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Public university in Florianópolis, the capital city of Santa Catarina in southern Brazil.
Proper citation: Federal University of Santa Catarina; Santa Catarina; Brazil (RRID:SCR_021535) Copy
System includes automated cell counter for trypan blue viability for cell lines and bright field imaging and pattern recognition software to quickly and accurately identify and count individual cells. Cell count, concentration, diameter, and % viability are automatically calculated and reported.
Proper citation: McKinley: Cellometer Auto T4 (RRID:SCR_021656) Copy
https://github.com/flatironinstitute/CaImAn
Open source software tool for scalable calcium imaging data analysis. Used for large scale calcium imaging analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
Proper citation: Calcium Imaging data Analysis (RRID:SCR_021533) Copy
https://hackaday.io/project/181604-mri-stereoscope
Project provides miniature mirror stereoscope system for MRI-scanner. System takes advantage of commonly used display equipment, MRI head coil, and display screen. Miniature Wheatstone stereoscope is used for human neuroimaging.
Proper citation: MRI-stereoscope project (RRID:SCR_021655) Copy
https://spikeforest.flatironinstitute.org/about
Open source and reproducible software suite that benchmarks performance of automated spike sorting algorithms across extensive, curated database of ground truth electrophysiological recordings, displaying results interactively on continuously updating website.
Proper citation: Spike Forest (RRID:SCR_021532) Copy
https://edspace.american.edu/openbehavior/project/openfeeder/
Project related to studying reward and feeding behavior. Provides open source automatic feeding system that can be customized for food types from seeds to pellets.System integrates plexiglass tubes, Arduino Uno, motor driver, and piezo sensor to reliably deliver accurate amounts of food, and can also be built using 3D printed parts.
Proper citation: OpenFeeder (RRID:SCR_021552) Copy
Project related to auditory behavioral task data collection.Provided high throughput operant conditioning in mouse homecage system was developed by University of Maryland,College Park, scientists.Automated system for training up to hundreds of mice in auditory behavioral task features custom Matlab GUI running on desktop which connects to Raspberry Pi to administer auditory stimuli from USB soundcard and collects auditory data as well as licking data from water spout with commercially available capacitive sensors. Parts list and build instructions are readily available from paper and associated GitHub repository.
Proper citation: ToneBox (RRID:SCR_021548) Copy
https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md
Software tool for accurate, fast and versatile mapping/quantification of single cell and single nucleus RNA-seq data. Used for mapping, demultiplexing and quantification for single cell RNA-seq. Comprehensive turnkey solution for quantifying gene expression in single-cell/nucleus RNA-seq data, built into RNA-seq aligner STAR.
Proper citation: STARsolo (RRID:SCR_021542) Copy
https://circexplorer2.readthedocs.io/en/latest/
Software package for comprehensive and integrative circular RNA analysis. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. Used to annotate circRNAs, de novo assemble novel circular RNA transcripts and chracterize various of alternative (back-)splicing events of circular RNAs.
Proper citation: CIRCexplorer2 (RRID:SCR_021664) Copy
https://github.com/ratcave/ratcave
Software 3D graphics python package for cognitive psychology experiments. Open source, cross platform Python library that adds 3D stimulus support to all OpenGL-based 2D Python stimulus libraries. These libraries include VisionEgg, Psychopy, Pyglet, and PyGam.
Proper citation: Ratcave (RRID:SCR_021599) Copy
https://sourcemd.toolforge.org/index_old.php
Web tool as prototype service to automatically generate Wikidata items using metadata from scholarly publications. Citation lookup tool in Wikipedia platform. Takes persistent identifier for scholarly article and processes it by importing bibliographic metadata into Wikidata items. In August 2018, it was merged with ORCIDator into single tool that allows for fully automated batch processing based on ISBN-13, DOI, ORCID iD, PubMed ID, PMCID identifiers.
Proper citation: SourceMD (RRID:SCR_021633) Copy
https://github.com/mne-tools/mne-cpp
Software tool for real time processing of electrophysiological data.
Proper citation: MNE Scan (RRID:SCR_021530) Copy
https://services.healthtech.dtu.dk/service.php?NetMHC-4.0
Web tool for binding prediction of peptides to MHC class I molecules. The newest version NetMHC- 4.0 is used for prediction of peptide MHC class I binding affinity using gapped sequence alignment that allows insertions and deletions in alignment.
Proper citation: NetMHC (RRID:SCR_021651) Copy
https://cumulus.readthedocs.io/en/stable
Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data.
Proper citation: Cumulus (RRID:SCR_021644) Copy
https://pypi.org/project/jcvi/
Software tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.
Proper citation: jcvi (RRID:SCR_021641) Copy
https://hpap.pmacs.upenn.edu/about-pancdb
Portal to make all Human Pancreas Analysis Program data available to anyone in research community and to interact with and connect scientific community. Stores clinical, molecular, cellular, immunology, imaging, and pathology data from pancreatic tissue and cell samples from organ donors with and without type 1 or type 2 diabetes.
Proper citation: PANC-DB (RRID:SCR_021860) Copy
Software tool as biophysical simulation model for livestock systems. It has flexible interface for setting up and running simulations with extensive graphical and data output.
Proper citation: Sustainable Grazing System Pasture Model (RRID:SCR_021854) Copy
https://www.research.va.gov/mvp/
National research program to learn how genes, lifestyle, and military exposures affect health and illness.
Proper citation: Million Veteran Program (RRID:SCR_021731) Copy
https://pypi.org/project/fuzzywuzzy/
Software pacakge that uses Levenshtein Distance to calculate differences between sequences for string matching.
Proper citation: FuzzyWuzzy (RRID:SCR_021699) Copy
https://pdf.medicalexpo.com/pdf/ge-healthcare-life-sciences/amersham-imager-600/80554-135352.html
Amersham Imager 600 is CCD camera system that produces digitial images of samples in gels or membranes in three different modes: chemiluminescence, colorimetric and fluorescent image capture. Provides imaging system to capture and analyze protein and DNA sample gels and membranes in high resolution.
Proper citation: GE: Amersham Imager 600 (RRID:SCR_021853) Copy
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