Curator Dashboard

THIS 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.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone. Software for bacterial microscopy image analysis. It is designed to detect and outline bacterial cells in microscopy images and to analyze fluorescence signal inside them.

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• RRID-Legacy
• 9 years ago - by Anonymous

Core provides JEOL 400 MHz NMR equipped with auto sampling and automatic tuning and matching. Instrument can perform temperature and kinetic studies as well as x-nuclei and 2D experiments.

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

Non-profit research center dedicated to the study of the human genome. Expert staff and pioneering programs in the fields of personalized medicine, cell biology, cytogenetics, genotyping, and biobanking drive our mission. The emerging field of personalized medicine draws upon a person's genomic information to tailor treatments and prescription drug dosing to optimize health outcomes. The Coriell Personalized Medicine Collaborative (CPMC) research study is seeking to understand the usefulness of genetic risk and pharmacogenomics in clinical decision-making and healthcare management. Coriell has a distinguished history in cell biology. We are building upon this expertise by playing an important role in induced pluripotent stem (iPS) cell research. These powerful cells, which can be made from skin cells or blood, are revolutionizing the way human disease is studied and how drugs are developed. The decline of neurons afflicted with Alzheimer's disease or pancreatic cells fighting diabetes can be studied in a Petri dish. By proving efficacy within the diseased environment prior to clinical trial, drugs can move through the pipeline quicker to reach patients sooner. In addition to pioneering cutting-edge research initiatives, Coriell offers custom research services including cell culture, cytogenetic analyses, and molecular biology to the scientific community. Furthermore, Coriell's Genotyping and Microarray Center is one of the nation's largest centers, with high-throughput DNA analysis systems from Illumina and Affymetrix. The Center is CLIA-certified in 48 states.

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• SciCrunch
• 17 years ago - by Anonymous

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Database of digitized plant specimens. Used for finding plant name, type, specimens and their label data.The collection also includes partner contributed reference works and primary sources. Used for research and teaching in botany, ecology, and conservation studies.

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• RRID
• 2 years ago - by Anonymous

Ontology of the international classification for nursing practice.

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• SciCrunch
• 13 years ago - by Anonymous

Software for handling multimedia files. FFmpeg can record, convert and stream audio and video.

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• RRID-Legacy
• 9 years ago - submitted by Samuel Nastase

Software R package for generating circular multi-track plots.

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• RRID
• 2 years ago - submitted by Yi Liu

Software tool for detecting differential RNA processing from RNA-Seq data. It implements two statistical tests, rDiff.parametric and rDiff.nonparametric, to detect changes of the RNA processing between two samples.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. Used for concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation as a high-resolution microbial tree of life with taxonomic annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software application as fast, extensible progress bar for Python and CLI.

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• RRID
• 2 years ago - by Anonymous

Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories.

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• SciCrunch
• 13 years ago - by Anonymous

Image reconstruction software for MRI. Its library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms.

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• RRID-Legacy
• 9 years ago - by Anonymous

Facility specializes in training users in both solution phase and solid state NMR across all active nuclei and multiple NMR experients

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

Brain imaging data collected from a large population of normal, healthy children that have been used to construct pediatric brain templates, which can be used within statistical parametric mapping for spatial normalization, tissue segmentation and visualization of imaging study results. The data has been processed and compiled in various ways to accommodate a wide range of possible research approaches. The templates are made available free of charge to all interested parties for research purposes only. When processing imaging data from children, it is important to take into account the fact that the pediatric brain differs significantly from the adult brain. Therefore, optimized processing requires appropriate reference data be used because adult reference data will introduce a systematic bias into the results. We have shown that, in the in the case of spatial normalization, the amount of non-linear deformation is dramatically less when a pediatric template is used (left, see also HBM 2002; 17:48-60). We could also show that tissue composition is substantially different between adults and children, and more so the younger the children are (right, see also MRM 2003; 50:749-757). We thus believe that the use of pediatric reference data might be more appropriate.

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• SciCrunch
• 17 years ago - by Anonymous

The Bioinformatics Center is located within the Department of Diabetes and Cancer Discovery Science at City of Hope and was established in 2014 to support the Human Islet Research Network (HIRN). The overall objective of the Bioinformatics Center is to advance type 1 diabetes knowledge generated through HIRN by providing the bioinformatics capability and infrastructure needed to support the Network. To achieve this goal, the Bioinformatics Center provides investigators with tools, processes, and methods to facilitate long term sharing, maintenance, and management of HIRN developed resources, including datasets, technologies, documents, and bioreagents. Collaboration and communication are cultivated through consultation and outreach activities. In 2019, HIRN received funding to continue HIRN Coordinating Center (CC) and Bioinformatics Center (BC) as Human Islet Research Enhancement Center (HIREC).

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• dkNET
• 9 years ago - submitted by Ko-Wei Lin

One of several isotope labs in Department of Geology and Environmental Science formerly known as Regional Stable Isotope Lab for Earth and Environmental Science Research, has capacity for wide variety of isotopic measurements in multitude of sample media. Capabilities include: Nitrate (?15N, ?18O, D17O);Greenhouse and trace gases like carbon dioxide (?13C, ?18O), nitrous oxide (?15N, ?18O), methane (?13C); Nitrogen, carbon, and sulfur (?15N, ?13C, ?34S) in organic and other solid materials (e.g., biota, soils);Ammonium (?15N); Dry reactive nitrogen deposition (?15N-NH3, ?15-NO2, and ?15N-HNO3); and Carbonates (?13C, ?18O).

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

Database that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC).

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• SciCrunch
• 17 years ago - by Anonymous

Algorithm for co-registration of pairs and groups of neuron morphologies based on maximization of spatial overlap. The algorithm is written in Python and work with SWC files.

• RRID-Legacy
• 9 years ago - submitted by Ajayrama Kumaraswamy