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on page 1 showing 20 out of 45 results from 1 sources

Cite this (AnimalTFDB, RRID:SCR_001624)

URL: http://www.bioguo.org/AnimalTFDB/

Resource Type: Resource, data or information resource, database

A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading.

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Cite this (Bpod, RRID:SCR_015943)

URL: https://github.com/sanworks

Resource Type: Resource, software resource

Software for a measurement and control system for behavior research, most often used to implement operant (Go/NoGo, 2AFC) tasks. This software controls a hierarchy of hardware modules, each powered by an Arduino-programmable microcontroller.

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Cite this (BrainMaps.org, RRID:SCR_006878)

URL: http://brainmaps.org

Resource Type: Resource, service resource, storage service resource, atlas, image repository, data repository, data or information resource

An interactive multiresolution brain atlas that is based on over 20 million megapixels of sub-micron resolution, annotated, scanned images of serial sections of both primate and non-primate brains and integrated with a high-speed database for querying and retrieving data about brain structure and function. Currently featured are complete brain atlas datasets for various species, including Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, Tyto alba and many other vertebrates. BrainMaps is currently accepting histochemical, immunocytochemical, and tracer connectivity data, preferably whole-brain. In addition, they are interested in EM, MRI, and DTI data.

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Cite this (Computerized Anatomical Reconstruction and Editing Toolkit, RRID:SCR_006260)

URL: http://brainvis.wustl.edu/wiki/index.php/Caret:About

Resource Type: Resource, software resource, software application, image processing software, data visualization software, data processing software

A free, open-source, software package used to visualize and analyze the structural and functional characteristics of cerebral and cerebellar cortex in humans, nonhuman primates, and rodents. It runs on Apple (Mac OSX), Linux, and Microsoft Windows operating systems. The software includes two main programs, caret5 and caret_command. caret5 is a graphical user interface (GUI) for interactively manipulating and viewing neuroimaging data. caret_command is a command line program that allows batch processing of neuroimaging data. Caret 5.61 Functionality * Atlases and associated experimental data (see (Caret:Atlases Atlases)). * Capture images and create movies of surface, volume, and contour (border) data. * Caret-command script builder and executor for algorithm testing and batch processing. * Classify regions of a surface using border and paint operations. * Connect and transfer data to and from the (Sums:About SuMS database). * Flexible overlay system for displaying a variety of data in layers on surfaces or volumes. * Map neuroimaging activation foci (stereotaxic coordinates) to surfaces and volumes. * Map functional and other volume data to surfaces. * Map surface-based data (e.g., cortical areas) onto volumes. * Metadata handling that can encode processing steps, vocabularies, citations. * Multiple windows for simultaneous display of contours, surfaces, and volumes. * Read and write many file formats (Analyze, AFNI, Caret, FreeSurfer, GIfTI, NIfTI, and many others). * Surface-based statistics (based on sulcal depth and other shape characteristics). * Surface inflation and flattening. * Surface reconstruction via segmentation of anatomical volume data (SureFit method). * Surface reconstruction from contours. * Surface region of interest operations. * Visualization of contour, surface, and volumetric data. WebCaret allows Caret-like online visualization of data sets in the Sums DB database without downloading software or data.

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Cite this ( CURE - Digestive Diseases Research Center Animal Models Core , RRID:SCR_015217)

URL: http://www.cure.med.ucla.edu/cores/animal-models

Resource Type: Resource, service resource, resource, core facility, access service resource

Core that provides in vivo characterization of normal and pathophysiological mechanisms of hormonal and neural regulation of gastrointestinal (GI) function and brain-gut interactions in rodents to members and associate members of the CURE: DDRCC.

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Cite this ( DGAP , RRID:SCR_003036)

URL: http://www.diabetesgenome.org

Resource Type: Resource, narrative resource, data or information resource, resource, experimental protocol, database

Produce resources to unravel the interface between insulin action, insulin resistance and the genetics of type 2 diabetes including an annotated public database, standardized protocols for gene expression and proteomic analysis, and ultimately diabetes-specific and insulin action-specific DNA chips for investigators in the field. The project aims to identify the sets of the genes involved in insulin action and the predisposition to type 2 diabetes, as well as the secondary changes in gene expression that occur in response to the metabolic abnormalities present in diabetes. There are five major and one pilot project involving human and rodent tissues that are designed to: * Create a database of the genes expressed in insulin-responsive tissues, as well as accessible tissues, that are regulated by insulin, insulin resistance and diabetes. * Assess levels and patterns of gene expression in each tissue before and after insulin stimulation in normal and genetically-modified rodents; normal, insulin resistant and diabetic humans, and in cultured and freshly isolated cell models. * Correlate the level and patterns of expression at the mRNA and/or protein level with the genetic and metabolic phenotype of the animal or cell. * Generate genomic sequence from a panel of humans with type 2 diabetes focusing on the genes most highly regulated by insulin and diabetes to determine the range of sequence and expression variation in these genes and the proteins they encode, which might affect the risk of diabetes or insulin resistance. The DGAP project will define: * the normal anatomy of gene expression, i.e. basal levels of expression and response to insulin. * the morbid anatomy of gene expression, i.e., the impact of diabetes on expression patterns and the insulin response. * the extent to which genetic variability might contribute to the alterations in expression or to diabetes itself.

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Cite this ( Einstein-Mount Sinai Diabetes Research Center Animal Physiology Core , RRID:SCR_015076)

URL: http://www.einstein.yu.edu/centers/diabetes-research/diabetes.aspx?id=1286&ekmensel=15074e5e_4046_4048_28715_1

Resource Type: Resource, service resource, resource, core facility, access service resource

Core which assists with the in vivo assessment of glucose and fatty acid metabolism, insulin sensitivity and energy homeostasis in mice and rats. It provides tools to understand the behavior and physiology mediating the relationships among diabetes, nutrient sensing, obesity and diabetic cardiovascular complications in rodents.

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Cite this ( Einstein-Mount Sinai Diabetes Research Center Human Islet and Adenovirus Core , RRID:SCR_015066)

URL: http://www.einstein.yu.edu/centers/diabetes-research/human-Islet-and-adenovirus-core/

Resource Type: Resource, service resource, resource, core facility, access service resource

Core which provides methodologies, technology and infrastructure to support investigators in the use of human islets for research studies for the Einstein-Mount Sinai Diabetes Research Center. It isolates and prepares human and rodent islets/beta cells and cell lines for investigator-initiated research and generates specific viral vectors (adenovirus and lentivirus) for gene delivery of cDNAs and shRNAs of interest to beta cells and other islet cell types.

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Cite this (Emory University Rodent Behavioral Core, RRID:SCR_012499)

URL: http://www.scienceexchange.com/facilities/rodent-behavioral-core-emory

Resource Type: Resource, service resource, core facility, access service resource

Provides planning, execution, and analysis of behavioral experiments examining activity, arousal, coordinated movement, learning and memory, anxiety, depression, seizure susceptibility, reward/reinforcement, and aggression in mice and rats. Additional tests can potentially be developed on a case-by-case basis. The Behavioral Core also offers several rodent surgical services and assistance in IACUC protocol preparation.

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Cite this (Ensembl, RRID:SCR_002344)

URL: http://www.ensembl.org/

Resource Type: Resource, catalog, data or information resource, database

A collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. The goal of Ensembl is to automatically annotate the genome, integrate this annotation with other available biological data and make the data publicly available via the web. The range of available data has also expanded to include comparative genomics, variation and regulatory data. Ensembl allows users to: upload and analyze data and save it to an Ensembl account; search for a DNA or protein sequence using BLAST or BLAT; fetch desired data from the public database, using the Perl API; download the databases via FTP in FASTA, MySQL and other formats; and mine Ensembl with BioMart and export sequences or tables in text, HTML, or Excel format. The DNA sequences and assemblies used in the Ensembl genebuild are provided by various projects around the world. Ensembl has entered into an agreement with UCSC and NCBI with regard to sequence identifiers in order to improve consistency between the data provided by different genome browsers. The site also links to the Ensembl blog with updates on new species and sequences as they are added to the database.

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Cite this (Feeding Experimentation Device, RRID:SCR_015942)

URL: https://github.com/KravitzLab/fed/wiki

Resource Type: Resource, software resource

Software for a home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers a alternative to commercial feeders, with the convenience of use in tradition colony rack caging.

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Cite this ( George M. O'Brien Kidney Research Core Center - UT Southwestern Medical Center Cell Biology and Imaging Core , RRID:SCR_015297)

URL: http://www.utsouthwestern.edu/research/core-facilities/obrien-kidney/core-services/cell-biology-imaging-core.html

Resource Type: Resource, service resource, resource, core facility, access service resource

Core that provides services such as imaging of rodent kidney and heart including functional MRI, processing of tissues for routine paraffin embedding, and single tubule isolation and immunocytochemistry.

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Cite this (GOblet, RRID:SCR_006998)

URL: http://goblet.molgen.mpg.de/cgi-bin/goblet2008/goblet.cgi

Resource Type: Resource, data analysis service, production service resource, analysis service resource, software application, service resource, software resource

Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms.

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Cite this (Hippocampome.org, RRID:SCR_009023)

URL: http://hippocampome.org

Resource Type: Resource, data or information resource, database

A curated knowledge base of the circuitry of the hippocampus of normal adult, or adolescent, rodents at the mesoscopic level of neuronal types. Knowledge concerning dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex is distilled from published evidence and is continuously updated as new information becomes available. Each reported neuronal property is documented with a pointer to, and excerpt from, relevant published evidence, such as citation quotes or illustrations. Please note: This is an alpha-testing site. The content is still being vetted for accuracy and has not yet undergone peer-review. As such, it may contain inaccuracies and should not (yet) be trusted as a scholarly resource. The content does not yet appear uniformly across all combinations of browsers and screen resolutions.

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Cite this (Image & Data Archive, RRID:SCR_007283)

URL: https://ida.loni.usc.edu/login.jsp

Resource Type: Resource, data analysis service, database, analysis service resource, production service resource, image collection, service resource, storage service resource, data repository, data or information resource

Environment for archiving, searching, sharing, tracking and disseminating neuroimaging and related clinical data. It accommodates MRI, PET, MRA, DTI and other imaging modalities for human, rodent and primate data. The IDA is utilized for dozens of neuroimaging research projects across North America and Europe and accommodates MRI, PET, MRA, DTI and other imaging modalities. A flexible data de-identification engine and encrypted file transmission help ensure compliance with patient-privacy regulations. All data are stored on redundant servers with daily and weekly on- and off-site backups. Archiving data in the IDA is simple, secure and requires no specialized hardware, software or personnel. All that is required is a computer with internet access and web browser software. The IDA automatically extracts relevant metadata from the de-identified image files allowing data to be searched within moments of archival. Once archived, data may be downloaded and/or streamed into the LONI Pipeline processing environment. Integration of the LONI Debabeler file format translation engine allows users to download image data in a number of file formats in addition to the original file format.

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Cite this ( Indiana Diabetes Research Center Islet and Physiology Core , RRID:SCR_015081)

URL: http://cdmd.indiana.edu/research-core/the-islet-core/

Resource Type: Resource, service resource, resource, core facility, access service resource

Core that provides services for islet transplantation and will assist investigators who wish to perform immunohistochemistry, immunofluorescence, and/or analysis of beta cell mass on whole pancreata from mouse and rat models. It also offers services for rodent metabolic characterization, including performance of insulin and glucose tolerance testing, analysis of body composition and metabolic cage analysis using the TSE System cages.

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Cite this ( Indiana O'Brien Center for Advanced Microscopic Analysis Probe Delivery Core , RRID:SCR_015274)

URL: http://medicine.iupui.edu/neph/obrien/probe

Resource Type: Resource, service resource, resource, core facility, access service resource

Core facility which develops and characterizes methods for expressing fluorescent biosensors in the rodent kidney to be paried with intravital microscopy.

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Cite this ( Indiana University Cooperative Center of Excellence in Hematology Optical Microscopy Core , RRID:SCR_015347)

URL: http://medicine.iupui.edu/ICBM

Resource Type: Resource, service resource, resource, core facility, access service resource

Core facility which provides access to and training on optical microscopy instruments to Indiana University researchers.

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Cite this (JIP Analysis Toolkit, RRID:SCR_009588)

URL: http://www.nmr.mgh.harvard.edu/~jbm/jip/

Resource Type: Resource, software resource, image analysis software, software toolkit, data processing software, software application

Software toolkit for analysis of rodent and non-human primate fMRI data. The toolkit consists of binary executables, highly portable open-source c code, and image resources that enable 1) Automated registration based upon mutual information (affine, non-linear warps), with flexible control and visualization of each step; 2) visualization of 4-dimensional data using either mosaic or tri-planar display of the z/slice dimension, and integration of a general linear model for graphical display of time series analysis; 3) A simple and flexible 1st-order GLM for fMRI time series analysis, a 1st-order GLM analysis for PET data within the SRTM framework, plus a 2nd-order GLM analysis following the Worsley 2002 scheme, and 4) MRI templates to place your rodent and non-human primate data into standardized spaces.

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Cite this ( Joslin Diabetes Center Animal Physiology Core , RRID:SCR_009876)

URL: https://joslinresearch.org/drc-cores/Animal-Physiology-Core

Resource Type: Resource, service resource, resource, core facility, access service resource

Core that provides technically advanced physiological evaluation of metabolism in diabetes, obesity, and their associated complications in rodents for DRC investigators and outside users. It also provides training of investigators and trainees in several physiological procedures.

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