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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: Sep 14, 2019)

Physical Resource or Software Tool Software

101 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
PROTOTYPE - Suspected Overlap Among OBO Foundry Candidate OntologiesResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Service that determines the Suspected Overlap Among OBO Foundry Candidate Ontologies.SCR_008834(PROTOTYPE - Suspected Overlap Among OBO Foundry Candidate Ontologies, RRID:SCR_008834)National Center for Biomedical Ontology Last checked downnlx_144632
GOALIEResource, software resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Generalized Ontological Algorithmic Logical Invariants Extractor (GOALIE) is a tool for the construction of time-course dependent enrichments. Requires an ODBC connection to an instance of the GO database. Platform: Windows compatible, Mac OS X compatible, Linux compatiblegene ontology, statistical analysis, time-courseSCR_000088(GOALIE, RRID:SCR_000088)NYU Bioinformatics Group listed by: Gene Ontology ToolsLast checked downnlx_149255
FluWikie.comResource, topical portal, portal, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. Flu Wikie is a topical portal on the flu. Major categories include health, Flu Symptoms, Avian Influenza, Swine Flu, Cold, Vaccination, Pandemic, Vitamin D, and Immune System. Many articles on topic are included.virusSCR_000506(FluWikie.com, RRID:SCR_000506)Last checked downnlx_22823
EDACResource, software resource, software applicationTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.gene, genetic, genomicSCR_000829(EDAC, RRID:SCR_000829)listed by: Genetic Analysis SoftwareLast checked downnlx_154078http://www.biostat.wustl.edu/~gc/cgi-bin/calcpwr.cgi
2LDResource, software resource, software applicationTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software program for calculating linkage disequilibrium (LD) measures between two polymorphic markers.gene, genetic, genomic, cSCR_000826(2LD, RRID:SCR_000826)listed by: Genetic Analysis SoftwareLast checked downnlx_154006http://www.mrc-epid.cam.ac.uk/Personal/jinghua.zhao/software.htm
DCHIP LINKAGEResource, software resource, software applicationTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.gene, genetic, genomic, c++, ms-windowsSCR_000835(DCHIP LINKAGE, RRID:SCR_000835)listed by: Genetic Analysis SoftwareLast checked downnlx_154280
ZAPLOResource, software resource, software applicationTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016.gene, genetic, genomic, linux, unix, solarisSCR_009426(ZAPLO, RRID:SCR_009426)listed by: Genetic Analysis SoftwareLast checked downnlx_154692
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
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
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
GCG/SeqWebResource, this resource is no longer in service, data analysis software, data processing software, software application, text-mining software, nif annotation standard, narrative resource, standard specification, software resource, availability annotation standard, data or information resourceThe Core Facility provides the software and support for computer assisted protein and DNA sequence analysis and database access. The Genetics Computer Group GCG-Wisconsin package is currently available on PBRC's UNIX platform that is accessible via modem or direct connection. The package can be accessed via three interfaces: the command-line interface (UNIX C-shell), the web-based interface (SeqWeb) and the X-Windows based graphics interface (SeqLab). Applications in the package include sequence editing, alignment, comparison, primer design, restriction analysis, mapping, data presentation, database browsing, etc. In addition to local databases, access to remote databases (BLAST) is integrated into the package. The local databases are updated quarterly. Databases available include GenBank, EMBL, PIR-Protein, SWISS-PROT and Restriction Enzymes (REBASE). THIS RESOURCE IS NO LONGER IN SERVCE, documented January 28, 2019.bioinformatics, data mining, statistical analysis, dna microarray, molecular modeling, genetic analysis, protein, dna, sequence analysisSCR_003454(GCG/SeqWeb, RRID:SCR_003454)University of Hawaii at Manoa listed by: BiositemapsLast checked downnif-0000-33361http://core.biotech.hawaii.edu/b-gcg.htm
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_10193http://www.sander.ebi.ac.uk/dali/fssp/
HealthGrid WikiResource, wiki, narrative resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. HealthGrid is a wiki dedicated to grids for health. It is maintained as a dynamic knowledge resource for the healthgrid community. The HealthGrid community (a world-wide initiative) gathers individuals from the public and private domain world-wide who are actively exploring the beneficial impact of healthgrid technology on healthcare provision and research.SCR_003572(HealthGrid Wiki, RRID:SCR_003572)Last checked downnlx_12797
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
M2Gen BiorepositoryResource, biomaterial supply resource, material resource, tissue bankTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The M2Gen Biorepository offers the world's largest cancer-focused tissue biobank linked to longitudinal clinical and molecular data. We provide well-annotated, high quality tissue and clinical data to support research and clinical partnerships. M2Gen's Biorepository team includes dedicated pathologists, biobanking specialists and licensed laboratory staff. Quality control assessment is performed by board-certified pathologists.biorepository, tissue bank, commercial, health informaticsSCR_004332(M2Gen Biorepository, RRID:SCR_004332)listed by: One Mind Biospecimen Bank ListingLast checked downnlx_35112http://www.moffitt.org/Site.aspx?spid=C54AF116F69244D49BACE202F69BC2A6
Open HHS BlogResource, blog, narrative resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. In the Open HHS Blog, Chief Technology Officer, Todd Park, writes about harnessing the power of data, technology and innovation to improve the health and welfare of the nation.SCR_004429(Open HHS Blog, RRID:SCR_004429)Data.gov Last checked downnlx_42950
Gray MattersResource, narrative resource, podcast, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on September 06, 2013. Gray Matters is a radio series on brain topics that has been produced since 1994 by Public Radio International in association with the Dana Alliance. More than 25 programs have been created on topics ranging from stress, neuroethics, learning throughout life and sports, fitness and the Brain. Dana Alliance members serve as advisers to Gray Matters programming and are interviewed during the programs. The transcripts are also available.SCR_004433(Gray Matters, RRID:SCR_004433)The Dana Foundationrelated to: Integrated Podcasts, used by: NIF Data FederationLast checked downnlx_54435
LifeTek OrthoBiologicsResource, biomaterial supply resource, material resource, tissue bankTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. LifeTek is a full service International Tissue Bank, with recovery and processing partners in the United States, Spain and Mexico. Our goal is to provide safe, quality allograft implants, therefore serving donor families, physicians and recipients. Following regulations established by state and federal agencies, including the United States Food and Drug Administration, specific steps are taken to ensure donor suitability, including serologic testing performed by CLIA certified laboratories. LifeTek aseptically process tissues in Class 100 Cleanrooms, significantly reducing the risk of airborne contaminants. Equipment and reagents used are sterilized in steam autoclaves. Grafts are further processed and sterilized using Clearant Technology. LifeTek allografts are provided either freeze-dried or frozen. Freeze-dried allografts are stored at ambient temperatures, while frozen allografts are stored at -40 degrees C or colder. Freeze-dried allografts are provided with a maximum of two years expiration, frozen allografts are provided with a maximum of five years expiration.SCR_004488(LifeTek OrthoBiologics, RRID:SCR_004488)listed by: One Mind Biospecimen Bank ListingLast checked downnlx_47539
MD Anderson Clone BankResource, biomaterial supply resource, material resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The MD Anderson Cancer Center Clone Bank consists of 802 murine cDNA clones, purchased from Research Genetics, Inc. These clones were sequence verified. A listing of the following are available: * Currently available clones (xls) * Top five blast hits for incorrect sequences (xls)SCR_004581(MD Anderson Clone Bank, RRID:SCR_004581)University of Texas MD Anderson Cancer Center listed by: One Mind Biospecimen Bank ListingLast checked downnlx_57463
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