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http://www.mmpc.org

Center mission is to advance medical and biological research by providing the scientific community with standardized, high quality metabolic and physiologic phenotyping services for mouse models of diabetes, diabetic complications, obesity and related disorders.

Proper citation: National Mouse Metabolic Phenotyping Centers (RRID:SCR_008997) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://ageing-map.org/

Database of age-related changes covering different biological levels, including molecular, physiological, psychological and pathological age-related data, to create an interactive portal that serves as a centralized collection of human aging changes and pathologies. To facilitate integrative, system-level studies of aging, the DAA provides a centralized source for aging-related data as well as basic tools to query and visualize the data, including anatomical models. Data in the DAA is manually curated from the literature and retrieved from public databases. For more detailed analyses users are able to download the entire database. More information on how to use the DAA is available on the help page. The DAA primarily focuses on human aging, but also includes supplementary mouse data, in particular gene expression data, to enhance and expand the information on human aging. If you would like to contribute to the database yourself, for instance if you have new data on aging, please use the contribute page to submit your data.

Proper citation: Digital Ageing Atlas (RRID:SCR_009020) Copy   

•   Source: SciCrunch Registry

http://opossum.cisreg.ca

A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences.

Proper citation: oPOSSUM (RRID:SCR_010884) Copy   

•   Source: SciCrunch Registry

http://annmap.picr.man.ac.uk/

A genome browser that includes mappings between genomic features and Affymetrix microarrays. Associated with annmap is: * a Bioconductor package, annmap that provides programmatic access to the underlying MySQL database tables (which are freely available for download on this site) * xmapbridge, a Bioconductor package that outputs numeric data in a form suitable for presentation in the browser. This is supported by XMapBridge, a Java client that sits on the local desktop and performs the graph rendering for the browser.

Proper citation: Annmap (RRID:SCR_011783) Copy   

•   Source: SciCrunch Registry

http://mitobreak.portugene.com/cgi-bin/Mitobreak_home.cgi

Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements.

Proper citation: MitoBreak (RRID:SCR_012949) Copy   

•   Source: SciCrunch Registry

http://www.rcsb.org/#Category-welcome

Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.

Proper citation: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) Copy   

•   Source: SciCrunch Registry

http://www.nabc.go.kr/sgd/

Database for ESTs (Expressed Sequence Tags), consensus sequences, bacterial artificial chromosome (BAC) clones, BES (BAC End Sequences). They have generated 69,545 ESTs from 6 full-length cDNA libraries (Porcine Abdominal Fat, Porcine Fat Cell, Porcine Loin Muscle, Liver and Pituitary gland). They have also identified a total of 182 BAC contigs from chromosome 6. It is very valuable resources to study porcine quantitative trait loci (QTL) mapping and genome study. Users can explore genomic alignment of various data types, including expressed sequence tags (ESTs), consensus sequences, singletons, QTL, Marker, UniGene and BAC clones by several options. To estimate the genomic location of sequence dataset, their data aligned BES (BAC End Sequences) instead of genomic sequence because Pig Genome has low-coverage sequencing data. Sus scrofa Genome Database mainly provide comparative map of four species (pig, cattle, dog and mouse) in chromosome 6.

Proper citation: PiGenome (RRID:SCR_013394) Copy   

•   Source: SciCrunch Registry

http://actimetrics.com/products/limelight/

A video tracking system designed for high-throughput behavioral experiments. LimeLight can track up to 4 arenas at once and can collect images at up to 30 frames per second for one animal or up to 8 frames per second when tracking 4 arenas at once. The tracking system has 2 different hardware configurations: the 1-camera system can be used to record 1 to 4 animals at once, while for multiple animals, each one is placed in a separate arena in one quadrant of the image. The software contains productivity features such as flexible arena setup, user-defined behavior scoring, stimulus control, and various analytical functions for quantifying behavior. The program is designed for experiments such as Open Field, Plus Maze, Radial Arm Maze, Zero Maze, Novel Object Recognition, Conditioned Place Preference, and Barnes Maze.

Proper citation: Limelight (RRID:SCR_014254) Copy   

•   Source: SciCrunch Registry

http://actimetrics.com/products/freezeframe/

A video-based system to detect animal movement in fear conditioning experiments, as well as movements in learned helplessness experiments. FreezeFrame can detect animal movements (as small as 1mm) and actions, including grooming, sniffing, turning, and rearing. It can also collect and process data for learned helplessness experiments, such as Tail Suspension and the Porsolt Forced Swim Test. This software can monitor animals for up to 15 times per second.

Proper citation: FreezeFrame (RRID:SCR_014429) Copy   

•   Source: SciCrunch Registry

http://www.sandiegoinstruments.com/any-maze-video-tracking/

Video tracking system used to automate testing in a variety of behavioral apparatus. ANY-maze can automatically track the tail, head, or body of a test animal in up to 16 pieces of apparatus. The software can record live images or digital files with different camera types and save the data in multiple formats. ANY-maze contains built in statistical tests and standard measures for distance, speed, mobility, duration, etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ANY-maze (RRID:SCR_014289) Copy   

•   Source: SciCrunch Registry

http://www.salk.edu/science/core-facilities/behavior-testing-core/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2024. Core facility that provides the resources to investigate sensory, motor and complex behavioral testing in rat and mouse models. The facility offers standard neurobehavioral tests, customized test batteries, training for independent use of the equipment, data interpretation and anlaysis.

Proper citation: Salk Institute Behavior Testing Core Facility (RRID:SCR_014840) Copy   

•   Source: SciCrunch Registry

http://mmpc.ucdavis.edu/index.php

Center that provides the scientific community with metabolic and physiologic phenotyping tests, services, and procedures for mouse models of diabetes, diabetic complications, obesity and related disorders in order to advance medical and biological research.

Proper citation: MMPC-University of California Davis (RRID:SCR_015357) Copy   

•   Source: SciCrunch Registry

http://mbm.cs.uga.edu/mouse/transcriptome_architecture/

Image collection of transcriptome architecture of adult mouse brain revealed by sparse coding of genome-wide in situ hybridization images.

Proper citation: Transcriptome architecture of adult mouse brain (RRID:SCR_015483) Copy   

•   Source: SciCrunch Registry

http://mmpc.med.umich.edu/

Research center which aims to contribute to a national database of metabolic phenotyping data in wild-type mouse strains and a broad range of mouse models relevant to the pathogenesis and treatment of diabetes, obesity and associated metabolic disorders. It also aims to foster continued technical development, refinement of assay sensitivity and specificity, data reproducibility, and transmission of best research practices within the areas of fundamental and applied diabetes and obesity research.

Proper citation: MMPC-University of Michigan Medical School (RRID:SCR_015373) Copy   

•   Source: SciCrunch Registry

http://m6asnp.renlab.org

Web server implemented in JAVA and PHP for annotating genetic variants by m6A function. It predicts and annotates N6-methyladenosine (m6A) alterations from genetic variants data such as germline SNPs or cancer somatic mutations. It employs two accurate prediction models for human and mouse using Random Forest algorithm. It conducts a statistical analysis for all the predicted m6A alterations. Provides statistical diagrams and a genome browser to visualize the topology characteristics of predicted m6A alterations.

Proper citation: m6ASNP: Annotation of genetic variants by m6A function (RRID:SCR_016048) Copy   

•   Source: SciCrunch Registry

http://stemcellcommons.org/

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   

•   Source: SciCrunch Registry

http://www.brainarchitecture.org/mouse-home

An atlas project whose goal is to enerate brainwide maps of inter-regional neural connectivity that specify the inputs and outputs of every brain region, at a "mesoscopic" level of analysis. A 3D injection viewer is used to view the mouse brain. To determine the outputs of a brain region, anterograde tracers are used which are taken up by neurons locally ("the input"), then transported actively down the axons to the "output regions." The whole brain is then sliced thinly, and each slice is digitally imaged. These 2-D images are reconstructed in 3D. The majority of the resulting 3-D brain image is unlabeled. Only the injected region and its output regions have tracer in them, allowing for identification of this small fraction of the connectivity map. This procedure is repeated identically, to account for individual variability. To determine the inputs to the same brain region as above, a retrograde tracer is injected in the same stereotaxic location ("the input"), and the process is repeated. In order to accumulate data from different mice (each of whom has a slightly different brain shape and size), 3-D spatial normalization is performed using registration algorithms. These gigapixel images of whole-brain sections can be zoomed to show individual neurons and their processes, providing a "virtual microscope." Each sampled brain is represented in about 500 images, each image showing an optical section through a 20 micron-thick slice of brain tissue. A multi-resolution viewer permits users to journey through each brain, following the pathways taken through three-dimensional brain space by tracer-labeled neuronal pathways. A key point is that at the mid-range "mesoscopic" scale, the team expects to assemble a picture of connections that are stereotypical and probably genetically determined in a species-specific manner. By dividing the volume of a hemisphere of the mouse brain into 250 equidistant, predefined grid-points, and administering four different kinds of tracer injections at each grid point -- in different animals of the same sex and age a complete wiring diagram that will be stitched together in "shotgun" fashion from the full dataset.

Proper citation: Mouse Brain Architecture Project (RRID:SCR_004683) Copy   

•   Source: SciCrunch Registry

http://variant.bioinfo.cipf.es/

Analysis tool that can report the functional properties of any variant in all the human, mouse or rat genes (and soon new model organisms will be added) and the corresponding neighborhoods. Also other non-coding extra-genic regions, such as miRNAs are included in the analysis. It not only reports the obvious functional effects in the coding regions but also analyzes noncoding SNVs situated both within the gene and in the neighborhood that could affect different regulatory motifs, splicing signals, and other structural elements. These include: Jaspar regulatory motifs, miRNA targets, splice sites, exonic splicing silencers, calculations of selective pressures on the particular polymorphic positions, etc. Software analysis pipelines used in the analysis of NGS data are highly modular, heterogeneous, and rapidly evolving. VARIANT can easily be incorporated into a NGS resequencing pipeline either as a CLI or invoked a webservice. It inputs data directly from the most widely used programs for SNV detection., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: VARIANT (RRID:SCR_005194) Copy   

•   Source: SciCrunch Registry

http://seqant.genetics.emory.edu/

A free web service and open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform. Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser. SeqAnt further identifies all loci harboring two or more coding sequence variants that help investigators identify potential compound heterozygous loci within exome sequencing experiments. In total, SeqAnt resolves a significant bottleneck by allowing an investigator to rapidly prioritize the functional analysis of those variants of interest.

Proper citation: SeqAnt (RRID:SCR_005186) Copy   

•   Source: SciCrunch Registry