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https://www.olympus-lifescience.com/en/downloads/detail-iframe/?0[downloads][id]=847249651

Software for image processing. Reads data captured by FV1200/FV1000/FV500/FV300 microscopes. Images saved with FV file format (OIF, OIB, FV Multi-Tiff) can be read.

Proper citation: Olympus FV10-ASW Viewer (RRID:SCR_024433) Copy   

•   Source: SciCrunch Registry

https://xdd.wisc.edu/

Software digital library and cyberinfrastructure facilitating discovery and utilization of data and knowledge in published documents.

Proper citation: XDD (RRID:SCR_024434) Copy   

•   Source: SciCrunch Registry

http://mpds.neist.res.in:8085/

Galaxy based disease specific web portal for drug discovery research of COVID-19. Open access disease specific drug discovery portal.

Proper citation: Molecular Property Diagnostic Suite Covid-19 (RRID:SCR_024545) Copy   

•   Source: SciCrunch Registry

https://prosite.expasy.org/scanprosite/

Web tool for detecting PROSITE signature matches in protein sequences.

Proper citation: ScanProsite (RRID:SCR_024425) Copy   

•   Source: SciCrunch Registry

https://github.com/STOmics/BatchEval

Software tool for evaluating batch effects in data integration. Tool to improve accuracy and reliability of experimental results. Used to evaluate batch effect of dataset integration and output comprehensive report.

Proper citation: BatchEval (RRID:SCR_024546) Copy   

•   Source: SciCrunch Registry

https://science.bostongene.com/kassandra/

Software bulk RNA-seq cellular deconvolution tool. Used for analysis of healthy tissue and tumor biopsies. Based on RNA-seq NGS data of biological sample, Kassandra predicts cellular composition including stromal and immune elements by analyzing gene expression.

Proper citation: Kassandra (RRID:SCR_024548) Copy   

•   Source: SciCrunch Registry

https://github.com/EwellNeuroLab?tab=repositories

Low cost platform for multianimal chronic Local Field Potential video monitoring with Graphical User Interface for seizure detection and behavioral scoring. Enables chronic monitoring of several animals simultaneously, synchronizes bilateral local field potential and video streams in real time, and parses recorded data into manageable file sizes. Hardware solution leverages Intan and Open Ephys acquisition systems and software solution is implemented in Bonsai. Data are synchronized and parsed in Bonsai, allowing for flexibility and scalability of up to 128 channels per animal. The use of Intan adapter board for LFP video recordings allows compatibility with large variety of recording devices. Custom made electrodes and cables were components for the chronic LFP recordings. Used as acquisition system for long term video neurophysiology recordings.

Proper citation: LFP Monitoring (RRID:SCR_024428) Copy   

•   Source: SciCrunch Registry

https://de.caeonline.com/buy/lab-equipment-and-accessories/tecan-infinite-m200/9076657

TECAN Infinite M200 is laboratory device and accessory for multiplex luminescence and fluorescence applications. Device features automated robotic arm for dispensing samples or reagents onto cuvettes or microplates, as well as range of high speed and throughput sample injection capabilities. Infinite M200 is integrated with TECAN's proven laser-based multi-channel detection technology, to measure multiple biological responses simultaneously. System features graphical user interface to configure instrument for single or multiple sample injection processes. Accommodates range of different cuvette and microplate vessels, suitable for both 1.5ml and 0.2ml tubes as well as plates up to 384 wells. Multichannel optical detector can detect up to four different signals in parallel, with wide range of detection wavelengths. Designed for high-throughput applications with sensitive fluorescence and luminescence. Features automated sample injection unit that enables hands-free operation of 96 or 1,536 up to eight-channel multipoint experiments, providing maximum flexibility. Comes with range of software, including intuitive data collection and analysis interface. Designed with automated calibration settings, providing reliable, accurate and reproducible results.

Proper citation: Tecan: Infinite M200 (RRID:SCR_024560) Copy   

•   Source: SciCrunch Registry

https://www.tecan.com/customer-news/tecan-granted-patent-for-revolutionary-nanoquant-plate-2117

Device designed for simultaneous measurement of multiple low volume samples. Consists of 16 precision manufactured quartz optics in user friendly format, offering precise, straightforward absorbance and fluorescence based measurements from sample volumes as low as 2 µl. Combined with Tecan’s Infinite series readers – the Infinite 200 PRO, Infinite F500 and Infinite M1000 PRO – the NanoQuant Plate provides solution for DNA or RNA quantification, allowing detection of concentrations down to 1 ng/µl for wide variety of applications.

Proper citation: Tecan: NanoQuantPlate (RRID:SCR_024561) Copy   

•   Source: SciCrunch Registry

https://www.leica-microsystems.com/products/confocal-microscopes/p/leica-tcs-sp8-dls/

Digital LightSheet full confocal with gentle single plane illumination microscope for easy light sheet imaging. TwinFlect mirror deflects illuminating light sheet at 90° angle, which allows integration of illumination and detection beam path into vertical axis of every inverted, Leica TCS SP8 confocal.

Proper citation: Leica: TCS SP8 DLS LightSheet microscope (RRID:SCR_024563) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/DrugSim2DR/

Software R package to predict drug functional similarity to drug repurposing.

Proper citation: DrugSim2DR (RRID:SCR_024564) Copy   

•   Source: SciCrunch Registry

https://ganjoho.jp/public/index.html

Portal provides information on Cancer Statistics in Japan. Official website operated by National Cancer Center for cancer information.

Proper citation: Cancer Information Service (RRID:SCR_024445) Copy   

•   Source: SciCrunch Registry

https://www.sfwmd.gov/our-work/cerp-project-planning

Platform provides framework for restoring, protecting and preserving the greater Everglades ecosystem. The plan is partnership between State of Florida and federal government.

Proper citation: Comprehensive Everglades Restoration Plan (RRID:SCR_024557) Copy   

•   Source: SciCrunch Registry

https://diagnostics.roche.com/ch/de/products/instruments/cobas-c-311-ins-2043.html

Autoanalyzer is standalone system that provides consolidated testing from range of clinical chemistry applications. Allows determination of sodium, potassium and chloride in serum, plasma and urine using ion selective electrodes. Measurement of HbA1c levels in whole blood can also be performed.

Proper citation: Roche: Cobas C311 (RRID:SCR_024559) Copy   

•   Source: SciCrunch Registry

https://github.com/torognes/vsearch

Software versatile open source tool for metagenomics. Used for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data.

Proper citation: VSEARCH (RRID:SCR_024494) Copy   

•   Source: SciCrunch Registry

https://www.tomocube.com/product/tomostudio/

Software tool for acquisition and analysis, visualization and analysis of RI tomograms. Used to color code the image according to the refractive index and identify various types of quantitative data.

Proper citation: TomoStudio (RRID:SCR_024498) Copy   

•   Source: SciCrunch Registry

https://github.com/howisonlab/softcite-dataset

Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale.

Proper citation: SoftCite (RRID:SCR_024411) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/spliceai/

Software package annotates genetic variants with their predicted effect on splicing. Used to identify splice variants.

Proper citation: Splice AI (RRID:SCR_024532) Copy   

•   Source: SciCrunch Registry

https://www.photometrics.com/products/ocular

Scientific image acquisition software. Software allows color and monochrome cameras to capture high quality images and videos from their microscope or lens system.

Proper citation: Ocular (RRID:SCR_024490) Copy   

•   Source: SciCrunch Registry

https://github.com/SharonLutz/Umediation

Software R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for mediator exposure interaction on the outcome. Enables to simulate unmeasured confounding in mediation analysis in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding.

Proper citation: Umediation (RRID:SCR_024492) Copy   

•   Source: SciCrunch Registry