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Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development)
Proper citation: Pathbase (RRID:SCR_006141) Copy
http://interactome.baderlab.org/
Project portal for the Human Reference Protein Interactome Project, which aims generate a first reference map of the human protein-protein interactome network by identifying binary protein-protein interactions (PPIs). It achieves this by systematically interrogating all pairwise combinations of predicted human protein-coding genes using proteome-scale technologies.
Proper citation: Human Reference Protein Interactome Project (RRID:SCR_015670) Copy
https://sedfitsedphat.nibib.nih.gov/software/default.aspx
Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.
Proper citation: SEDFIT (RRID:SCR_018365) Copy
http://www.cbs.dtu.dk/services/BepiPred/index.php
Sequential B-Cell Epitope Predictor. Web server predicts B-cell epitopes from protein sequence. Sequence-based B-cell epitope prediction using conformational epitopes. Sequences of protein of interest should be in fasta format. BepiPred 2.0 is available as stand alone software package, with same functionality as web service., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: BepiPred-2.0 (RRID:SCR_018499) Copy
https://mass-spec.stanford.edu/instruments
Advanced benchtop tandem quadrupole mass spectrometer which expands scope of ultimate sensitivity analysis. Fatures probe design which allows users much easier maintenance, optimization and improved reproducibility between operators. Method transfer onto Xevo TQ-XS is made simple by Xtended Dynamic Range detector which allows six orders of linear dynamic range. Wider compound coverage without changing ionization technique is delivered by the revolutionary UniSpray source option.
Proper citation: Xevo TQ-XS mass spectrometer (RRID:SCR_018510) Copy
Portal for research on urinary stones in adults and children in order to learn more about who forms kidney stones, treatments and prevention. Network comprises of experts including adult and pediatric urologists, adult and pediatric nephrologists, pediatricians, emergency department physicians, clinical trialists, nutritionists, behavioral scientists, and radiologists. Duke Clinical Research Institute is Scientific Data Research Center and with clinical sites including University of Pennsylvania Children Hospital of Philadelfia, University of Texas Southwestern Medical Center, University of Washington, Washington University in St. Louis, work together in planning, executing, and analyzing results from USDRN studies.
Proper citation: Urinary Stone Disease Research Network (RRID:SCR_019059) Copy
Portal for human electrophysiological data, supports, sharing and in depth analysis of identified human neuroelectromagnetic brain data including scalp EEG, its magnetic counterpart, MEG, and, intracranial iEEG and ECoG. Open access EEG and MEG data archives, analysis, and visualization. Neuroelectromagnetic data, tools, and compute resource.
Proper citation: NEMAR (RRID:SCR_019100) Copy
https://run.biosimulations.org
Web tool for executing broad range of modeling studies and visualizing their results. Provides web interface for reusing any model. Models, simulations, and visualizations are available under licenses specified for each resource.
Proper citation: runBioSimulations (RRID:SCR_019110) Copy
Searchable table of datasets. Data generated from projects through BRAIN Initiative Cell Census Network. Datasets can be filtered by species, research investigator, grant number or experimental technique. Includes links to data directories at data archives and links to protocols.
Proper citation: BICCN Cell Registry (RRID:SCR_017267) Copy
Portal to facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health or by other agencies that support human genomics research. Resource for genomic scientific community, that leverages cloud based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic related data sets. Component of federated data ecosystem, and is expected to collaborate and integrate with other genomic data resources through adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from scientific community. Will provide collaborative environment, where datasets and analysis workflows can be shared within consortium and be prepared for public release to broad scientific community through AnVIL user interfaces.
Proper citation: Analysis, Visualization, and Informatics Lab-space (AnVIL) (RRID:SCR_017469) Copy
http://grantome.com/grant/NIH/U01-DK099919-04S1
Consortium to design and conduct pilot and feasibility studies of novel therapies to reduce morbidity and mortality for patients treated with maintenance hemodialysis. Data Coordinating Center (DCC) for consortium provides scientific expertise and operational support for pilot studies that will be conducted at HDPSC Participating Clinical Centers. Data Coordinating Center for Hemodialysis Pilot Studies Consortium.
Proper citation: Hemodialysis Pilot Studies Consortium (RRID:SCR_017468) Copy
https://bioinfo3d.cs.tau.ac.il/PatchDock/
Web server for molecular docking. Performs structure prediction of protein–protein and protein–small molecule complexes. Molecular docking algorithm based on shape complementarity principles.
Proper citation: PatchDock (RRID:SCR_017589) Copy
Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions.
Proper citation: immuneXpresso (RRID:SCR_017578) Copy
https://www.synapse.org/#!Synapse:syn22345748/wiki/605339
Reference dataset of multiplexed immunofluorescence microscopy images collected at HMS Laboratory of Systems Pharmacology. Includes set of images of different types for development and benchmarking of computational methods for image processing. As of 4/2/2021, EMIT comprises tissue microarray containing cores from 34 cancer, non-neoplastic diseases, and normal tissue collected from clinical discards under IRB supervised protocol. TMA was imaged using cyclic immunofluorescence method. Additional extensions of EMIT are currently in the planning stages. Long term goal is to compose ImageNet like resource for highly multiplexed images of tissues and tumors by consolidating high quality curated datasets.
Proper citation: Exemplar Microscopy Images of Tissues (RRID:SCR_021052) Copy
https://nwb-extensions.github.io/
Community led catalog of extensions to Neurodata Without Borders data standard.
Proper citation: Neurodata Extensions Catalog (RRID:SCR_021340) Copy
https://github.com/marbl/MashMap
Software tool as fast approximate aligner for long DNA sequences. Used for computing local alignment boundaries between long DNA sequences.
Proper citation: MashMap (RRID:SCR_022194) Copy
https://mass-spec.stanford.edu/instruments
System includes Thermo Orbitrap Eclipse Tribid mass spectrometer and Waters M-Class Acquity nanoUPLC. This platform features sequential acquisition capabilities and multiple fragmentation types, enabling complex, in depth proteomic experiments.
Proper citation: Thermo Orbitrap Eclipse nanoLC/MS system (RRID:SCR_022212) Copy
https://kidsfirstdrc.org/portal/portal-features/
Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects.
Proper citation: Kids First Data Resource Portal (RRID:SCR_016493) Copy
https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#bewith
Software tool for discovering relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions.
Proper citation: BeWith (RRID:SCR_016573) Copy
https://www.mousephenotype.org/imits/
This resource has been replaced by GenTaR. Software tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC products.
Proper citation: iMITS (RRID:SCR_016552) Copy
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