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https://github.com/lmb-embrapa/machado
Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code.
Proper citation: Machado (RRID:SCR_018428) Copy
Open source virtual screening software for computational drug discovery with intuitive user interface. Runs on operating systems Linux, Windows, and Mac OS. Used to screen libraries of compounds against potential drug targets.
Proper citation: PyRx (RRID:SCR_018548) Copy
https://prosa.services.came.sbg.ac.at/prosa.php
Web service is extension of classic ProSA program used for refinement and validation of experimental protein structures and in structure prediction and modeling.
Proper citation: ProSA-web (RRID:SCR_018540) Copy
https://github.com/quest-bih/barzooka
Software automated screening tool that detects bar graphs of continuous data in preprints submitted to bioRxiv. Used for detection of bar graphs for continuous data in BioRxiv preprints.
Proper citation: Barzooka (RRID:SCR_018508) Copy
https://github.com/OHDSI/CohortMethod
Software R package for performing new user cohort studies in observational database in OMOP Common Data Model.
Proper citation: CohortMethod (RRID:SCR_018511) Copy
https://www.mpbio.com/fastprep-24-5g-instrument
Sample disruption instrument that can homogenize, grind, or lyse biological samples. Samples are added to individual lysing matrix tubes and shaken in tridimensional motion.
Proper citation: MP Biochemicals: FastPrep24 Sample Preparation (RRID:SCR_018599) Copy
https://mass-spec.stanford.edu/instruments
Advanced benchtop tandem quadrupole mass spectrometer which expands scope of ultimate sensitivity analysis. Fatures probe design which allows users much easier maintenance, optimization and improved reproducibility between operators. Method transfer onto Xevo TQ-XS is made simple by Xtended Dynamic Range detector which allows six orders of linear dynamic range. Wider compound coverage without changing ionization technique is delivered by the revolutionary UniSpray source option.
Proper citation: Waters: Xevo TQ-XS mass spectrometer (RRID:SCR_018510) Copy
http://covidnlp.tavlab.iiitd.edu.in/
Web Application for distilling systemic implications of COVID-19 pandemic with Natural Language Processing.
Proper citation: CovidNLP (RRID:SCR_018513) Copy
https://www.thelabworldgroup.com/mettler-toledo-pb303-precision-balance
Miligram balance that is used for weighing, tarring, percent weighing, and dynamic weighing for unstable samples. Has maximum capacity of 310 grams. Lab balance utilizes mono block weighing technology with permanent shock protection and built in overload protection as well as automatic calibration.
Proper citation: Mettler: PB303-S Milligram Balance (RRID:SCR_018592) Copy
Invitrogen benchtop automated cell counter. Can perform cell counts, viability calculations, hemocytometry, fluorescent protein expression, and measure fluorescence capabilities. There are also reusable slides, fluorescence capabilities, and brightfield fluorescence channels.
Proper citation: Thermo Fisher: Life Technologies: Countess Automated Cell Counter (RRID:SCR_018591) Copy
http://shiny.ieis.tue.nl/sprite/
Web app to generate possible distributions of data matching given mean, SD, sample size, and range. Used for recovering data from summary statistics. Implementation of SPRITE in R programming environment.
Proper citation: rSPRITE (RRID:SCR_018524) Copy
https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
Web tool for conserved domains searching within protein or coding nucleotide sequence.
Proper citation: Conserved Domains Search (RRID:SCR_018729) Copy
https://www.microscopyu.com/museum/model-smz1500-stereomicroscope
SMZ1500 stereoscopic zoom microscope is system with apochromatic objectives, zoom ratio of 15 to 1, range of magnifications from 0.75x to 11.25x for total magnifying capability of 3.75x up to 540x, and is best for in depth imaging.Zoom knob allows to zoom from 1x to 11x at 1x-intervals without interrupting observations. Other facets include high eyepoint eyepieces with built-in diopter adjustments, wide field of view, and built-in aperture diaphragm for achieving optimal depth of focus and improved photomicrography.Provides options of either low eye-level viewing tube or tilting eyepiece tube, with or without eye-level risers. Three different diascopic stands with built-in power supplies may also be utilized with instrument, or standard stand that features low profile for increased clearance.
Proper citation: Nikon: SMZ1500 Zoom Stereoscope (RRID:SCR_018605) Copy
https://github.com/yanzhanglab/Graph2GO
Software tool as graph based representation learning method for protein function prediction. Multi modal graph based representation learning model that can integrate heterogeneous information including multiple types of interaction networks including sequence similarity network and protein-protein interaction network, and protein features including amino acid sequence, sub cellular location and protein domains, to predict protein functions on Gene Ontology.
Proper citation: Graph2GO (RRID:SCR_018726) Copy
https://www.gmi-inc.com/product/packard-cobra-gamma-counter-series/
Gamma counter available in single, five, or ten detector configurations. Can count RIA tubes, 16x100mm and variety of smaller micro tubes using available adapter.This instrument has dot Matrix Printer, tube racks, and protocol ID tags.Single detector model is available in 2 inch or 3 inch crystal configurations for research grade capabilities.
Proper citation: Packard: Cobra 5000 Gamma Counter (RRID:SCR_018609) Copy
https://mass-spec.stanford.edu/instruments
Shimadzu 8030 triple quadrupole mass spectrometer used for targeted quantitation applications. Listed by Stanford University Mass Spectrometry Vincent Coates Foundation Instruments.
Proper citation: Stanford Shimadzu 8030 LC/MS mass spectrometer (RRID:SCR_018699) Copy
Dual channel fluorimeter for fluorescence measurements when calibrated with known concentration to measure compounds at low concentration with low assay volume.
Proper citation: Promega: TBS-380 Fluorimeter (RRID:SCR_018615) Copy
Microplate luminometer that features two optional injectors and reads both glow- and flash-luminescent reactions in 96-well plates. The sensitivity and range enable a wide range of luminescent assays, including Promega bioluminescent reporter, cell-based and biochemical assays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Promega: GloMax 96 Microplate Luminometer (RRID:SCR_018614) Copy
http://www.pirx.com/iMol/index.shtml
Software molecular visualization application for Mac OS X operating system. Tool for chemists and molecular biologists used for handling small and large molecules, loading multiple molecules, moving and rotating them independently, or displaying molecular dynamics trajectory. Allows loading molecules using file formats: PDB, XYZ, MOL2, HIN, CAR, ALC, BIO.
Proper citation: iMol (RRID:SCR_018735) Copy
https://www.biosimulations.org/
Web tool for sharing and re-using biomodels, simulations, and visualizations of simulations results. Supports variety of modeling frameworks including kinetic, constraint based, and logical modeling, model formats including BNGL, CellML, SBML, and simulation tools including COPASI, libRoadRunner/tellurium, NFSim, VCell.
Proper citation: BioSimulations (RRID:SCR_018733) Copy
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