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http://www.vislab.ucl.ac.uk/cogent_2000.php
MATLAB Toolbox for presenting stimuli and recording responses with precise timing. It also provides additional utilities for the manipulation of sound, keyboard, mouse, joystick, serial port, parallel port, subject responses and physiological monitoring hardware.
Proper citation: Cogent 2000 (RRID:SCR_015672) Copy
https://singularityhub.github.io/sregistry
Web application and registry for institutional deployment of Singularity containers.
Proper citation: Singularity Registry (RRID:SCR_016249) Copy
Research forum portal to address brain status by acquiring comprehensive, multimodal data from healthy humans across the lifespan to characterize brain status, assess its change over time, and associate composite descriptors of brain status. Specifically, the measurements are acquired noninvasively by existing neuroimaging technologies (structural MRI, functional MRI, magnetic resonance spectroscopy, diffusion MRI, and magnetoencephalography); in addition, genetic, cognitive, language, and lifestyle data are acquired. Goals: * Derive the Brain Health Index- An integrative assessment of brain status derived from multimodal measurements of brain structure, function, and chemistry. * Continue acquiring data to construct the first-ever databank on brain, cognitive, language and genetic measurements for healthy people across the lifespan. * Provide a novel and unique dataset by which to: characterize brain status, assess its change over time, and associate it with genetic makeup, cognitive function, and language abilities. * Forecast future brain health and disease based on current measurements and guide physicians towards new interventions and evaluate interventions as they develop. * Extend to siblings and other family members to further assess the genetic influences and inheritability.
Proper citation: HBP: Healthy Brain Project (RRID:SCR_013137) Copy
http://crn2m.univ-mrs.fr/pub/recherche/equipe-t-brue/jullien-nicolas/programmation/amplifx/?lang=fr
A software for managing, testing, and drawing primers. The software can locate primers for target sequences, calculate the quality score, predict amplified fragments and dimers, and create graphic representations of the primers.
Proper citation: AmplifX (RRID:SCR_014465) Copy
http://www.cytoskeleton.com/antibodies
An Antibody supplier
Proper citation: Cytoskeleton (RRID:SCR_013532) Copy
http://www.proteomesoftware.com/products/scaffold/
Software for MS/MS proteomic experiments to compare samples, identify biological relevance, and identify isoforms and protein PTMs. These proteins can be classified based on molecular function or organelle. Users can investigate spectrum details and counts, as well as use high through-put batch processing. Tutorials and a free trial are available through the main site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Scaffold Proteome Software (RRID:SCR_014345) 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
A software provider which supplies researchers with software that enables remote monitoring and management of experiments. TetraScience provides software for managing lab cameras, sensors, electrical switches, adapters, and timers. Users are notified by text or email of lab proceedings and alerts.
Proper citation: TetraScience (RRID:SCR_013977) Copy
Software that analyzes intestinal microbiota data. This environment is composed of a framework to process and analyze microbiota data from raw sequences to taxonomic and functional assignations.
Proper citation: ASaiM (RRID:SCR_015878) Copy
http://ced.co.uk/products/signal
A sweep-based data acquisition and analysis software package. Its uses range from a simple storage oscilloscope to complex applications requiring stimulus generation, data capture, control of external equipment and custom analysis. A built-in script language automates tasks and provides additional tools for custom analyses and applications. Signal includes functions for specific application areas, including dynamic clamp, whole cell and patch clamp electrophysiology, and evoked response including control of magnetic and other stimulus devices. Video tutorials and a demo version of Signal is available on the main page.
Proper citation: Signal (RRID:SCR_014276) Copy
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.
Proper citation: Psykinematix (RRID:SCR_014830) Copy
Site for collection and distribution of clinical data related to genetic analysis of drug abuse phenotypes. Anonymous data on family structure, age, sex, clinical status, and diagnosis, DNA samples and cell line cultures, and data derived from genotyping and other genetic analyses of these clinical data and biomaterials, are distributed to qualified researchers studying genetics of mental disorders and other complex diseases at recognized biomedical research facilities. Phenotypic and Genetic data will be made available to general public on release dates through distribution mechanisms specified on website.
Proper citation: National Institute on Drug Abuse Center for Genetic Studies (RRID:SCR_013061) Copy
https://glimmpse.samplesizeshop.org/#/
Web based software tool that calculates power and sample size for study designs with normally distributed outcomes. Permits power calculations for clinical trials, randomized experiments, and observational studies with clustering, repeated measures, and both, and almost any testable hypothesis. GLIMMPSE Version 3 release back end has been refactored in Python, interface has been simplified, requiring user decisions about only one topic per screen, new menu improves specification of both between-participant and within-participant hypothese, recursive algorithm permits computing covariances for up to ten levels of clustering., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GLIMMPSE (RRID:SCR_016297) Copy
http://www.nitrc.org/projects/nihlungseg/
A segmentation tool for the segmentation of a lung from CT images. The sofware can be run in two modes: fully automatic and semi-automatic with manual seeding by the user. The software also allows the user to perform basic filtering operations and manual correction to the segmentation. The VTK-based rendering implementation, along with option to view in axial, coronal, and sagittal, provides the user with better visualization of the segmented lung.
Proper citation: NIH-CIDI Lung Segmentation Tool (RRID:SCR_014150) Copy
http://erilllab.umbc.edu/research/software/xfitom/
A fully customizable program that uses a graphical user interface to locate transcription factor-binding sites in genomic sequences. xFITOM scans DNA or RNA sequences for putative binding sites as defined by a collection of aligned known sites, a consensus sequence in IUPAC degenerate-base format, or a combination of the two.
Proper citation: xFITOM (RRID:SCR_014445) Copy
https://atgu.mgh.harvard.edu/plinkseq/
An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software)
Proper citation: PLINK/SEQ (RRID:SCR_013193) Copy
https://github.com/csb-toolbox/CSB
Software package as an application framework and a Python class library. It is designed for reading, storing and analyzing biomolecular structures in a variety of formats with rich support for statistical analyses.
Proper citation: Computational Structural Biology Toolbox (RRID:SCR_016065) Copy
https://www.niaid.nih.gov/diseases-conditions/coronaviruses
Information about coronaviruses, including COVID-19. NIAID provides research funding and resources for scientific community to facilitate development of vaccines, therapeutics, and diagnostics for infectious diseases, including those caused by coronaviruses.
Proper citation: NIAID Overview of Coronaviruses (RRID:SCR_018290) Copy
https://github.com/davidaknowles/leafcutter/
Software tool for identifying and quantifying RNA splicing variation. Used to study sample and population variation in intron splicing. Identifies variable intron splicing events from short read RNA-seq data and finds alternative splicing events of high complexity. Used for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs).
Proper citation: LeafCutter (RRID:SCR_017639) Copy
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