SciCrunch

Transgenic Huntington's Disease Monkey Resources

Center for resources to facilitate basic and preclinical applications of the transgenic Huntington's disease (HD) monkey model to advance scientific knowledge and the discovery of a cure for HD. Their resources include longitudinal biomaterials and MRI data, postmortem biomaterials, and research proposal assistance.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

DynaMine

An NMR based method for protein folding prediction. Users can enter a UniProt identifier, FASTA sequences, or upload a file containing FASTA sequences and results are returned., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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RRID-Legacy
10 years ago - submitted by Anita Bandrowski

Protein Prospector

A package of over twenty mass spectrometry-based tools primarily geared toward proteomic data analysis and database mining. It can be run from the command line, but is primarily used through a web browser, and there is a public website that allows anyone to use the software without local installation. Tandem mass spectrometry analysis tools are used for database searching and identification of peptides, including post-translationally modified peptides and cross-linked peptides. Support for isotope and label-free quantification from this type of data is provided. MS-Viewer software allows sharing and displaying of annotated spectra from many different tandem mass spectrometry data analysis packages. Other tools include software for analyzing peptide mass fingerprinting data (MS-Fit); prediction of theoretical fragmentation of peptides (MS-Product); theoretical chemical or enzymatic digestion of proteins (MS-Digest); and theoretical modeling of the isotope distribution of any chemical, including peptides (MS-Isotope). Searches using amino acid sequence can be used to identify homologous peptides in a database (MS-Pattern); the use of the combination of amino acid sequence and masses can be used for homologous peptide and protein identification using MS-Homology. Tandem mass spectrometry peak list files can be filtered for the presence of certain peaks or neutral losses using MS-Filter. Given a list of proteins, MS-Bridge can report all potential cross-linked peptide combinations of a specified mass. Given a precursor peptide mass and information about known amino acid presence, absence, or modifications, MS-Comp can report all amino acid combinations that could lead to the observed mass.

Resource
RRID-Legacy
10 years ago - by Anonymous

BioBlend Library

A Python library which provides Python access to and interaction with Galaxy's API and CloudMan. The library allows users to create a CloudMan compute cluster via an API and directly from a local machine, reconnect to an existing CloudMan instance and manipulate it, and interact with Galaxy via a straightforward API and an object-oriented API. The library itself can be used with either service irrespective of the other.

Resource
RRID-Legacy
10 years ago - by Anonymous

ELIXIR Tools and Data Services Registry

Elixir Interoperability Platform to help people and machines to discover, access, integrate and analyse biological data. Encourages life science community to adopt standardized file formats, metadata, vocabularies and identifiers and works internationally to achieve its goals. Bioinformatics resource registry that provides scientific and technical information about analytical tools and data services for bioinformatics. Gateway to databases and tools for life science data analysis.Provides comprehensive and up-to-date catalogue of resources that are interactive and downloadable, and that offer programmatic access. The registry also allows the community to upload their own resources to the registry following a simple log in procedure.

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RRID-Legacy
10 years ago - by Anonymous

cBioPortal

A portal that provides visualization, analysis and download of large-scale cancer genomics data sets.

SciCrunch
10 years ago - submitted by Anita Bandrowski

Aging Dementia and Traumatic Brain Injury Study

The Aging, Dementia and Traumatic Brain Injury Study is a detailed neuropathologic, molecular and transcriptomic characterization of brains of control and TBI exposure cases from a unique aged population-based cohort from the Adult Changes in Thought (ACT) study. The study contains six data sets: histology and immunohistochemistry, in situ hybridization, rna-seq, protein quantification by luminex, isoprostane quantification, and specimen metadata.

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Aging
10 years ago - by Anonymous

UCSF Brain and Spinal Injury Center (UCSF-BASIC)

A center that conducts basic science and clinical research concerning spinal cord injury located at both the University of California San Francisco and the Zuckerberg San Francisco General Hospital.

odc-sci
10 years ago - submitted by Adam Ferguson

CRAIG H. NEILSEN FOUNDATION

A non-profit organization that awards grants to a broad spectrum of charities, including those that benefit spinal cord injury efforts. The Foundation is primarily dedicated to funding extensive research, education and quality of life programs for improving the lives of people affected by spinal cord injury.

odc-sci
10 years ago - submitted by Maryann Martone

Olympus cellSens Software

Software suite for image acquisition and analysis. The software can be paired with high-quality cameras to maximize output quality and export it for sharing and research applications.

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SciCrunch
10 years ago - submitted by Gabrielle Pine

dotSlide Software

An imaging system that can be used in lieu of conventional light microscopy. The specimen, rather than being viewed through the eyepiece of the microscope, is displayed a monitor after the system has scanned it at the desired resolution. This is done by a series of scans of single images acquired through the scanning process being automatically stitched together to make the ultimate seamless overview image through the "virtual slide". The digital images can be saved to a web-based database so that it can be accessible for online conferences.

Resource
SciCrunch
10 years ago - submitted by Gabrielle Pine

FluorChem Q Imager

A software used for quantitative Western blot imaging and analysis. This software is compatible with several dyes and kits, providing extra flexibility for application. This software is designed to be able to look at multiple proteins simultaneously on a single assay. This software is sensitive enough to distinguish co-migrating proteins, such as phosphorylated and unphosphorylated isoforms.

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SciCrunch
10 years ago - submitted by Gabrielle Pine

Pixel-Wise Modeling Tool

A software to apply modeling techniques directly to individual pixels within an image and create a parametric map from it. The resulting outcomes show the values within the model parameter in each image pixel. This is used to make quantitative tissue properties easier to visualize and compare with information from other sources. Furthermore, the quantitative maps can then be statistically analyzed within the software using a step-by step method. This tool is designed to be used with the PKIN tool.

Resource
SciCrunch
10 years ago - submitted by Gabrielle Pine

ASIPro

An image analysis software.

SciCrunch
10 years ago - submitted by Gabrielle Pine

AFQ: Automated Fiber Quatification

A framework for generating Tract Profiles of tissue properties for major fiber tracts in healthy and diseased brains. Online documentation can be found at: https://github.com/yeatmanlab/AFQ/wiki. AFQ has been tested for MATLAB r2009b through MATLAB r2014b. It requires functions from the MATLAB stats toolbox, vistasoft and SPM.

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RRID-Legacy
10 years ago - submitted by Maryann Martone

Preclinical Data Forum Network

A forum for preclinical data sharing and interpretation to enhance its utility for clinical research and development. The forum allows researchers to communicate and collaborate on modern preclinical issues and data sharing.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

AbMiner

A tool that allows users to search for appropriate, commercially available antibodies for research purposes, and to match each antibody to its respective genomic identifiers. The antibodies are screened by Western blot and the results are listed on AbMiner. AbMiner also includes the diluitons used and vendor information for all antibodies. Users can conduct general or advanced searches and browse antibodies by gene.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

DataJoint

MATLAB and Python 3 high-level programming interface for MySQL databases to support data processing chains in science labs. Specifically designed to provide robust and intuitive data model for scientific data processing chains.Used for scientific data pipelines and workflow management.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

MobiDB

A database of protein disorder and mobility annotations. The database features three levels of annotation: manually curated data (which are extracted from the DisProt database), indirect data, and predicted data. Additional annotations are included from external sources, including UniProt, Pfam, PDB, and STRING.

Resource
SciCrunch
10 years ago - submitted by Kristen Jensen

NIRSPORT

A commercial cap product that records fNIR signals from the participant. NIRSport integrates for concurrent measurements with EEG, fMRI, eye-tracking, cochlear implants, TMS, tDCS, EMG, pulse oximetry, and other modalities for concurrent measurements. Researchers can conduct tandem studies with two separate systems synchronized to operate simultaneously.

RRID-Legacy
10 years ago - submitted by Anita Bandrowski

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