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https://mass-spec.stanford.edu/instruments

System includes Thermo Orbitrap Fusion Tribrid mass spectrometer and Waters M-Class Acquity nanoUPLC. This platform features sequential acquisition capabilities and multiple fragmentation types, enabling complex, in depth proteomic experiments.

Proper citation: Thermo Fisher: Orbitrap Fusion nanoLC/MS system (RRID:SCR_018702) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://mygene.info/

Web service for querying or retrieving gene annotation data.

Proper citation: MyGene.info (RRID:SCR_018660) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.thermofisher.com/us/en/home/life-science/gene-expression-analysis-genotyping/laser-capture-microdissection/arcturus-laser-capture-microdissection-lcm-instrument.html

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   

•   Source: SciCrunch Registry

https://www.labx.com/product/thermo-scientific-cytomat-6001-and-6001-c4-automated-wide-range-incubator

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   

•   Source: SciCrunch Registry

http://www.mediacy.com/imagepro

Software platform to perform image processing, analysis, and data reporting for microscope-based research and quality inspection.

Proper citation: Image Pro (RRID:SCR_016497) Copy   

•   Source: SciCrunch Registry

https://www.humancellatlas.org

Software tool as a catalog of comprehensive reference of human cells based on their stable properties, transient features, locations and abundances. Map to show the relationships among its elements. Open data international collaborative project involving diverse scientific communities to provide a framework for understanding cellular dysregulation in human disease.

Proper citation: Human Cell Atlas (RRID:SCR_016530) Copy   

•   Source: SciCrunch Registry

https://ihg.helmholtz-muenchen.de/cgi-bin/hw/hwa1.pl

Software tool for performing tests for deviation from Hardy-Weinberg equilibrium and tests for association. Used in population-based genetic association studies to identify susceptibility genes for complex diseases.

Proper citation: Tests for deviation from Hardy-Weinberg equilibrium (RRID:SCR_016496) Copy   

•   Source: SciCrunch Registry

http://www.broadcvdi.org/

Platform for analysis of the genetics of cardiovascular disease.Used for searching and analysis of human genetic information linked to myocardial infarction, atrial fibrillation and related traits while protecting the integrity and confidentiality of the data.

Proper citation: Cardiovascular Disease Knowledge Portal (RRID:SCR_016536) Copy   

•   Source: SciCrunch Registry

http://www.ajnr.org/content/25/6/945.long

Software tool written in Java that reads DICOM-files from Dynamic Susceptibility Contrast (DSC) Magnetic Resonance Imaging (MRI) and calculates standardized Time-to-Peak (stdTTP) parameter. Maps from this calculation are provided as RGB- and Monochrom2-Dicom files and may be sent to a PACS automatically. Works on windows® platforms on PC’s (Intel® CPUs from Pentium I up to the I7-octo cores) together with the Philips 1.5T ACS-NT up to the Ingenia Systems (n> 20.000), with the Philips 3.0T Systems (n ~ 1.000), the Siemens 1.5T Avanto (SQ-machine) (n> 10.000) and the Siemens 3.0T TimTrio (n ~ 200) so far. Works with uncompressed DICOM-standard files.

Proper citation: jPerfusionModule (RRID:SCR_016534) Copy   

•   Source: SciCrunch Registry

http://www.cyto.purdue.edu/cdroms/micro1/7_spon/vaytek/voxblast.htm

Software application for science and medicine which offers 3-D Measurement, 3-D Volume Visualization, and 3-D Rendering for any 3-D data. It accepts stacks of registered 2-D images and creates 3-D projections from any viewpoint.

Proper citation: VoxBlast (RRID:SCR_016491) Copy   

•   Source: SciCrunch Registry

https://doi.org/10.1016/j.neuroimage.2018.07.046

Software package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions.

Proper citation: nonparametricGGC_toolbox (RRID:SCR_016539) Copy   

•   Source: SciCrunch Registry

https://github.com/INM-6/NetworkUnit

Library of a test driven framework for formally validating scientific models against experimental data used for validation testing of spiking neuron network simulations on the network activity level.

Proper citation: NetworkUnit (RRID:SCR_016543) Copy   

•   Source: SciCrunch Registry

https://github.com/mpi2/HARP

Software as a cross platform application for automating the processing of μCT and OPT image data. Used for standarization of embryo images prior to export to the PhenoDCC. Capable of processing other image modalities and specimens. Can be download as a stand alone release.

Proper citation: HARP (RRID:SCR_016546) Copy   

•   Source: SciCrunch Registry