Curator Dashboard

Core is involved in procurement and processing of human tissue and other biospecimens for basic, translational, and clinical research.Provides laboratory support services for clinical trials, tissue samples from remnant surgical resection and autopsy specimens linked to clinicopathologic data while maintaining patient confidentiality. Provides biorepository of human specimens.Offers advanced histology services including multi color immunohistochemistry, in situ hybridization, tissue microarrays, slide scanning, computerized image analysis, NanoString spatial profiling.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core specializes in oral microbial genomics, taxonomy, phylogenetics and the next generation sequence (NGS) data analysis with both in house and cloud high performance computational resource. In addition to supporting funded bioinformatics projects, Bioinformatics Core will also provide computational support to Forsyth and other researchers for processing, analyzing, and interpreting biological data.

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• SciCrunch
• 13 years ago - by Anonymous

Software R package for analysis of paths from spatial tracking experiments such as Morris water maze and calculation of goal finding strategies. Used for in depth analysis of tracking coordinates from video.

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• RRID
• 4 years ago - submitted by Samantha White

The Forsyth Center for Clinical and Translational Research (CCTR) is a unique clinical facility with 6 fully-equipped dental units and associated laboratories that are specifically dedicated to conduct clinical research in oral and related systemic diseases. Clinical trials following FDA guidelines are performed at all levels, from early phase 1 trials to large, multicenter definitive clinical trials, with the goal of improving outcomes and the long-term health of patients. We routinely conduct studies in the oral environment, that include standard clinical measurement protocols for dental caries, dental calculus, gingivitis, periodontal diseases, intraoral local anesthetic evaluation, tooth restoration and tooth whitening evaluation. In addition, the clinic is equipped for obtaining and processing microbiological samples, gingival crevice fluid samples, blood and saliva samples for analysis of bacteria, inflammatory mediators, as well as for genomic and proteomic analyses. Under the new leadership of Dr. Thomas Van Dyke, Vice President of Clinical Research at The Forsyth Institute, the Center proposes new goals/efforts in discovering new techniques, testing new ideas and searching for valuable biomarkers for preventing and treating periodontal diseases and associated systemic inflammatory conditions. The CCTR is actively involved with the design and conduct of clinical research under Good Clinical Practices for submission to regulatory agencies. It has a published international reputation in evaluating intraoral local drug delivery devices, oral diagnostic systems, local anesthesia, restorative materials, tooth whitening systems and the association of oral diseases with systemic conditions. Forsyth''s Institutional Review Board is a member of the Harvard Catalyst Regulatory Group and meets on a monthly basis providing complete review of clinical protocols.

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• SciCrunch
• 13 years ago - by Anonymous

Center that imports, archives, maintains, and distributes mutant mouse alleles as live mice, frozen germplasm, stem cells, and molecular vectors for use in biomedical research. The MMRRC Davis receives transgenics, knockouts, and other kinds of mutant mouse lines at no cost to the donor, and after re-derivation and cryopreservation, distributes breeding stock, germplasm, cells, or tissues of genetically-defined and pathogen-free mice for a small fee to requesting investigators.

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• SciCrunch
• 8 years ago - submitted by Isabella Froman

Core facility that provides the following services: Magnetic Resonance Spectroscopy Service, Magnetic Resonance Imaging Service.

The Musculoskeletal Imaging Research Core (MIRC) offers specialized imaging techniques including quantitative computed tomography (QCT), magnetic resonance (MR) spectroscopy of muscle and high-resolution soft tissue MR imaging. QCT is a technique widely employed for studies evaluating body composition and bone mineral density. MR spectroscopy is a technique that allows non-invasive quantification of metabolites in human tissues.

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• SciCrunch
• 13 years ago - by Anonymous

Gastric cancer gene mutation data sample and clinical information data set.

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• RRID
• 4 years ago - submitted by Zhenzhang Li

A list of Wordpress plugins that are useful for authoring scientific papers. Listed plugins include BibTeX Importer, Link to Link, Broken Link Checker, and Contact Info Options, among many others.

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• SciCrunch
• 14 years ago - by Anonymous

Software R package for post alignment quality assessment of ATAC-seq data. Package also contains functions to preprocess aligned ATAC-seq data for subsequent peak calling.

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• RRID
• 4 years ago - submitted by Anita Bandrowski

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2012. (no longer being funded) The NIH Microarray Consortium provides for-fee services to a community of NIH grantees, together with a more limited set of services to the public. The primary goal of this consortium is to move basic and translational research forward through acquisition and dissemination of high quality genomic data. This site includes a repository of microarray data sets and offers one-click links to public projects. These datasets were generated by various researchers on these platforms: Affymetrix, Agilent, Ambion, cDNA, Illumina, and Operon. The species currently covered are: Arabidopsis, Bovine, chicken, C. Elegans, Drosophila, Human, Macaca mulatta (Rhesus macaque), Mouse, Rat, Songbird, Xenopus, Yeast, and zebra finch. Basic search functions allows users to choose multiple options for finding the projects that interest them, and raw data files can also be downloaded after user registration. Web-based data analysis tools are also available. Scientists can analyze microarray data from the consortium repository or investigators can upload outside data for analysis.

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• SciCrunch
• 17 years ago - by Anonymous

ChemBank is a public, web-based informatics environment that includes freely available data derived from small molecules and small-molecule screens, and resources for studying the data so that biological and medical insights can be gained. ChemBank is intended to guide chemists synthesizing novel compounds or libraries, to assist biologists searching for small molecules that perturb specific biological pathways, and to catalyze the process by which drug hunters discover new and effective medicines. ChemBank stores an increasingly varied set of cell measurements derived from, among other biological objects, cell lines treated with small molecules. Analysis tools are available and are being developed that allow the relationships between cell states, cell measurements and small molecules to be determined. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the ICG in collaborations involving biomedical researchers worldwide. These scientists have agreed to perform their experiments in an open data-sharing environment. The goals of ChemBank are to provide life scientists unfettered access to biomedically relevant data and tools heretofore available almost exclusively in the private sector. We intend for ChemBank to be a planning and discovery tool for chemists, biologists, and drug hunters anywhere, with the only necessities being a computer, access to the Internet, and a desire to extract knowledge from public experiments whose greatest value is likely to reside in their collective sum.

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• SciCrunch
• 17 years ago - by Anonymous

GD library is an open source code library for the dynamic creation of images by programmers. GD is written in C, and wrappers are available for Perl, PHP and other languages. GD creates PNG, JPEG and GIF images, among other formats. GD is commonly used to generate charts, graphics, thumbnails, and most anything else, on the fly. While not restricted to use on the web, the most common applications of GD involve website development. gd is a graphics library. It allows your code to quickly draw images complete with lines, arcs, text, multiple colors, cut and paste from other images, and flood fills, and write out the result as a PNG or JPEG file. This is particularly useful in World Wide Web applications, where PNG and JPEG are two of the formats accepted for inline images by most browsers. gd is not a paint program. If you are looking for a paint program, you are looking in the wrong place. If you are not a programmer, you are looking in the wrong place, unless you are installing a required library in order to run an application. gd does not provide for every possible desirable graphics operation. It is not necessary or desirable for gd to become a kitchen-sink graphics package, but version 2.0 does include most frequently requested features, including both truecolor and palette images, resampling (smooth resizing of truecolor images) and so forth. What if I want to use another programming language? Not all of these tools are necessarily up to date and fully compatible with 2.0.33. PHP A variant of gd 2.x is included in PHP 4.3.0. It is also possible to patch PHP 4.2.3 for use with gd 2.0.33; see the gd home page for a link to that information. It would be a Good Idea to merge all of the things that are better in mainstream gd and all of the things that are better in PHP gd at some point in the near future. Perl gd can also be used from Perl, courtesy of Lincoln Stein''s GD.pm library, which uses gd as the basis for a set of Perl 5.x classes. Highly recommended. OCaml gd can be used from OCaml, thanks to Matt Gushee''s GD4O project. Tcl gd can be used from Tcl with John Ellson''s Gdtclft dynamically loaded extension package. Pascal Pascal enthusiasts should look into the freepascal project, a free Pascal compiler that includes gd support. REXX A gd interface for the REXX language is available. Any Language The fly interpreter performs gd operations specified in a text file. You can output the desired commands to a simple text file from whatever scripting language you prefer to use, then invoke the interpreter.

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• SciCrunch
• 17 years ago - by Anonymous

Repository of metadata and data that describes and provides access to diverse data sets generated by Arctic and Antarctic researchers. The metadata records follow ISO 19115 and Federal Geographic Data Committee (FGDC) standard formats to provide exchange with other data centres. The records cover a wide range of disciplines from natural sciences and policy, to health and social sciences. The PDC Geospatial Search tool is available to the public and researchers alike and allows searching data using a mapping interface and other parameters.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Randomized controlled clinical trial to understand how increasing hemodialysis to six times a week from the standard of three times a week may result in improved heart health. Subjects were recruited from dialysis units associated with designated Clinical Centers in the U.S. and Canada and followed for 1 year. Subjects will be randomized to either conventional hemodialyis Daily HD delivered for at least 2.5 hours (typically 3 to 4 hours), 3 days per week, or to more frequent hemodialysis delivered for 1.5 - 2.75 hours, 6 days per week. The study has two co-primary outcomes: 1) a composite of mortality with the change over 12 months in left ventricular mass by magnetic resonance imaging, and 2) a composite of mortality with the change over 12 months in the SF-36 RAND physical health composite (PHC) quality of life scale. In addition, main secondary outcomes have been designated for each of seven outcome domains: 1) cardiovascular structure and function (change in LV mass), 2) health-related quality of life/physical function (change in the PHC), 3) depression/burden of illness (change in Beck Depression Inventory), 4) nutrition (change in serum albumin), 5) cognitive function (change in the Trail Making Test B), 6) mineral metabolism (change in average predialysis serum phosphorus), and 7) clinical events (rate of non-access hospitalization or death). Hypertension and anemia are also main outcome domains, but without designation of single first priority outcomes.

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• dkNET
• 14 years ago - by Anonymous

Electron Microscopy Resource supports ultra-structural interrogation of tissues, biologic solutions and nanomaterials for investigators utilizing transmission electron microscopy (TEM), scanning electron microscopy (SEM) and cryo-TEM.

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• SciCrunch
• 14 years ago - by Anonymous

Software tools for read pair collation based algorithms on BAM files including * bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name * bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field * bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column * bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading. * bamsort: reads BAM and writes BAM resorted by coordinates or query name * bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name

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• SciCrunch
• 12 years ago - by Anonymous

NIH HIV Reagent Program has been managed under contract by American Type Culture Collection (ATCC) since 2020. ATCC shall maintain the NIH HIV Reagent Program through identification, acquisition, production, receipt, storage, maintenance, distribution and disposal of biological and chemical research organisms and materials for HIV and other infectious diseases for use in basic and translational research.

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• RRID
• 4 years ago - submitted by Edyta Vieth

A sequence aligner software program that is 10-100x faster and simultaneously more accurate than existing tools like BWA, Bowtie2 and SOAP2. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools. This gives SNAP up to 2x lower error rates than existing tools and lets it match larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting, duplicate marking, and BAM indexing.

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• SciCrunch
• 13 years ago - by Anonymous

Provides germ free and gnotobiotic mice, space in which investigators can complete their own studies or hire core to complete experimental manipulations.Facility includes 12 large soft sided vinyl isolators for breeding and 8 small soft sided vinyl isolators for experiments. There is option between using Allentown positive pressure racks and static cage for experimental use.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

The Primary Immunodeficiency Disease Ontology Project is developing an ontology for the phenotypic description of Primary Immunodeficiency Diseases. The ontology can be used for integrative research in both biomedical and clinical research. Primary Immunodeficiency Diseases (PIDs) are Mendelian diseases, caused by defects or deletions of genes involved in the development, regulation and maintenance of the immune system. They usually affect newborns and toddlers, but can also manifest much later in life. Information about PIDs is often widely scattered across the research literature and a number of databases. PIDO is an attempt to develop both a machine- as well as a human-comprehensible representation of these diseases, starting with a phenotypic descriptions of disease.

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• SciCrunch
• 15 years ago - by Anonymous