, tourettes syndrome, treatmentSCR_002719(Movement Disorder Virtual University (MDVU): Resource Library, RRID:SCR_002719)Last checked downnif-0000-23698
SumsDBResource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, atlas, image repository, data repository, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figuressegmentation, volume, neuroimaging, brain, fmri, stereotaxic foci, stereotaxic coordinate, brain-mapping, foci, structural mri, mri, cerebral cortex, cerebellar cortex, afni brik, analyze, atlas, nifti, registration, rendering, spatial transformation, surface analysis, surface rendering, visualization, volume rendering, brain mapping, neuroanatomySCR_002759(SumsDB, RRID:SCR_002759)Washington University School of Medicine in St. Louis; Missouri; USA Mental disease, Neurological disorder, NormalHuman Brain Project, NASA, National Partnership for Advanced Computational Infrastructure, NCI, NIMH, NLM, NSFrelated to: Computerized Anatomical Reconstruction and Editing Toolkit, Integrated Manually Extracted Annotation, used by: NIF Data Federation, listed by: Biositemaps, NeuroImaging Tools and Resources Collaboratory (NITRC), re3data.orgLast checked downnif-0000-00016
GenomEUtwinResource, disease-related portal, topical portal, database, biomaterial supply resource, research forum portal, portal, material resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Study of genetic and life-style risk factors associated with common diseases based on analysis of European twins. The population cohorts used in the Genomeutwin study consist of Danish, Finnish, Italian, Dutch, English, Australian and Swedish twins and the MORGAM population cohort. This project will apply and develop new molecular and statistical strategies to analyze unique European twin and other population cohorts to define and characterize the genetic, environmental and life-style components in the background of health problems like obesity, migraine, coronary heart disease and stroke, representing major health care problems worldwide. The participating 8 twin cohorts form a collection of over 0.6 million pairs of twins. Tens of thousands of DNA samples with informed consents for genetic studies of common diseases have already been stored from these population-based twin cohorts. Studies targeted to cardiovascular traits are now being undertaken in MORGAM, a prospective case-cohort study. MORGAM cohorts include approximately 6000 individuals, drawn from population-based cohorts consisting of more than 80 000 participants who have donated DNA samples.genetic, environment, lifestyle, gene, diseaseSCR_002843(GenomEUtwin, RRID:SCR_002843)University of Helsinki; Helsinki; Finland TwinEuropean Unionrelated to: KI Biobank - TwinGene, listed by: One Mind Biospecimen Bank ListingLast checked downnif-0000-25218
International HapMap ProjectResource, narrative resource, data or information resource, experimental protocol, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project.genetic variant, disease, genetic sequence, genetic variation, single nucleotide polymorphism, genetic diversity, dna, sequence, catalog, genome, chromosomeSCR_002846(International HapMap Project, RRID:SCR_002846)NCBI Chinese Academy of Sciences, Chinese Ministry of Science and Technology, Delores Dore Eccles Foundation, Genome Canada, Genome Quebec, Hong Kong Innovation and Technology Commission, Japanese Ministry of Education Culture Sports Science and Technology MEXT, National Natural Science Foundation of China, NIH, SNP Consortium, University Grants Committee of Hong Kong, Wellcome Trust, W. M. Keck Foundationrelated to: SNAP - SNP Annotation and Proxy Search, Haploview, NHGRI Sample Repository for Human Genetic Research, DistiLD - Diseases and Traits in LD, SNP at Ethnos, GBrowse, used by: BioSample Database at EBI, listed by: OMICtoolsLast checked downnif-0000-02940, OMICS_00273
Coddle-Codons Optimized to Discover Deleterious LEsionsResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Web-accessible program that identifies the region(s) of a user-selected gene and of its coding sequence (CDS) where the anticipated point mutations are most likely to result in deleterious effects on the gene's function. CODDLe separately handles 1) the prediction of changes which should truncate the protein and destabilize the RNA - nonsense changes and splice junction changes, and 2) the prediction of missense changes which should alter function of the gene product - those in conserved amino acid blocks in the CDS. Because the region(s) identified will be PCR amplified by the user and that amplicon will be used for polymorphism discovery, the application delivers primer pairs selected by Primer3 (Steve Rozen, Helen J. Skaletsky (1996,1997,1998)Primer3.) After selecting a primer pair, CODDLe returns a window with the selected amplicon and tabulates the effects of all possible polymorphisms which could be detected in that amplicon. CODDLe will not identify the regions of a gene where polymorphisms are most likely to be discovered. Others have shown that naturally occurring SNPs are found more often in the untranslated regions of a gene.codon, deleterious lesion, gene, coding, sequence, mutation, primer, protein sequence, cdna, sequence alignment, coding sequenceSCR_003003(Coddle-Codons Optimized to Discover Deleterious LEsions, RRID:SCR_003003)Fred Hutchinson Cancer Research Center DOE, Office of Energy Researchlisted by: 3DVCLast checked downnif-0000-30262
AlzSWAN Knowledge BaseResource, portal, knowledge environment, community building portal, knowledgebase, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A community-driven knowledgebase of Alzheimer disease, in which researchers can annotate scientific claims, data, and information, putting these into the context of testable hypotheses and treatment discovery. This SWAN project adds a collection of hand-curated hypotheses to a research paper, which are then related through a set of discourse relationships. They can be browsed and relations between claims, as well as support networks for a specific claim, are made and visualized. AlzSWAN is where you explore scientific knowledge about Alzheimer disease and share your own ideas, comments and questions in a semantically structured system. AlzSWAN is enabled by Semantic Web technology, a new standard for knowledge organization and transfer on the Web. AlzSWAN organizes and manages knowledge using formal knowledge descriptions called ontologies. Using these formal knowledge descriptions, they can tie statements made in scientific publications or on the Web to scientific evidence, biological terminologies, and knowledgebases, and to claims and counterclaims made by other researchers.hypothesis, claim, research paper, relationship, semantics, annotationSCR_003017(AlzSWAN Knowledge Base, RRID:SCR_003017)Alzheimer's Research Forum Alzheimer's, Ellison Medical Foundationrelated to: Semantic Web Applications in Neuromedicine (SWAN) Ontology, listed by: FORCE11PMID:17510163Last checked downnif-0000-00524
PDP++ Software Home PageResource, software resource, software application, simulation softwareTHIS RESOURCE IS NO LONGER SUPPORTED, documented August 23, 2016. The PDP++ software is a neural-network simulation system written in C++. It represents the next generation of the PDP software originally released with the McClelland and Rumelhart Explorations in Parallel Distributed Processing Handbook, MIT Press, 1987. It is easy enough for novice users, but very powerful and flexible for research use. The new version of PDP++, released 8/21/07, is now called Emergent.feedforward, backpropagation, graphical representations, long short term memory, metadata, model, neural network, simulation, softwareSCR_003064(PDP++ Software Home Page, RRID:SCR_003064)Carnegie Mellon University; Pennsylvania; USA related to: EmergentLast checked downnif-0000-00172
Rat Gene Symbol TrackerResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Database for defining official rat gene symbols. It includes rat gene symbols from three major sources: the Rat Genome Database (RGD), Ensembl, and NCBI-Gene. All rat symbols are compared with official symbols from orthologous human genes as specified by the Human Gene Nomenclature Committee (HGNC). Based on the outcome of the comparisons, a rat gene symbol may be selected. Rat symbols that do not match a human ortholog undergo a strict procedure of comparisons between the different rat gene sources as well as with the Mouse Genome Database (MGD). For each rat gene this procedure results in an unambiguous gene designation. The designation is presented as a status level that accompanies every rat gene symbol suggested in the database. The status level describes both how a rat symbol was selected, and its validity. Rat Gene Symbol Tracker approves rat gene symbols by an automatic procedure. The rat genes are presented with links to RGD, Ensembl, NCBI Gene, MGI and HGNC. RGST ensures that each acclaimed rat gene symbol is unique and follows the guidelines given by the RGNC. To each symbol a status level associated, describing the gene naming process.gene, orthology, naming, gene symbol, nomenclature, human, mouseSCR_003261(Rat Gene Symbol Tracker, RRID:SCR_003261)RatMap Erik Philip-Sorensen Foundation, Nilsson-Ehle Foundation, Sven and Lilly Lawski Foundation, Swedish MRC, SWEGENE Foundation, Wilhelm and Martina Lundgren Research Foundationrelated to: Rat Genome Database (RGD), Entrez Gene, Ensembl, Mouse Genome Informatics (MGI), HGNCPMID:18215257Last checked downnif-0000-31426
Cancer Biomedical Informatics GridResource, organization portal, portal, knowledge environment, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented July 19, 2016. It has been integrated into the National Cancer Informatics Program (NCIP). The National Cancer Institute launched the cancer Biomedical Informatics Grid (caBIG) to create a virtual network of interconnected data, individuals, and organizations that worked together to redefine how cancer research is conducted. caBIG capabilities allowed researchers and clinicians to collaborate more effectively so that complex research questions might be asked and answered faster and more effectively. The mission of caBIG was to develop a truly collaborative information network that accelerated the discovery of new approaches for the detection, diagnosis, treatment, and prevention of cancer, ultimately improving patient sharingSCR_003328(Cancer Biomedical Informatics Grid, RRID:SCR_003328)National Cancer Institute NCIrelated to: caTIES - Cancer Text Information Extraction System, caArrayLast checked downnif-0000-31949
PINdbResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Relational database containing the compositions of multi-protein complexes in the nucleus of budding yeast and human cells. Its content is limited to information curated from the proteomics literature and primarily comprises of components of the general transcription and DNA repair machinery. In addition to database browsing and searching capabilities, the PINdb web portal also includes user-friendly interactive tools for comparative analysis of the composition of multiple protein complexes and for clustering and visualizing network of protein complexes. Currently, PINdb contains mostly protein complexes that may be involved in gene transcription. To facilitate comparative analyses and identification of protein complexes, the compositional information is integrated with standardized gene nomenclature, annotation and protein sequences from public databases. The PINdb web interface provides a number of tools for (1) comparison of protein complexes, (2) search for a protein complex by its published name or by a partial list of its components and (3) browsing specific subsets or a functional classification of the complexes.nuclear protein complex, protein interaction, targeted proteomics, network visualization, protein, nucleus, proteomics, protein complex, gene transcriptionSCR_003348(PINdb, RRID:SCR_003348)related to: ConsensusPathDBPMID:15087322Last checked downnif-0000-03290
FSSP - Families of Structurally Similar ProteinsResource, data set, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank. The database currently contains an extended structural family for each of 330 representative protein chains. Each data set contains structural alignments of one search structure with all other structurally significantly similar proteins in the representative set (remote homologs, below 30%% sequence identity), as well as all structures in the Protein Data Bank with 70-30%% sequence identity relative to the search structure (medium homologs). Very close homologs (above 70 % sequence identity) are excluded as they rarely have marked structural differences. The alignments of remote homologs are the result of pairwise all-against-all structural comparisons in the set of 330 representative protein chains. All such comparisons are based purely on the 3D co-ordinates of the proteins and are derived by automatic (objective) structure comparison programs. The significance of structural similarity is estimated based on statistical criteria. The FSSP database is available electronically and by anonymous ftp (file transfer protocol).computer algorithm, modular protein design, protein folding, protein structure alignment, protein structure, gold standardSCR_003534(FSSP - Families of Structurally Similar Proteins, RRID:SCR_003534)European Bioinformatics Institute Commission of the European Communities and Human Frontiers Science Program, EMBOPMID:1304898Last checked downnlx_10193
Sage Bionetworks PodcastsResource, narrative resource, podcast, data or information resourceTHIS RESOURCE IS NO LONGER SUPPORTED, documented September 6, 2016. Sage Bionetworks video podcasts feature the plenary talks from the April 2011 Commons Congress in San Francisco. The Keynote and project update video posts are in reverse chronological order; the full agenda is available at There are also several excellent podcasts from the January 2011 Symposium on Human Data Interoperability. The podcasts are also available on iTunes where you can subscribe and receive new podcasts automatically when posted. Upcoming posts will feature presentations and interviews on network biology, genomics, healthcare and open science. All these podcasts feature research and thought leaders as well as policy advocates, scientists working at the coal-face and patients. The topics span technical and strategic issues and include fact and opinion. The goal is to engage, educate and inspire non-scientists and scientists alike.SCR_003542(Sage Bionetworks Podcasts, RRID:SCR_003542)Sage Bionetworks Last checked downnlx_10797
National Brain DatabankResource, data set, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. A publicly accessible data repository to provide neuroscience investigators with secure access to cohort collections. The Databank collects and disseminates gene expression data from microarray experiments on brain tissue samples, along with diagnostic results from postmortem studies of neurological and psychiatric disorders. All of the data that is derived from studies of the HBTRC collection is being incorporated into the National Brain Databank. This data is available to the general public, although strict precautions are undertaken to maintain the confidentiality of the brain donors and their family members. The system is designed to incorporate MIAME and MAGE-ML based microarray data sharing standards. Data from various types of studies conducted on brain tissue in the HBTRC collection will be available from studies using different technologies, such as gene expression profiling, quantitative RT-PCR, situ hybridization, and immunocytochemistry and will have the potential for providing powerful insights into the subregional and cellular distribution of genes and/or proteins in different brain regions and eventually in specific subregions and cellular subtypes.cellular, cortex, sequence data, molecular neuroanatomy resource, gene expression, microarray, brain tissue, post-mortem, neurological disorder, mental disease, human, gene expression profiling, quantitative rt pcr, in situ hybridization, immunocytochemistry, schizophrenia, bipolar disorder, huntington's disease, parkinson's diseaseSCR_003606(National Brain Databank, RRID:SCR_003606)Harvard Brain Tissue Resource Center Schizophrenia, Huntington's disease, Parkinson's disease, bipolar disorderNIMH, NINDSLast checked downnif-0000-00071
GLIDERSResource, software resource, software applicationTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016.gene, genetic, genomicSCR_009210(GLIDERS, RRID:SCR_009210)listed by: Genetic Analysis SoftwareLast checked downnlx_154359
Massachusetts Human Stem Cell BankResource, biomaterial supply resource, material resource, cell repositoryTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. Stem cell research, particularly human embryonic stem cell (hESC) research, holds tremendous promise to discover therapeutic options and perhaps cures for insidious diseases such as cancer, juvenile diabetes, Alzheimer's and Parkinson's. The Massachusetts Human Stem Cell Bank provides the biomedical research community with expertly maintained human ES (hES) and reprogrammed (iPS) cell lines to facilitate studies into the properties and potential therapeutic applications of pluripotent stem cells. The Bank cultures, characterizes and distributes quality controlled hES and iPS cell lines derived in Massachusetts and beyond. The Bank is a 15,000 square foot facility that contains research and training space for visiting investigators. In addition, the Education and Training division provides technical training and programs to educate the community.SCR_004141(Massachusetts Human Stem Cell Bank, RRID:SCR_004141)University of Massachusetts Medical School; Massachusetts; USA Massachusetts Life Sciences Centerlisted by: One Mind Biospecimen Bank ListingLast checked downnlx_16360
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