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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 19, 2019)

Physical Resource or Software Tool Software

280 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
UCSCinResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Beta software used to align and browse a genome.genomeSCR_000571(UCSCin, RRID:SCR_000571)University of Toronto; Ontario; Canada Last checked downnlx_144379
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
MetaGeneProfilerResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Meta Gene Profiler (MetaGP) is a web application tool for discovering differentially expressed gene sets (meta genes) from the gene set library registered in our database. Once user submits gene expression profiles which are categorized into subtypes of conditioned experiments, or a list of genes with the valid pvalues, MetaGP assigns the integrated p-value to each gene set by combining the statistical evidences of genes that are obtained from gene-level analysis of significance. The current version supports the nine Affymetrix GeneChip arrays for the three organisms (human, mouse and rat). The significances of GO terms are graphically mapped onto the directed acyclic graph (DAG). The navigation systems of GO hierarchy enable us to summarize the significance of interesting sub-graphs on the web browser. Platform: Online toolgene, gene expression, differentially expressed, gene ontology, meta gene, gene set, statistical analysisSCR_005794(MetaGeneProfiler, RRID:SCR_005794)Institute of Statistical Mathematics; Tokyo; Japan related to: Gene Ontology, listed by: Gene Ontology ToolsLast checked downnlx_149271
Expression ProfilerResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice.other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, geneSCR_005821(Expression Profiler, RRID:SCR_005821)European Bioinformatics Institute Estonian Science Foundation, European Union, Wellcome Trustrelated to: Gene Ontology, listed by: Gene Ontology ToolsPMID:15215431Last checked downnlx_149323
MAP-O-MATResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. MAP-O-MAT is a web-based server for automated linkage mapping of human polymorphic DNA markers. The server uses publicly available genotype data for over 15,000 markers. It facilitates the verification of order and map distances for custom mapping sets using genotype data from the CEPH database, and from the Marshfield, SNP Consortium and Rutgers linkage maps. The CRI-MAP program is used for likelihood calculations and some mapping algorithms, and physical map positions are provided from the human genome assembly.general human genetics databases, automated, distance, dna, genotype, human, linkage, map, mapping, marker, polymorphic, position, verificationSCR_008197(MAP-O-MAT, RRID:SCR_008197)Rutgers University; New Jersey; USA Last checked downnif-0000-21251http://compgen.rutgers.edu/mapomat/
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
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
MD Anderson Pancreas Tissue BankResource, biomaterial supply resource, data or information resource, material resource, tissue bank, databaseTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. A clinical database and PTB were created in 1990 and 2000, respectively, to collect clinical information and biospecimens from patients with suspected or confirmed pancreatic cancer, other pancreatic diseases, and tumors of the duodenum, ampulla of Vater, and distal bile duct. Standard procedures for biospecimen collection and data entry were developed. The use of human tissue for research is an invaluable tool to understand the basic mechanisms of tumor biology, which will hopefully lead to the development of new therapeutic approaches to pancreatic cancer treatment. The cornerstone of any large translational research program is the development of an accurate and comprehensive tumor bank. All tumors removed in the operating room are sampled for careful pathologic study and the remainder of the tumor is promptly stored in our Pancreas Tissue Bank (PTB) to be used for research. Other samples, including blood, pancreatic juice and biopsy material, can also be utilized to identify early markers for pancreatic cancer. The molecular profile of tumors in the PTB can be linked to information in our clinical database to provide insight on the relationship between molecular events and clinical outcome. Patients may contribute to the tissue banking effort by choosing to participate in select research protocols. Protecting patient privacy is of great importance and thus, to maintain the confidentiality of health information, the PTB complies with all federal and institutional regulations governing research with human participants.clinical, tumor, cancer, bodily fluid, tissue, tumor, blood, pancreatic juice, biopsy material, pancreatic cancer, pancreatic disease, tumor of the duodenum, tumor of the ampulla of vater, tumor of the distal bile ductSCR_004983(MD Anderson Pancreas Tissue Bank, RRID:SCR_004983)University of Texas MD Anderson Cancer Center Pancreatic cancer, Pancreatic disease, Tumor of the duodenum, Tumor of the ampulla of Vater, Tumor of the distal bile ductlisted by: One Mind Biospecimen Bank ListingPMID:18256882Last checked downnlx_94016http://www.mdanderson.org/education-and-research/research-at-md-anderson/basic-science/research-programs/pancreatic-cancer-research/from-bench-to-bedside/human-tumor-bank-database-expansion.html
Taizhou BiobankResource, biomaterial supply resource, material resourceTHIS RESOURCE IS NOT IN SERVICE, documented August 9, 2016. A genetic biobank in Taizhou, China which plans to collect five million samples in 10 years.biobank, china, taizhouSCR_000935(Taizhou Biobank, RRID:SCR_000935)Last checked upnlx_88700
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
Adenoma Polyp Tissue BankResource, biomaterial supply resource, material resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The Adenoma Polyp Tissue Bank (APTB) receives whole blood from patients enrolled in the Prevention of Sporadic Colorectal Adenomas with Celecoxib clinical trial. We have reached our accrual on blood submissions, so we will no longer be receiving blood specimens The objectives of this trial are as follows: A. To determine the efficacy and safety of celecoxib versus placebo in preventing the occurrence of newly detected colorectal adenomas in subjects at increased risk for colorectal carcinoma. In addition to incidence, other established risk factors will be evaluated for their association with occurrence of new colorectal adenomas, including cancer family history and adenoma size, histopathologic grade, multiplicity and location. Primary assessment of treatment efficacy will be the reduction in the number of subjects with adenomas at colonoscopy after Year 1 and Year 3 of study drug use. Secondary assessments of treatment efficacy will be 1) the number of adenomas 2) the histopathologic grade of adenomas and 3) the size of adenomas, also measured after one year and three years of study drug use. These factors will be incorporated into a risk model for predicting adenoma occurrence and response to celecoxib. B. To determine the efficacy of celecoxib versus placebo in modulating one or more of a panel of biomarkers for colorectal cancer at the cellular and molecular level sampled in a subset of subjects at selective sites at baseline and after Year 1 and Year 3 of study drug use. These biomarkers will include measurements of aberrant crypt foci (ACF), proliferation (index and crypt distribution), apoptosis (index and crypt distribution), COX expression and activity. If modulation of one or more mucosal biomarkers occur, we will explore whether it correlates with the development of incident colorectal neoplasia (adenomas/carcinomas), thereby attempting to validate the surrogacy of that biomarker. C. To develop a specimen bank. Serum and white blood cells are isolated from whole blood and adenoma tissue blocks and slides are banked. Banked specimens will become available for use in correlative science studies at a later point. This project began in 1999 and will be extended through 2006. The lead principal investigator is Monica M. Bertagnolli, MD, Brigham and Women''s Hospital, Boston, MA, and the APTB Director is Scott Jewell, Ph.D., Department of Pathology, The Ohio State University. The APTB is supported by the NIH, NCI Division of Cancer Prevention, in connection with the Strang Cancer Prevention Center, Cornell University, New York.blood, serum, white blood cell, adenoma tissue, tissue, whole blood, block, slide, colorectal adenoma, celecoxib, adenoma, cancer, colorectal cancer, clinical trial, polyp, risk factorSCR_005366(Adenoma Polyp Tissue Bank, RRID:SCR_005366)Human Tissue Resource Network Increased risk for colorectal carcinomaNCIlisted by: One Mind Biospecimen Bank ListingLast checked downnlx_144435
Loyola University Medical Center / Hines VA Brain BankResource, biomaterial supply resource, material resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. A medical center with a neuropathology research program focused on the normal and abnormal aging process of the central nervous system and a funding source for research. The center serves as a collection site for brains in order to study normal aging and neurodegenerative diseases like Alzheimer's.late adult human, neuropathology, autopsy, alzheimer's disease, neurodegenerative disease, age-matched control, normal control, muscle, nerve, brain, brain tissue, tissue, neuropathologySCR_013277(Loyola University Medical Center / Hines VA Brain Bank, RRID:SCR_013277)Loyola University Chicago Stritch School of Medicine; Illinois; USA Alzheimer's disease, Neurodegenerative disease, Age-matched control, Aginglisted by: One Mind Biospecimen Bank ListingLast checked downnlx_144052http://www.stritch.luc.edu/depts/path/residency/anatomic_pathology.htm#Neuropathology
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
SpinalGraft Technologies LLCResource, biomaterial supply resource, material resource, instrument supplierTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 02, 2016.spinal graft, medtronics, commercialSCR_000937(SpinalGraft Technologies LLC, RRID:SCR_000937)Last checked downnlx_92159
BayGenomicsResource, biomaterial supply resource, material resource, organism supplier, tissue bankTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The BayGenomics gene-trap resource provides researchers with access to thousands of mouse embryonic stem (ES) cell lines harboring characterized insertional mutations in both known and novel genes. The major goal of BayGenomics is to identify genes relevant to cardiovascular and pulmonary disease.embryonic, expression, gene, bioinformatic, cardiopulmonary, cell, clone, disease, genomic, germline, insertional, line, mouse, mutant, mutation, pulmonary, stem, cardiovascular, pulmonary diseaseSCR_008168(BayGenomics, RRID:SCR_008168)University of California at San Francisco; California; USA listed by: One Mind Biospecimen Bank ListingLast checked downnif-0000-21042
BC Fisheries Living Gene BankResource, biomaterial supply resource, material resource, tissue bankTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. An ichtyological gene bank with data from fisheries in British Columbia, Canada.SCR_000917(BC Fisheries Living Gene Bank, RRID:SCR_000917)Last checked downnlx_17177
LifeCell CorporationResource, biomaterial supply resource, material resource, tissue bankTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016.SCR_013593(LifeCell Corporation, RRID:SCR_013593)Last checked downnlx_12927
Medical College of Georgia Tumor BankResource, biomaterial supply resource, material resource, tissue bankTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. The MCG Tumor Tissue and Serum Repository or tumor bank, located in the Department of Pathology, Murphey Pathology Building, was established with support from the Georgia Cancer Coalition (GCC). Its mission is to provide researchers access to high quality annotated specimens, an essential requirement for cancer research. The repository collection includes a variety of specimen types, such as tumor tissue and cells, blood and other biofluids as well as normal specimens used as controls. The quality of all specimens is reviewed by a pathologist, and the information is captured in the tumor bank''s database. An imaging system will be used in the future to capture this information. Human-derived specimens are a very precious resource, and therefore the operations of the tumor bank are overseen by an advisory board, representing GHSU and other stakeholders, to ensure that the specimens are properly utilized and the privacy of specimen donors is protected.SCR_004336(Medical College of Georgia Tumor Bank, RRID:SCR_004336)Medical College of Georgia; Georgia; USA Tumorlisted by: One Mind Biospecimen Bank ListingLast checked downnlx_35211http://www.mcg.edu/CANCER/shared/tumor/
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
Dana Farber Tissue BankResource, biomaterial supply resource, material resource, tissue bankTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. The Dana-Farber/Harvard Cancer Center Pathology Specimen Locator (PSL) is a core developed to facilitate translational research requiring human specimens. The PSL is a distributed network of databases containing de-identified pathology reports and other specimen information from IRB-approved repositories within Dana-Farber/Harvard Cancer Center affiliated institutions. Using the PSL, researchers can work with the pathology departments to find appropriate specimens for their research. The Harvard VLS currently contains approximately two million de-identified pathology reports from the four main Harvard Teaching Hospitals.SCR_004352(Dana Farber Tissue Bank, RRID:SCR_004352)Dana-Farber Cancer Institute listed by: One Mind Biospecimen Bank ListingLast checked downnlx_37203
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