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http://genecodis.cnb.csic.es/

Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GeneCodis (RRID:SCR_006943) Copy   

•   Source: SciCrunch Registry

http://crcns.org

Website for brain experimental data and other resources such as stimuli and analysis tools. Provides marketplace and discussion forum for sharing tools and data in neuroscience. Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS offers funding for new class of proposals focused on data sharing and other resources.

Proper citation: CRCNS (RRID:SCR_005608) Copy   

•   Source: SciCrunch Registry

http://www.oeb.harvard.edu/faculty/hartl/old_site/lab/publications/GeneMerge.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: GeneMerge (RRID:SCR_005744) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/

A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.

Proper citation: Synapse (RRID:SCR_006307) Copy   

•   Source: SciCrunch Registry

https://github.com/scimemia/M-Track

Source code that allows users to simultaneously track the movement of individual paws during spontaneous grooming episodes and walking in multiple freely-behaving mice/rats. This toolbox provides a simple platform to perform trajectory analysis of paw movement.

Proper citation: M-Track (RRID:SCR_015865) Copy   

•   Source: SciCrunch Registry

https://ratgenes.org/

Portal includes information about genetic studies of drug abuse in outbred rats. Data center created in 2014 to perform genome wide association studies on numerous behavioral traits that have well established relevance to drug abuse using outbred rats.

Proper citation: NIDA center for genetic studies of drug abuse in outbred rats (RRID:SCR_021788) Copy   

•   Source: SciCrunch Registry

http://datahub.io/dataset/kupkb

A collection of omics datasets (mRNA, proteins and miRNA) that have been extracted from PubMed and other related renal databases, all related to kidney physiology and pathology giving KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. Some microarray raw datasets have also been downloaded from the Gene Expression Omnibus and analyzed by the open-source software GeneArmada. The Semantic Web technologies, together with the background knowledge from the domain's ontologies, allows both rapid conversion and integration of this knowledge base. SPARQL endpoint http://sparql.kupkb.org/sparql The KUPKB Network Explorer will help you visualize the relationships among molecules stored in the KUPKB. A simple spreadsheet template is available for users to submit data to the KUPKB. It aims to capture a minimal amount of information about the experiment and the observations made.

Proper citation: Kidney and Urinary Pathway Knowledge Base (RRID:SCR_001746) Copy   

•   Source: SciCrunch Registry

https://www.cmtk.org/

A Python-based open source toolkit for magnetic resonance connectome mapping, data management, sharing, visualization and analysis. The toolkit includes the connectome mapper (a full DMRI processing pipeline), a new file format for multi modal data and metadata, and a visualization application.

Proper citation: Connectome Mapping Toolkit (RRID:SCR_001644) Copy   

•   Source: SciCrunch Registry

https://rgd.mcw.edu/rgdweb/portal/home.jsp?p=4

An integrated resource for information on genes, QTLs and strains associated with diabetes. The portal provides easy acces to data related to both Type 1 and Type 2 Diabetes and Diabetes-related Obesity and Hypertension, as well as information on Diabetic Complications. View the results for all the included diabetes-related disease states or choose a disease category to get a pull-down list of diseases. A single click on a disease will provide a list of related genes, QTLs, and strains as well as a genome wide view of these via the GViewer tool. A link from GViewer to GBrowse shows the genes and QTLs within their genomic context. Additional pages for Phenotypes, Pathways and Biological Processes provide one-click access to data related to diabetes. Tools, Related Links and Rat Strain Models pages link to additional resources of interest to diabetes researchers.

Proper citation: Diabetes Disease Portal (RRID:SCR_001660) Copy   

•   Source: SciCrunch Registry

http://neuromorpho.org/index.jsp

Centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact.

Proper citation: NeuroMorpho.Org (RRID:SCR_002145) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/rat/public/index_main.html

Data set of pictures representing genetic linkage maps of the rat resulting from the integration of two F2 intercrosses (SHRSP x BN and FHH x ACI). Markers in common between the two crosses are connected by a line to define integration points. There are a total of 4,786 markers on these maps; 4375 WIBR/MIT CGR markers; 223 markers from the previously released Mit/Mgh rat maps and 188 markers from the National Institute of Arthritis and Musculoskeletal and Skin Diseases Arb rat maps. Pictures are drawn to a scale of 5cm (Kosombi) per inch. The changes in color of the backbone of the chromosome for each cross represents the space between any two framework loci. Markers in blue type are framework loci. Markers in green type are unique placement loci. Markers in black type are bouncy placement loci.

Proper citation: Genetic Maps of the Rat Genome (RRID:SCR_002266) Copy   

•   Source: SciCrunch Registry

http://www.rrrc.us/

Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models.

Proper citation: Rat Resource and Research Center (RRID:SCR_002044) Copy   

•   Source: SciCrunch Registry

http://ccdb.ucsd.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented June 5, 2017. It has been merged with Cell Image Library. Database for sharing and mining cellular and subcellular high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging that makes unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. Techniques range from wide field mosaics taken with multiphoton microscopy to 3D reconstructions of cellular ultrastructure using electron tomography. Contributions from the community are welcome. The CCDB was designed around the process of reconstruction from 2D micrographs, capturing key steps in the process from experiment to analysis. The CCDB refers to the set of images taken from microscope the as the Microscopy Product. The microscopy product refers to a set of related 2D images taken by light (epifluorescence, transmitted light, confocal or multiphoton) or electron microscopy (conventional or high voltage transmission electron microscopy). These image sets may comprise a tilt series, optical section series, through focus series, serial sections, mosaics, time series or a set of survey sections taken in a single microscopy session that are not related in any systematic way. A given set of data may be more than one product, for example, it is possible for a set of images to be both a mosaic and a tilt series. The Microscopy Product ID serves as the accession number for the CCDB. All microscopy products must belong to a project and be stored along with key specimen preparation details. Each project receives a unique Project ID that groups together related microscopy products. Many of the datasets come from published literature, but publication is not a prerequisite for inclusion in the CCDB. Any datasets that are of high quality and interest to the scientific community can be included in the CCDB.

Proper citation: Cell Centered Database (RRID:SCR_002168) Copy   

•   Source: SciCrunch Registry

http://biodev.extra.cea.fr/interoporc/

Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8.

Proper citation: InteroPorc (RRID:SCR_002067) Copy   

•   Source: SciCrunch Registry

http://spine.rutgers.edu/microarray/

Database which provides on-line searching of microarray datasets generated from rat spinal cord after contusion injury. Both the primary injury site and a site 5 mm distal to the injury site were assayed. Tissue was obtained from Long Evans rats subject to spinal cord contusion injury using the MASCIS impactor (formerly known as the NYU impactor). RNA expression was assayed at the site of injury and distal to the site of injury using the Affymetrix Rat Neuro U34 chip.

Proper citation: Gene Expression Profiling in Spinal Cord Injury (RRID:SCR_003260) Copy   

•   Source: SciCrunch Registry

http://brainarray.mbni.med.umich.edu/Brainarray/Database/ProbeMatchDB/ncbi_probmatch_para_step1.asp

Matches a list of microarray probes across different microrarray platforms (GeneChip, EST from different vendors, Operon Oligos) and species (human, mouse and rat), based on NCBI UniGene and HomoloGene. The capability to match protein sequence IDs has just been added to facilitate proteomic studies. The ProbeMatchDB is mainly used for the design of verification experiments or comparing the microarray results from different platforms. It can be used for finding equivalent EST clones in the Research Genetics sequence verified clone set based on results from Affymetirx GeneChips. It will also help to identify probes representing orthologous genes across human, mouse and rat on different microarray platforms.

Proper citation: ProbeMatchDB 2.0 (RRID:SCR_003433) Copy   

•   Source: SciCrunch Registry

http://synapses.clm.utexas.edu

A portal into the 3D ultrastructure of the brain providing: Anatomy of astrocytes, axons, dendrites, hippocampus, organelles, synapses; procedures of 3D reconstruction and tissue preparation; as well as an atlas of ultrastructural neurocytology (by Josef Spacek), online aligned images, and reconstructed dendrites. Synapse Web hosts an ultrastructural atlas containing more than 500 electron micrographs (added to regularly) that identify unique ultrastructural and cellular components throughout the brain. Additionally, Synapse Web has raw images, reconstructions, and quantitative data along with tutorial instructions and numerous tools for investigating the functional structure of objects that have been serial thin sectioned for electron microscopy.

Proper citation: Synapse Web (RRID:SCR_003577) Copy   

•   Source: SciCrunch Registry

http://www.fda.gov/downloads/Drugs/DevelopmentApprovalProcess/DrugDevelopmentToolsQualificationProgram/UCM294644.pdf

Serum / plasma biomarkers, Cardiac troponins T (cTnT) and I (cTnI), in safety assessment studies for rats, dogs, and monkeys are qualified biomarkers for the following contexts of use: # When there is previous indication of cardiac structural damage with a particular drug, cardiac troponin testing can help estimate a lowest toxic dose or a highest non-toxic dose to help choose doses for human testing. In this case, cardiac troponins may serve as a clinical chemistry correlate to the histology. For example, in a safety assessment study, lower doses without increases in cardiac troponins may be used to support a no observed effect level (NOEL) identified by histology. # When there is known cardiac structural damage with a particular pharmacologic class of a drug and histopathologic analyses do not reveal structural damage, circulating cardiac troponins may be used to support or refute the inference of low cardiotoxic potential. # When unexpected cardiac structural toxicity is found in a nonclinical study, the retroactive (reflex) examination of serum or plasma from that study for cardiac troponins can be used to help determine a no observed adverse effect level (NOAEL) or lowest observed adverse effect level (LOAEL). The results of this testing may support inclusion of cardiac troponin testing in subsequent safety assessment studies.

Proper citation: O'Brien Reagan York and Jacobsen Drug-induced Cardiotoxicity Biomarkers (RRID:SCR_003717) Copy   

•   Source: SciCrunch Registry

http://www.fda.gov/downloads/Drugs/DevelopmentApprovalProcess/DrugDevelopmentToolsQualificationProgram/UCM285010.pdf

Urinary kidney biomarkers, Clusterin and Renal Papillary Antigen-1 (RPA-1), that sponsors may use to determine more conservative NOAELs for estimating starting doses in the initial human clinical trial of a drug that displays nonclinical nephrotoxicity as determined by histopathology. When tested with a limited number of nephrotoxic compounds, the Receiver Operating Characteristic (ROC) analyses showed that urinary clusterin and renal papillary antigen-1 (RPA-1) have better sensitivity and specificity than BUN and creatinine for the detection of specific kidney pathologies in male rats. Clusterin and RPA-1 provide additional and complementary information to BUN, serum creatinine (sCr), and histopathology for the detection of acute drug-induced nephrotoxicity in safety assessment studies.

Proper citation: ILSI HESI Drug-induced Nephrotoxicity Biomarkers (RRID:SCR_003716) Copy   

•   Source: SciCrunch Registry

http://actimetrics.com/products/clocklab/

Point and click program used to quickly analyse circadian activity data using algorithms and embedded controls to make every graph interactive and useful for data analysis. The analysis program has been used for a variety of species including mice, hamsters, rats, sheep, Drosophila, and humans. This program has three separate applications: one for data collection, one for analysis, and a chamber control program.

Proper citation: Clocklab (RRID:SCR_014309) Copy   

•   Source: SciCrunch Registry