Curator Dashboard

Flow cytometry core which offers a wide range of routine and custom flow cytometry, mass cytometry, cell sorting services, data analysis, strategic planning for novel assays, user training, and full scale research collaborations.

• Resource
• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Core Facility provides support for short or long-term projects requiring expertise the analysis of biological datasets. The services provided include the analysis of large-scale datasets (e.g. next-gen sequencing data, microarrays, etc.), the development of customized databases and reusable analysis pipelines, guidance on experimental design, support with technical sections of manuscripts and grants, and training on analysis software packages. All services are charged at our hourly rate.

• Resource
• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Standalone solution dedicated to Visual Psychophysics running on Mac OS X. Psykinematix runs standard psychophysical protocols, presents complex stimuli, collects subject's responses, and analyzes results on the fly. It consists of a unique OpenGL-based software package that does not require any programming skill to create and run complex experiments.

• Resource
• RRID-Legacy
• 10 years ago - by Anonymous

Commercial organization which provides hardware and software products for life science research and teaching.

• Organization
• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Image analysis software that learns modular models of things such as cell shape, nuclear shape, vesicular organelle distribution and microtubule distribution directly from 2D or 3D images and can produce specific instances of cell geometries without the need to create them by hand or to segment microscope images. These geometries can be combined with biochemical models to perform spatially realistic cell simulations if used in conjunction with MCell.

• Resource
• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Computing platform for biomolecular NMR available to not-for-profit or government users. It consists of a virtual machine (VM) provisioned with dozens of widely-used NMR software packages, and is available as a cloud-based Platform-as-a-Service (PaaS) or as a downloadable VM for local execution.

• Resource
• SciCrunch
• 10 years ago - submitted by Jeffrey Hoch

Database and repository of tissues relating to mouse models of breast cancer. Users can search and share models, and members can enter details of available material to share on a collaborative basis.

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• SciCrunch
• 10 years ago - submitted by Anita Bandrowski

Server used to create spreadsheets with ontology based data validations. Webulous can process populated templates and transform them into OWL/RDF using design patterns expressed in OPPL. It also has an add-on with Google spreadsheets which supports loading templates from a Webulous server and allows users to submit populated spreadsheets back to the Webulous server for transformation into OWL.

• Resource
• SciCrunch
• 10 years ago - submitted by Jamie Li

Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data.

• RRID-Legacy
• 10 years ago - submitted by Mihai Capotă

Brightfield image analysis software for the FACS-like analysis of samples stained with immunohistochemical or other stains.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Image analysis software for cells and stained areas in samples stained with immunofluorescent markers.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Data acquisition and analysis software used for xCELLigence Real Time Cell Analysis SP, DP and MP instruments. The software is used to program and execute experiments and analyze data.

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• RRID-Legacy
• 10 years ago - by Anonymous

RZ6 processor tool designed for rapid animal screening. It automates the process of presenting stimulus signals and averaging response signal data. It automates the process of presenting stimulus signals and averaging response signal data by giving users control over the stimulus signal parameters used to generate stimuli that vary across successive presentations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

• Resource
• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.

• Resource
• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software tool designed for mapping short reads onto a reference genome generated from Illumina, Ion Torrent, and 454 NGS platforms. Its features include paired end alignment, methylation status analysis, automatic base quality calibration, and in built adapter trimming and base quality trimming.

• Resource
• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Full featured, excitation and emission, FRET and ratio-imaging software module which allows users to view and change setup parameters as images are being acquired. It is a standard component of ISee Analytical Imaging Software.

• Resource
• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Portal specializes in visualizing and disseminating single cell data. Allows you to use natural language and faceted search to discover other scientists’ research and share your own findings. Each study includes information on cell types, singular or multiple gene expression, and spatial transcriptomics. Interactive visualizations allow to explore cell clusters and search for related genes.

• Resource
• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Integrated pipeline for tractography-based brain parcellation with automatic processing and massive parallel computing. ATPP offers a CLI version for parcellating multiple brain regions and a GUI version for parcellating a specific brain region. " ATPP completely follows the scientific cultural shift to open science, which aims at making scientific research including journal papers, lab notes, data, and, of course, workflow tools, accessible and transparent to all levels of society. ATPP is publicly accessible in Neuroimaging Informatics Tools and Resources Clearinghouse8 (NITRC) (https://www.nitrc.org/projects/atpp). Its source codes are hosted in GitHub9 (https://github.com/haililihai/ATPP_CLI; https://github.com/haililihai/ATPP_GUI), under the GNU generic purpose license version 310 (GPLv3), and are welcome to download and fork. The Digital Object Identifiers (DOIs) providing a persistent way to make digital data easily and uniquely citable was created from Zenodo11 platform with those GitHub repositories (ATPP CLI v2.0.0, doi: https://doi.org/10.5281/zenodo.239702; ATPP GUI v2.0.0, doi: https://doi.org/10.5281/zenodo.239705). "

• Resource
• RRID-Legacy
• 10 years ago - by Anonymous

Graphical user interface that has been implemented as a 3D Slicer plugin (scripted module). It serves to display a corresponding set of cortical regions from functional connectivity matrix in an explorable 3D scene that represents brain anatomical environment. In addition to grey matter regions, MultiXplore automatically finds and extracts deterministic fiber bundles which exist between selected region(s) and adds them to the 3D environment. This feature helps in generating region-based fiber bundles given a desired whole-brain tractography data.

• Resource
• NIF
• 10 years ago - submitted by Matt Travers

Software for automated optical tracking for freely moving and head-fixed animals. It provides real-time and post-hoc tracking methods.

• RRID-Legacy
• 10 years ago - submitted by Mostafa Nashaat