SciCrunch

Washington University Digestive Diseases Research Core Center

Research center whose purpose is to advance research in digestive disease with a focus on interactions between host and environment. It provides research resources to basic and translational investigators through various core facilities.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

Vanderbilt Digestive Disease Research Center Flow Cytometry Core

Core facility whose services include training, acquisition and analysis on cytometers for experiments that include different fluorochromes, imaging cytometry, and mass cytometry.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

Vanderbilt Digestive Disease Research Center Cellular Imaging Core

Core facility whose goals include furnishing professional guidance in experimental design and data interpretation and providing access to optical and electron microscopy. Its services include confocal microscopy, wide-field microscopy, transmission electron microscopy, and processing and embedment of tissue or cells for EM.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

Imspector Software

Software toolkit for data aquisition and analysis. Its features include remote control of Abberior Instruments microscopes via a Python/MATLAB script, third-party compatibility with other data-analysis softwares/methods, and the easyCommander graphical user interface for experimental set up.

Resource
RRID-Legacy
10 years ago - by Anonymous

Statgraphics Centurion

Data analysis and visualization software with features that include a R interface, demographic maps, bivariate density estimation, multiple time series visualization, repeated ANOVA measures, and a multivariate visualizers.

Resource
RRID-Legacy
10 years ago - by Anonymous

LTR_Finder

Web software capable of scanning large-scale sequences for full-length LTR retrotranspsons., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Resource
SciCrunch
10 years ago - by Anonymous

Ilastik

Tool for interactive image classification, segmentation and analysis, built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection.

Resource
NIF
10 years ago - submitted by Maryann Martone

WholeBrain

Software suite that provides an efficient way for scientist with minimal knowledge of computers to create anatomical maps and integrate this information with behavioral and physiological data for sharing on the web. It uses R for data analysis and graphical plotting and uses OpenCV for image analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Resource
NIF
10 years ago - submitted by Maryann Martone

jModelTest

Software tool used to carry out statistical selection of best-fit models of nucleotide substitution without the aid of PAUP*. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests, Akaike and Bayesian information criteria, and a decision theory method. It also provides estimates of model selection uncertainty, parameter importances, and model-averaged parameter estimates.

Resource
RRID-Legacy
10 years ago - by Anonymous

Phandango

Interactive web visualization tool for populations of bacterial genomes linked by a phylogeny.

Resource
RRID-Legacy
10 years ago - by Anonymous

Neurodata Without Borders

Data standard for neurophysiology, providing common standard to share, archive, use, and build common analysis tools for neurophysiology data. NWB:N is designed to store variety of neurophysiology data, including data from intracellular and extracellular electrophysiology experiments, data from optical physiology experiments, and tracking and stimulus data. Project includes NWB format and broad range of software for data standardization and application programming interfaces (APIs) for reading and writing data as well as high value data sets that have been translated into NWB data standard. NWB format is implemented in Hierarchical Data Format (HDF5) and is designed to store data in self documenting way. Storage schema is described by specification language and it is extensible to support future scientific needs as well as lab specific requirements.

Resource
NIF
10 years ago - submitted by Maryann Martone

Neuromembrane Simulator

Simulator to help students understand basic properties of excitable membranes, particularly ion flow across an excitable membrane. The simulator is based on the equations developed by Alan Hodgkin and Andrew Huxley following their research on the excitability properties of the squid giant axon.

Resource
NIF
10 years ago - submitted by Maryann Martone

Atomify LAMMPS

Mobile simulation app for visualizing molecular interactions in liquids, solids and gases. The simulations are performed with the molecular dynamics code LAMMPS.

Resource
NIF
10 years ago - submitted by Maryann Martone

Center for the Study of Inflammatory Bowel Disease Immunology Core

Core whose focus is on modern approaches to the study of the human immune system and their application to the study of IBD and related disorders. Its services include routine immunology tools, specialized immunology services, and education and training services.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

Center for the Study of Inflammatory Bowel Disease Genetic Animal Models Core

Core whose services include breeding and maintenance of mutant mouse stocks, characterization of murine models, bone marrow transfers and adoptive T cell transfers, in vivo tracking of fluorescently labeled bacteria and cells, and whole body imaging of bioluminescent and fluorescent signals.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

USC Liver Transplant Program and Center for Liver Disease

Center whose goal is the facilitation and fostering of interdisciplinary collaborative research in the field of pathobiology of diseases of the liver and digestive tract and the development of new treatments for these diseases.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

USC Liver Transplant Program and Center for Liver Disease Liver Histology Core

Core that provides standard and customized slide preparation, liver histochemistry and immunohistochemistry as well as laser-capture microscopy.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

Washington University Center for Diabetes Translation Research Administrative Core in Diabetes Research Core

THIS RESOURCE IS LONGER IN SERVICE. Documented on June 15,2026. Management core whose main functions include organizing and managing membership committees, coordinating communication with the NIH and other research bases, and overseeing the use of funds.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

USC Liver Transplant Program and Center for Liver Disease Cell and Tissue Imaging Core

Core that provides instrumentation (confocal and fluorescence microscopy) and technical support for cell biology and pathophysiology studies.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

USC Liver Transplant Program and Center for Liver Disease Cell Separation and Culture Core

Core facility which provides primary hepatocytes cultures of normal and diseased mice and rats and various cell lines to investigators. The cell separation subcore plays a role in translational research in DILI and alcoholic hepatitis, supporting funded studies of the role of innate and adaptive immune systems in elucidating pathophysiology, identifying biomarkers, and predicting response to treatments.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

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