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https://github.com/viromelab/tracespipe
Software tool as hybrid pipeline for reconstruction and analysis of viral and host genomes at multi-organ level. Pipeline for identification, assembly, and analysis of viral genomes, that combine DNA sequence data from multiple organs. Cooperation between compression based prediction, sequence alignment, and de-novo assembly. Provides transmission and storage of data.
Proper citation: TRACESPipe (RRID:SCR_018831) Copy
https://github.com/TMinchington/sass
Software tool as custom analysis code combining single-cell traces and spot detection from live imaging movies and using Imaris output.
Proper citation: Simple Assignment of Spots to Surfaces (RRID:SCR_018797) Copy
http://www.harvardapparatus.com/media/harvard/pdf/Inspira_557058_9.pdf
Volume Controlled Ventilator delivers desired tidal volume to animal by precisely controlling stroke of piston. Since actual stroke length may be modified for given stroke, sigh breaths are supported.
Proper citation: Harvard Apparatus: Inspira Advanced Safety Ventilator, Volume Controlled (RRID:SCR_018834) Copy
http://m-cdn.adinstruments.com/owners-guides/PowerLab%20SP%20Series%20OG.pdf
Integrated system of hardware and software designed to record, display, and analyse experimental data. Consists of PowerLab recording unit and possible ancillary devices, software that run on computer to which PowerLab is connected. PowerLab/4SP has four inputs for recording external signals.
Proper citation: ADInstruments: PowerLab/4SP acquisition system (RRID:SCR_018833) Copy
https://millar.com/Clinical/Control-Units-and-Accessories/
Pressure Control Unit is two channel, patient isolated, line powered bridge amplifier for connecting one or two single sensor Millar Mikro-Tip catheters to clinical patient monitor or standalone data acquisition system. Provides built in ridge excitation eliminating need for separate bridge amplifier. Analog output signal level of 1V/100 mmHg is compatible with most pressure monitors and data acquisition systems. In line power supply adapts automatically to line voltages from 100 to 240 volts AC.
Proper citation: Millar: PCU-2000 Pressure Control Unit with Patient Isolation (RRID:SCR_018840) Copy
https://science-products.com/en/shop/491/23/data-aquisition/interfaces/micro1401-3
Unit records waveform data, digital event and marker information and can simultaneously generate waveform and digital outputs in real time for multi tasking experimental control.
Proper citation: CED: Micro1401-4 data acquisition unit (RRID:SCR_018846) Copy
Web tool as protein structure prediction service. Provides automated structure prediction and analysis tools that can be used to infer protein structural information from genomic data. Produces model for entire protein sequence in presence or absence of sequence homology to protein of known structure.
Proper citation: Robetta (RRID:SCR_018805) Copy
http://protein.ict.ac.cn/FALCON/
Web tool as high throughput protein structure prediction service. High throughput server for protein structure prediction.
Proper citation: FALCON (RRID:SCR_018804) Copy
https://somapp.ucdmc.ucdavis.edu/pharmacology/bers/maxchelator/webmaxc/webmaxcE.htm
Web tool for computing metal ion concentrations in physiological solutions. Used for determining free metal concentration in presence of chelators or total metal given desired free concentration.
Proper citation: WEBMAXC EXTENDED (RRID:SCR_018807) Copy
https://rippleneuro.com/ripple-products/grapevine-processors/
Interface processor as 512 channel stimulation and recording electrophysiology tool. Designed to be safe for human subjects.
Proper citation: Ripple Neuro: Grapevine Neural Interface Processor (RRID:SCR_018897) Copy
Web prediction tool for molecular binding in simulation of immune system. Agent based simulator of immune response that represents pathogens, as well as lymphocytes receptors, by means of their amino acid sequences and makes use of bioinformatics methods for T and B cell epitope prediction.Calculates immune response to generic pathogenic secondary structure. Allows users to submit antigen protein sequence and specify schedule of its injection as well as host haplotype.
Proper citation: C-IMMSIM (RRID:SCR_018775) Copy
Software experimental data table management system to make research data accessible and available for reuse with minimal effort on part of data provider. Allows any scientist or data researcher to be able to explore dataset and then extract some or all of data according to their needs. Designed to manage experimental data tables in quick and easy way for users.
Proper citation: ODAM (RRID:SCR_018774) Copy
https://www.leica-microsystems.com/products/light-microscopes/p/leica-dm4000-b/
Fluorescent microscope which supports fluorescence contrast techniques. This product is archived and has been replaced by the Leica DM4000 B LED.
Proper citation: Leica: DM4000 B Microscope (RRID:SCR_018895) Copy
https://millar.com/Research/PressureVolume-Loop-System/
Pressure volume loop system with seven available volume segments, range of gain settings, integrated internal ECG circuit and dual pressure amplifiers. System can be used in either large or small animal subjects, depending on which size catheter is used.
Proper citation: Millar: MPVS Ultra Pressure Volume Loop System (RRID:SCR_018894) Copy
https://github.com/aplbrain/saber
Library of containerized tools and workflow deployment system for enabling processing of large neuroimaging datasets. Provides canonical neuroimaging workflows specified in standard workflow language (CWL), integration with workflow execution engine (Airflow), imaging database (bossDB), and parameter database (Datajoint) to deploy workflows at scale, and tools to automate deployment and optimization of neuroimaging pipelines.
Proper citation: Scalable Analytics for Brain Exploration Research (RRID:SCR_018812) Copy
https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_phd.html
Web tool for secondary structure prediction. Used for network protein sequence analysis.
Proper citation: PHD SECONDARY STRUCTURE (RRID:SCR_018778) Copy
https://github.com/biocatiit/musclex
Software suite as collection of programs intended to assist with analyzing diffraction X-ray images. MuscleX diffraction X-ray image analyzing toolkit. Data reduction software for X-ray fiber diffraction data.
Proper citation: Muscle X (RRID:SCR_018811) Copy
http://www.genscript.com/psort/psort2.html
Web tool for prediction of protein sorting signals and localization sites in amino acid sequencies. Recommended for animal/yeast sequences. Analyzes input sequence by applying stored rules for various sequence features of known protein sorting signals to report possiblity for input protein to be localized at each candidate site with additional information.
Proper citation: PSORT II (RRID:SCR_018772) Copy
https://www.beckman.com/flow-cytometry/instruments/moflo-astrios-eq
High speed flow cytometry sorter.
Proper citation: Beckman Coulter: Life Sciences MoFlo Astrios EQ Cell Sorter (RRID:SCR_018893) Copy
https://github.com/chris-mcginnis-ucsf/DoubletFinder
Software R package that predicts doublets in single cell RNA sequencing data. Doublet detection in single cell RNA sequencing data using artificial nearest neighbors. Identifies doublets using only gene expression data.
Proper citation: DoubletFinder (RRID:SCR_018771) Copy
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