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https://mass-spec.stanford.edu/instruments
LTQ XL ion trap mass spectrometer with Agilent 1100 HPLC system for metabolite identification, stability testing, degradation products, and high abundance quantitation.
Proper citation: Thermo Fisher: LTQ XL LC/MS system (RRID:SCR_018701) Copy
https://github.com/wangdingkang/DiscreteMorse
Discrete Morse based pipeline for neuron tracing on tracer injection and single neuron data sets. Automatically generates set of trees summarization of given neuron imaging data. Used to extract tree skeletons of individual neurons from volumetric brain image data, and to summarize collections of neurons labelled by tracer injections.
Proper citation: Discrete Morse (RRID:SCR_018662) Copy
https://bioconductor.org/packages/minet/
Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data.
Proper citation: minet (RRID:SCR_018661) Copy
Web service for querying or retrieving gene annotation data.
Proper citation: MyGene.info (RRID:SCR_018660) 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
http://labx.com/product/stratagene-stratalinker-1800
UV crosslinker designed to crosslink DNA or RNA to nylon, nitrocellulose, or nylon reinforced nitrocellulose membranes in 25 to 50 seconds. It is equipped with internal photodetector to compensate for aging ultraviolet bulbs.
Proper citation: Stratagene: 1800 UV Crosslinker (RRID:SCR_018631) Copy
https://www.labx.com/product/sciex-4000-qtrap-
Hybrid triple quadrupole linear ion trap mass spectrometer for drug discovery and development, metabolite identification, contaminant testing, proteomic applications, post translationally modified proteins discovery, protein identification, and biomarker validation.
Proper citation: SCIEX: 4000 QTRAP Mass Spectrometer (RRID:SCR_018630) Copy
https://www.tainstruments.com/3200-system/
Mechanical testing apparatus with 225 N or 450 N maximum force and range of static to 300 Hz frequency response. Tests include torsion testing, creep under dynamic loading, special environment hot cold chambers, biomedical research, and engineered materials test applications..
Proper citation: TA Instruments: Electroforce 3200 Mechanical Testing Apparatus (RRID:SCR_018637) Copy
https://diagnostics.roche.com/global/en/products/instruments/discovery-xt-research-platform.html
Immunohistochemistry processor that can be used for immunohistochemistry and in situ hybridization slide preparation and processing.
Proper citation: Roche: Ventana Discovery XT Immunohistochemistry Processor (RRID:SCR_018643) Copy
Laser capture microdissection system that includes infrared lasers. It can be used for laser capture microdissection LCM, ultraviolet UV laser cutting, sanger sequencing, next generation sequencing, and quantitative PCR.
Proper citation: Thermo Fisher: Arcturus Cellect Laser Capture Microdissection System (RRID:SCR_018641) Copy
Automated wide range incubator used to minimize plate movement, receive samples, store plates, and track plates.Temperature range is from 10 to 50 degrees Celsius with humidity level of up to 95 rH.
Proper citation: Thermo Fisher: Cytomat 6001 Automated Wide Range Incubator (RRID:SCR_018646) 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://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.leica-microsystems.com/products/confocal-microscopes/p/dive/
Multiphoton confocal microscope with spectrally tunable detection. Equipped with 4Tune, tunable, non descanned detection unit.
Proper citation: Leica: SP8 DIVE multi photon microscope (RRID:SCR_018852) 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
https://cistrome.shinyapps.io/timer/
Web server for comprehensive analysis of tumor infiltrating immune cells. Web tool for systematical analysis of immune infiltrates across diverse cancer types. Allows users to input function specific parameters, with resulting figures dynamically displayed to access tumor immunological, clinical, and genomic features.
Proper citation: TIMER (RRID:SCR_018737) Copy
https://imspectordocs.readthedocs.io/en/latest/intro.html
Software tool for real time analysis and data visualization. Software system for experimental control and quantitative data analysis in microscopy and spectroscopy.Integration of data processing and acquisition allows real time analysis and visualization of experimental results.
Proper citation: Imspector (RRID:SCR_018863) Copy
Open source 3D printing software which supports multi part printing and has slicers.
Proper citation: Repetier Host (RRID:SCR_018901) Copy
https://www.sutter.com/MICROSCOPES/mom.html
Two photon microscope capable of imaging deep within living specimens when combined with Ti:Sapphire Laser. Provides 3D objective movement and rotation allowing specimen to remain stationary.
Proper citation: Sutter: Movable Objective Microscope (RRID:SCR_018860) Copy
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