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http://www.loni.usc.edu/BIRN/Projects/Mouse/

Animal model data primarily focused on mice including high resolution MRI, light and electron microscopic data from normal and genetically modified mice. It also has atlases, and the Mouse BIRN Atlasing Toolkit (MBAT) which provides a 3D visual interface to spatially registered distributed brain data acquired across scales. The goal of the Mouse BIRN is to help scientists utilize model organism databases for analyzing experimental data. Mouse BIRN has ended. The next phase of this project is the Mouse Connectome Project (https://www.nitrc.org/projects/mcp/). The Mouse BIRN testbeds initially focused on mouse models of neurodegenerative diseases. Mouse BIRN testbed partners provide multi-modal, multi-scale reference image data of the mouse brain as well as genetic and genomic information linking genotype and brain phenotype. Researchers across six groups are pooling and analyzing multi-scale structural and functional data and integrating it with genomic and gene expression data acquired from the mouse brain. These correlated multi-scale analyses of data are providing a comprehensive basis upon which to interpret signals from the whole brain relative to the tissue and cellular alterations characteristic of the modeled disorder. BIRN's infrastructure is providing the collaborative tools to enable researchers with unique expertise and knowledge of the mouse an opportunity to work together on research relevant to pre-clinical mouse models of neurological disease. The Mouse BIRN also maintains a collaborative Web Wiki, which contains announcements, an FAQ, and much more.

Proper citation: Mouse Biomedical Informatics Research Network (RRID:SCR_003392) Copy   

•   Source: SciCrunch Registry

http://edoctoring.ncl.ac.uk/Public_site/

Online educational tool that brings challenging clinical practice to your computer, providing medical education that is engaging, challenging and interactive. While there is no substitute for real-life direct contact with patients or colleagues, research has shown that interactive online education can be a highly effective and enjoyable method of learning many components of clinical medicine, including ethics, clinical management, epidemiology and communication skills. eDoctoring offers 25 simulated clinical cases, 15 interactive tutorials and a virtual library containing numerous articles, fast facts and video clips. Their learning material is arranged in the following content areas: * Ethical, Legal and Social Implications of Genetic Testing * Palliative and End-of-Life Care * Prostate Cancer Screening and Shared Decision-Making

Proper citation: eDoctoring (RRID:SCR_003336) Copy   

•   Source: SciCrunch Registry

http://portal.ncibi.org/gateway/mimiplugin.html

The Cytoscape MiMI Plugin is an open source interactive visualization tool that you can use for analyzing protein interactions and their biological effects. The Cytoscape MiMI Plugin couples Cytoscape, a widely used software tool for analyzing bimolecular networks, with the MiMI database, a database that uses an intelligent deep-merging approach to integrate data from multiple well-known protein interaction databases. The MiMI database has data on 119,880 molecules, 330,153 interactions, and 579 complexes. By querying the MiMI database through Cytoscape you can access the integrated molecular data assembled in MiMI and retrieve interactive graphics that display protein interactions and details on related attributes and biological concepts. You can interact with the visualization by expanding networks to the next nearest neighbors and zooming and panning to relationships of interest. You also can perceptually encode nodes and links to show additional attributes through color, size and the visual cues. You can edit networks, link out to other resources and tools, and access information associated with interactions that has been mined and summarized from the research literature information through a biology natural language processing database (BioNLP) and a multi-document summarization system, MEAD. Additionally, you can choose sub-networks of interest and use SAGA, a graph matching tool, to match these sub-networks to biological pathways.

Proper citation: MiMI Plugin for Cytoscape (RRID:SCR_003424) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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: Waters: Xevo TQ-XS mass spectrometer (RRID:SCR_018510) Copy   

•   Source: SciCrunch Registry

https://usdrn.org/

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   

•   Source: SciCrunch Registry

https://nemar.org

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://commonfund.nih.gov/hubmap

Project to facilitate research on single cells within tissues by supporting data generation and technology development to explore the relationship between cellular organization and function, as well as variability in normal tissue organization at the level of individual cells. Framework for functional mapping the human body with cellular resolution.Designed to support diverse spatial and non-spatial omics and imaging data types and to integrate with a wide range of analysis workflows.

Proper citation: The Human BioMolecular Atlas Program (RRID:SCR_016922) Copy   

•   Source: SciCrunch Registry

https://blake.bcm.edu/emanwiki/EMAN2

Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography.

Proper citation: EMAN (RRID:SCR_016867) Copy   

•   Source: SciCrunch Registry

https://github.com/dpeerlab/phenograph

Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity.

Proper citation: Phenograph (RRID:SCR_016919) Copy   

•   Source: SciCrunch Registry

https://biccn.org/data

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   

•   Source: SciCrunch Registry

https://anvilproject.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.immunexpresso.org

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   

•   Source: SciCrunch Registry

http://www.genetherapyreview.com/gene-therapy-research

The National Gene Vector Laboratories (NGVL) was established as a cooperative national effort to produce and distribute vectors for human gene transfer studies.

Proper citation: National Gene Vector Laboratories (RRID:SCR_015944) Copy   

•   Source: SciCrunch Registry

http://hyphy.org/

Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.

Proper citation: HyPhy (RRID:SCR_016162) Copy   

•   Source: SciCrunch Registry

https://gotrack.msl.ubc.ca/

Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis.

Proper citation: GOTrack (RRID:SCR_016399) Copy   

•   Source: SciCrunch Registry