Curator Dashboard

A Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Core which has adopted and incorporated a multidisciplinary, integrated approach that includes: genomics, analytical sciences, cellular sciences, and bioinformatics.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

Software R package implementation of Milo for testing for differential abundance in k-nearest neighbor graphs. Milo can identify perturbations that are obscured by discretizing cells into clusters. Used for differential abundance analysis on KNN graph from single-cell datasets.

• Resource
• RRID
• 2 years ago - submitted by Chrissy Weber-Schmidt

The Canadian Breast Cancer Foundation is the leading national volunteer-based organization in Canada dedicated to creating a future without breast cancer. Established in 1986 by a dedicated group of volunteers, the Foundation works collaboratively to fund, support and advocate for: * Relevant and innovative research, * Meaningful education and awareness programs, * Early diagnosis and effective treatment * A positive quality of life for those living with breast cancer. Our fundraising through our annual Canadian Breast Cancer Foundation CIBC Run for the Cure, special events, corporate sponsorship and donations has enabled the Foundation to allocate millions of dollars in grants for breast cancer projects and services since our inception. Addressing the needs of Canadians from coast to coast, the Canadian Breast Cancer Foundation has regional offices in British Columbia/Yukon Territory, Prairies/NWT, Ontario and the Atlantic Region. The Foundation''s central office is located in Toronto. Charitable Registration No. 12799 3608 RR0001

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Software tool as a framework for fitting and describing connectivity patterns between regions that is a simple extension from the current population receptive field models in the visual neuroscience literature. The connectivity from each voxel in a designated seed region to a mapping region is modeled as a 3-dimensional Gaussian, providing location parameters and spread parameters. This allows the direct description of the relative mapping from one region to another.

• Resource
• NIF
• 8 years ago - by Anonymous

Web tool to explore cluster TCRs that are predicted to bind the same MHC-restricted peptide antigen. When multiple donors have contributed to the clusters, and HLA genotypes for those donors are available, GLIPH additionally can provide predictions of which HLA-allele is presenting the antigen.

• Resource
• RRID
• 2 years ago - by Anonymous

A non-profit, community resource that works with volunteer donors to provide the highest quality blood and tissue components to patients. They collect and test more than 200,000 components of life-saving blood and tissue each year from volunteers all over South Texas. Because patients are in constant need of blood, blood components, and/or tissue, donors are essential. By using cutting-edge technology, the team of dedicated professionals have helped save hundreds of thousands of lives over more than 35 years. They are a member of the American Association of Blood Banks (AABB); American Association of Tissue Banks (AATB) and America''s Blood Centers (ABC). We are also one of the first blood centers in the country to be registered by the International Standards Organization.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Portal provides software library and python scripts for medical image processing. Open source set of software tools for medical image processing, medical image analysis, image registration, statistical analysis, quantitative MRI processing, image denoising and filtering, and segmentation developed by VISAGES/Empenn research team. Available as Github repository and compiled binaries for various OS including OSX, Fedora, Ubuntu, Windows.

• Resource
• RRID-Legacy
• 8 years ago - by Anonymous

Metapathways is an automated (meta)genomics annotation pipeline for predicting metabolic functions of given DNA sequences. It produces structured data products as pathway-genome databases with human-readable and machine-interpretable representations compatible with resources like PathwayTools and Metacyc from the Stanford Research Institute. A modular architecture, automated installation with Anaconda, and available containers on Quay.io maximize the accessibility, extensibility, and utility of Metapathways.

• Resource
• RRID
• 2 years ago - submitted by Tony Liu

The Center for Organ Recovery & Education (CORE) is one of 58 federally designated agencies in the United States known as a not-for-profit organ procurement organization (OPO). CORE is dedicated to promoting donation, education and research for the purpose of saving and improving the quality of life through organ, tissue and corneal transplantation. An innovative, responsive OPO, CORE plays a pivotal role between potential donors and patients awaiting transplantation. In addition to talking with families about the opportunity to donate, CORE coordinates the surgical recovery of organs, tissue and corneas, as well as the computerized matching of donated organs and placement of corneas. In 1995, CORE created the first donor card database in Pennsylvania. In 1996, the organization added tissue recovery and eye banking services to its organ recovery component. It enhanced its line of services by opening an internal laboratory in 1997, where CORE performs the necessary tests to help determine if the organs, tissue and corneas are healthy for transplantation. Since its inception more than 30 years ago, CORE has helped to provide more than 300,000 organs, tissue and corneas for transplantation. The chances for renewed health provided through CORE would not be possible without those who have said yes to donation.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Software R package for easily tidy data with spread and gather functions. Used for simplifying process of creating tidy data.

• Resource
• RRID-Legacy
• 8 years ago - by Anonymous

Offers access to microscopes and flow cytometry equipment for researchers. Available services include Upright and inverted widefield microscopy, Confocal Microscopy (Zeiss LSM 710), Super-Resolution Microscopy (Nikon SIMe), Live Cell Microscopy (Incucylte), Flow Cytometry (BD LSR Fortessa), Cell Sorting (BD Aria III).

• Resource
• SciCrunch
• 2 years ago - submitted by Edyta Vieth

Throughout the past 25 years, John Theurer Cancer Center at Hackensack University Medical Center has become one of the largest and most comprehensive cancer centers in the United States. Today, we are a top 50 U.S. News and World Report Best Hospitals for cancer the only cancer center in New Jersey with this prestigious designation. Its mission is to deliver extraordinary care that is multidisciplinary, personalized, innovative, and at the appropriate cost with superior outcomes to the most satisfied patients. Year after year, we have harnessed the newest technologies and retained world-class physicians, nurses and scientists to help service the needs of our patients within our 14 specialized cancer divisions.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Software tool to make artificial mate pairs from long sequences for scaffolding.

• Resource
• SciCrunch
• 8 years ago - submitted by Joseph Ryan

Joint effort by Harvard Medical School, Dana-Farber Cancer Institute, Boston Childrens Hospital, and Massachusetts General Hospital to provide cryo-EM instrumentation and expertise for Harvard structural biology community. Facility offers consultation and training by staff in specimen preparation, microscope operation, image acquisition, and data analysis.

• Resource
• SciCrunch
• 2 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. The Catalog of Fishes is the authoritative reference for taxonomic fish names, featuring a searchable on-line database. The Catalog of Fishes covers more than 53,000 species and subspecies, over 10,000 genera and subgenera, and includes in excess of 16,000 bibliographic references. The Catalog of Fishes consists of three hardbound volumes of 900-1000 pages each, along with a CD-ROM. The online database is updated about every 8 weeks and is now about twice the size of the published version. It is one of the oldest and most complete databases for any large animal group. References are over 30,000. Valid species are over 30,000. This work is an essential reference for taxonomists, scientific historians, and for any specialist dealing with fishes. Entries for species, for example, consist of species/subspecies name, genus, author, date, publication, pages, figures, type locality, location of type specimen(s), current status (with references), family/subfamily, and important publication, taxonomic, or nomenclatural notes. Nearly all original descriptions have been examined, and much effort has gone into determining the location of type specimens. The Genera are updated from Eschmeyer''s 1990 Genera of Recent Fishes. Both genera and species are listed in a classification using recent taxonomic schemes. Also included are a lengthy list of museum acronyms, an interpretation of the International Code of Zoological Nomenclature, and Opinions of the International Commission involving fishes.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Software R package for 3D visualisation and analysis of biological image data, especially tracings of single neurons.

• Resource
• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core provides services such as assistance in the development and successful completion of well-designed genetic studies, establishment and storage of EBV-transformed lymphoblastoid cell lines (LCLs), as well as PAXgene tubes, and specialized (e.g., the exome chip) single nucleotide polymorphism (SNP) testing, candidate gene sequencing, whole exome sequencing (WES), whole genome sequencing (WGS), and large-scale gene methylation analysis.

• Resource
• SciCrunch
• 10 years ago - submitted by Kristen Jensen

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches. It includes ''resource_type'', ''area of research'', and ''activity''. It is under development by a number of NIH-funded researchers who have a combined interest in classification of biomedical resources. The biositemaps site is no longer available but the biomedical resource ontology is still available via bioportal Biomedical Resource Ontology (BRO).

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Software package that evaluates correspondence between stated sexes, relationships, and ancestries in pedigree file and those inferred from genotypes in VCF file resulting from human whole genome sequencing or whole exome sequencing studies. Facilitates both automated and interactive, visual detection of sample swaps, poor sequencing quality, and other indicators of sample problems.

• Resource
• RRID-Legacy
• 7 years ago - by Anonymous