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https://www.visiopharm.com/solutions/oncotopix
Oncotopix Discovery is a comprehensive solution powered for whole slide image analysis of tissue sections, TMA slides across any image analysis application. Simple to program also for scientists without an IT background.
Proper citation: Oncotopix Discovery (RRID:SCR_015690) Copy
http://diseases.jensenlab.org/
Database that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. It also assigns confidence scores that facilitate comparison of the different types and sources of evidence.
Proper citation: DISEASES (RRID:SCR_015664) Copy
http://www.neurocaregroup.com/dc-stimulator-neuroconn.html
Device for administering transcranial electrical stimulation. It has applications in cranial electrotherapy that provides a weak direct current for non-invasive Interventional Neurophysiology.
Proper citation: Neurocare: Neuroconn DC-Stimulator Plus (RRID:SCR_015520) Copy
https://github.com/BRAHMS-SystemML/brahms
Simulation software that runs network simulations where the network is specified in its own format called SystemML. The components of the network can be implemented in C, C++, Python or Matlab and are used in SpineML_2_BRAHMS to provide a simulation back-end for SpineML models.
Proper citation: BRAHMS (RRID:SCR_015642) Copy
http://www.ebi.ac.uk/pdbe/pisa/
Web application for exploration of macromolecular interfaces. It calculates structural and chemical properties of macromolecular surfaces and interfaces, as well as quaternary structures (assemblies), their structural and chemical properties and dissociation patterns.
Proper citation: PISA (RRID:SCR_015749) Copy
https://compumedicsneuroscan.com/product/synamps-rt-64-channel-eeg-erp-ep-amplifier/
Equipment that is an EEG signal amplifier for 64-channel montages. It is suitable for recording data from high sampling rate (20,000 Hz) Auditory Brain Stem recordings and Spike Spindles to true DC recordings of CNV and P300.
Proper citation: Neuroscan SynAmps RT 64-channel Amplifier (RRID:SCR_015818) Copy
Equipment that provides physical support for cell cultures. These cell culture inserts feature attachment and suspension cells that can access media from both their apical and basolateral sides.
Proper citation: Sigma: Millicell Cell Culture Inserts (RRID:SCR_015799) Copy
Dataset that can be used to analyze cyber-attacks to an indoor real time localization system for autonomous robots. Data have been gathered in an indoor mock-up apartment using an autonomous robot with an on-board Real Time Location System (RTLS).
Proper citation: Real time localization system for autonomous robots Benchmark Dataset (RRID:SCR_015756) Copy
https://synbiobeta.com/antha-code-experiments-biology/
Software language for methods to simplify protocols into reusable components that can be exchanged or removed to produce simple, reproducible, and scalable workflows. It allows users to develop, execute, and analyse biological experiments faster, while also introducing standardization and modularity to bioengineering.
Proper citation: Antha (RRID:SCR_015761) Copy
Language standard for automating English language protocols. Autoprotocol specifies experimental protocols for biological research as a way to define experiments that could be run over the internet on remote robotic automation.
Proper citation: Autoprotocol (RRID:SCR_015764) Copy
https://www.olympus-lifescience.com/en/microscopes/inverted/ix53/
Equipment that is a microscope for routine inverted microscopic analysis. Its features include pre-centered phase contrast, relief contrast, and UIS2 DIC optics for visualization across all magnifications for both thin and thick specimens.
Proper citation: Olympus IX-53 (RRID:SCR_015801) Copy
http://ced.co.uk/products/power3
Data acquisition interface from Cambridge Electronic Design Limited. Works with Spike2 to provide continuous acquisition tasks. Records waveform data, digital and marker information, and can generate waveform and digital outputs simultaneously for real-time, multi-tasking experiment control.
Proper citation: CED: Power1401 (RRID:SCR_016040) Copy
University in Durham, England.
Proper citation: Durham University; Durham; England (RRID:SCR_016079) Copy
Software for a measurement and control system for behavior research, most often used to implement operant (Go/NoGo, 2AFC) tasks. This software controls a hierarchy of hardware modules, each powered by an Arduino-programmable microcontroller.
Proper citation: Bpod (RRID:SCR_015943) Copy
http://www.ebi.ac.uk/~zerbino/oases/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool as de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.
Proper citation: Oases (RRID:SCR_011896) Copy
https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/rnnotator
Software designed to assemble Illumina single or paired-end reads.
Proper citation: Rnnotator (RRID:SCR_011897) Copy
http://genome.cshlp.org/content/20/10/1432.full
A de novo transcriptome assembly from next-generation sequencing data.
Proper citation: STM (RRID:SCR_011898) Copy
http://tophat.cbcb.umd.edu/fusion_index.html
An algorithm for Discovery of Novel Fusion Transcripts with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome.
Proper citation: TopHat-Fusion (RRID:SCR_011899) Copy
http://www.cbcb.umd.edu/software/glimmer-mg/
A software system for finding genes in environmental shotgun DNA sequences.
Proper citation: Glimmer-MG (RRID:SCR_011932) Copy
http://whale.bio.titech.ac.jp/metagene/
A gene-finding software program for prokaryote and phage., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MetaGeneAnnotator (RRID:SCR_011934) Copy
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