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Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.
Proper citation: Reactome (RRID:SCR_003485) Copy
Urinary kidney biomarkers (KIM-1, albumin, total protein, 2-microglobulin, cystatin C, clusterin and trefoil factor-3) that are considered acceptable biomarkers for the detection of acute drug-induced nephrotoxicity in rats and can be included along with traditional clinical chemistry markers and histopathology in toxicology studies. These biomarkers may be used voluntarily as additional evidence of nephrotoxicity in nonclinical safety assessment studies to complement the standard data (BUN and sCr). In ROC analyses, some of these biomarkers showed better sensitivity and specificity than BUN and sCr relative to histopathological alterations considered to be the gold standard when tested with a limited number of nephrotoxicant and control compounds.
Proper citation: PSTC Nephrotoxicity Biomarkers (RRID:SCR_003709) Copy
A research- and development-oriented company based in Berlin that engineers and markets technology for animal behavior research offering unique, automated instrumentation. This includes specialized applications of virtual reality and touch screen technology for animal behavior environments and RFID (transponder) operated devices in home cage environments. Their experimental systems are used for behavioral phenotyping, brain research, experimental psychology, and the diagnostic characterization of animal models for translational medicine.
Proper citation: PhenoSys (RRID:SCR_004072) Copy
http://openconnectomeproject.org/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or which neurons synapse onto this one. Create your own annotations or browse others. *Sample Downloads - In addition to being able to select arbitrary downloads from the datasets, they have also collected a few choice volumes of interest. * Volume Viewer - A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. The code and program can be downloaded. * Machine Vision Pipeline - They are building a machine vision pipeline that pulls volumes from the 3ddb and outputs neural circuits. - a work in progress. As soon as we have a stable version, it will be released. * Mr. Cap - The Magnetic Resonance Connectome Automated Pipeline (Mr. Cap) is built on JIST/MIPAV for high-throughput estimation of connectomes from diffusion and structural imaging data. * Graph Invariant Computation - Upload your graphs or streamlines, and download some invariants. * iPad App - WholeSlide is an iPad app that accesses utilizes our open data and API to serve images on the go.
Proper citation: Open Connectome Project (RRID:SCR_004232) Copy
Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development.
Proper citation: Stem Cell Commons (RRID:SCR_004415) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17,2023. A database of genes and interventions connected with aging phenotypes including those with respect to their effects on life-span or age-related neurological diseases. Information includes: organism, aging phenotype, allele type, strain, gene function, phenotypes, mutant, and homologs. If you know of published data (or your own unpublished data that you'd like to share) not currently in the database, please use the Submit a Gene/Intervention link.
Proper citation: Aging Genes and Interventions Database (RRID:SCR_002701) Copy
The Rodent Brain WorkBench is the portal to atlases, databases and tools developed by the Neural Systems and Graphics Computing Laboratory (NeSys) at the Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway. The Rodent Brain WorkBench presents a collection of brain mapping and atlasing oriented database applications and tools. The main category of available data is high resolution mosaic images covering complete histological sections through the rat and mouse brain. A highly structured relational database system for archiving, retrieving, viewing, and analysing microscopy and imaging data, aiming at presentation in standardized brain atlas space, is used to present a series of web applications for individual research projects. * Brain Connectivity * Atlases of Mouse Brain Promoter Gene Expression * General Brain Atlas and Navigation Systems * Downloadable tools for 3-DVisualization Open Access: * Atlas 3D * Cerebro-Cerebellar I * Cerebro-Cerebellar II * Neurotransporter Atlas * Rat Hippocampus * Tet-Off Atlas I (PrP) * Tet-Off Atlas II (PrP/CamKII) * Whole Brain Connectivity Atlas The data presented have been produced in collaboration with a large number of laboratories in Europe and the United States.
Proper citation: Rodent Brain WorkBench (RRID:SCR_002727) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures
Proper citation: SumsDB (RRID:SCR_002759) Copy
Database of known and predicted mammalian and eukaryotic protein-protein interactions, it is designed to be both a resource for the laboratory scientist to explore known and predicted protein-protein interactions, and to facilitate bioinformatics initiatives exploring protein interaction networks. It has been built by mapping high-throughput (HTP) data between species. Thus, until experimentally verified, these interactions should be considered predictions. It remains one of the most comprehensive sources of known and predicted eukaryotic PPI. It contains 490,600 Source Interactions, 370,002 Predicted Interactions, for a total of 846,116 interactions, and continues to expand as new protein-protein interaction data becomes available.
Proper citation: I2D (RRID:SCR_002957) Copy
Portal for preclinical information and research materials, including web-accessible data and tools, NCI-60 Tumor Cell Line Screen, compounds in vials and plates, tumor cells, animals, and bulk drugs for investigational new drug (IND)-directed studies. DTP has been involved in the discovery or development of more than 70 percent of the anticancer therapeutics on the market today, and will continue helping the academic and private sectors to overcome various therapeutic development barriers, particularly through supporting high-risk projects and therapeutic development for rare cancers. Initially DTP made its drug discovery and development services and the results from the human tumor cell line assay publicly accessible to researchers worldwide. At first, the site offered in vitro human cell line data for a few thousand compounds and in vitro anti-HIV screening data for roughly 42,000 compounds. Today, visitors can find: * Downloadable in vitro human tumor cell line data for some 43,500 compounds and 15,000 natural product extracts * Results for 60,000 compounds evaluated in the yeast assay * In vivo animal model results for 30,000 compounds * 2-D and 3-D chemical structures for more than 200,000 compounds * Molecular target data, including characterizations for at least 1,200 targets, plus data from multiple cDNA microarray projects In addition to browsing DTP's databases and downloading data, researchers can request individual samples or sets of compounds on 96-well plates for research, or they can submit their own compounds for consideration for screening via DTP's online submission form. Once a compound is submitted for screening, researchers can follow its progress and retrieve data using a secure web interface. The NCI has collected information on almost half a million chemical structures in the past 50 years. DTP has made this information accessible and useful for investigators through its 3-D database, a collection of three-dimensional structures for more than 200,000 drugs. Investigators use the 3-D database to screen compounds for anticancer therapeutic activity. Also available on DTP's website are 127,000 connection tables for anticancer agents. A connection table is a convenient way of depicting molecular structures without relying on drawn chemical structures. As unique lists of atoms and their connections, the connection tables can be indexed and stored in computer databases where they can be used for patent searches, toxicology studies, and precursor searching, for example., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Developmental Therapeutics Program (RRID:SCR_003057) Copy
http://braininfo.rprc.washington.edu
Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures.
Proper citation: BrainInfo (RRID:SCR_003142) Copy
An information extracting and processing package for biological literature that can be used online or installed locally via a downloadable software package, http://www.textpresso.org/downloads.html Textpresso's two major elements are (1) access to full text, so that entire articles can be searched, and (2) introduction of categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., methods, etc). A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. The Textpresso project serves the biological and biomedical research community by providing: * Full text literature searches of model organism research and subject-specific articles at individual sites. Major elements of these search engines are (1) access to full text, so that the entire content of articles can be searched, and (2) search capabilities using categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or identify one (e.g., cell, gene, allele, etc). The search engines are flexible, enabling users to query the entire literature using keywords, one or more categories or a combination of keywords and categories. * Text classification and mining of biomedical literature for database curation. They help database curators to identify and extract biological entities and facts from the full text of research articles. Examples of entity identification and extraction include new allele and gene names and human disease gene orthologs; examples of fact identification and extraction include sentence retrieval for curating gene-gene regulation, Gene Ontology (GO) cellular components and GO molecular function annotations. In addition they classify papers according to curation needs. They employ a variety of methods such as hidden Markov models, support vector machines, conditional random fields and pattern matches. Our collaborators include WormBase, FlyBase, SGD, TAIR, dictyBase and the Neuroscience Information Framework. They are looking forward to collaborating with more model organism databases and projects. * Linking biological entities in PDF and online journal articles to online databases. They have established a journal article mark-up pipeline that links select content of Genetics journal articles to model organism databases such as WormBase and SGD. The entity markup pipeline links over nine classes of objects including genes, proteins, alleles, phenotypes, and anatomical terms to the appropriate page at each database. The first article published with online and PDF-embedded hyperlinks to WormBase appeared in the September 2009 issue of Genetics. As of January 2011, we have processed around 70 articles, to be continued indefinitely. Extension of this pipeline to other journals and model organism databases is planned. Textpresso is useful as a search engine for researchers as well as a curation tool. It was developed as a part of WormBase and is used extensively by C. elegans curators. Textpresso has currently been implemented for 24 different literatures, among them Neuroscience, and can readily be extended to other corpora of text.
Proper citation: Textpresso (RRID:SCR_008737) Copy
http://rgd.mcw.edu/rgdCuration/?module=portal&func=show&name=renal
An integrated resource for information on genes, QTLs and strains associated with a variety of kidney and renal system conditions such as Renal Hypertension, Polycystic Kidney Disease and Renal Insufficiency, as well as Kidney Neoplasms.
Proper citation: Renal Disease Portal (RRID:SCR_009030) Copy
https://i4sa.com/wp-content/uploads/2021/01/1025ManualRevJ.pdf
Magnetic resonance compatible monitoring and gating system, including software, that enables monitoring rectal temperature, electrocardiogram and respiration rate during magnetic resonance imaging scan time. The PC displays multiple waveforms, measured values, trends and gating pulses. The data Acquisition modules are controlled by menu driven software from the PC. Data acquisition modules are available to measure the following parameters: ECG, respiration (three ways), temperature (two ways), pressure including invasive blood pressure (two ways), oxygen saturation and end-tidal CO2.
Proper citation: SA Instruments: Model 1025 MR-compatible Small Animal Monitoring and Gating System (RRID:SCR_002090) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2017. Database of images depicting the spatial distribution of 2-deoxyglucose uptake evoked in the glomerular layer of the rat olfactory bulb in response to a wide range of defined odorant stimuli. A number of different display and comparison tools are provided allowing patterns to be viewed from different perspectives, and descriptions of the methods and interpretations of these data are provided. Some of the more advanced tools require you to download software.
Proper citation: Glomerular Activity Response Archive (RRID:SCR_002089) Copy
Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data.
Proper citation: GeneNetwork (RRID:SCR_002388) Copy
http://www.nitrc.org/projects/miva/
Software package that is a powerful graphical interface that displays, segments, aligns, manipulates, and blends image (pixel) and geometry (real-world coordinates) data simultaneously. Several applications are directly built into MIVA. Registration modes include interactive affine transformations. Fiducial registration tools facilitate rapid alignments for inter-modality volumes. Interactive Region of Interst (ROI) and Volume-of-Interest (VOI) tools exist to segment medical images. Virtually unique to MIVA are its 3D geometry tools and their compatibility with pixel based medical images. A full 3D interactive rat brain atlas is in an fMRI module which walks one through the necessary steps of fMRI. A multiple material surface routine takes segmented medical slices and creates 3D triangulated surfaces that align along all region boarders without overlap or gaps. These surfaces are the direct input into the MIVA tetrahedral mesh generator.
Proper citation: Medical Image Visualization and Analysis (RRID:SCR_002315) Copy
http://olympus.magnet.fsu.edu/galleries/ratbrain/index.html
An image gallery of the rat brain labeled via immunofluorescence in coronal, horizontal, and sagittal thick sections using laser scanning confocal microscopy.
Proper citation: Confocal Microscopy Image Gallery - Rat Brain Tissue Sections (RRID:SCR_002432) Copy
https://github.com/mjacquem/RodentThickness
An automatic cortical thickness measurement tool for rat brains. The pipeline consists of four steps: preprocessing to create binary mask and label map, thickness measurement which produces laplacian field and thickness map in order, run particle correspondence followed by statistical analysis resulting in mean thickness color map and t-test result. By running RodentThickness, you will need to fill in informations in a Graphical User Interface, and then compute. You can also run the tool in command line without using the GUI. Using the GUI, you will be able to save or load a dataset file or a configuration file. The tool needs these other tools to work, so be sure to have these installed on your computer: * ImageMath * measureThicknessFilter * GenParaMeshCLP * ParaToSPHARMMeshCLP * ShapeWorksRun * ShapeWorksGroom * SegPostProcessCLP * BinaryToDistanceMap * MeshPointsIntensitysampling
Proper citation: Rodent Cortical Thickness Analysis (RRID:SCR_002539) Copy
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