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https://zenodo.org/record/167621
Simulation environment that combines flexible script language user interface with computational tools in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level. It aims to include cell excitation, tissue/anatomy models, and stimulation protocols in BeatBox scripts so that simulation run either sequentially or in parallel (MPI) without re-compilation.
Proper citation: BeatBox (RRID:SCR_015780) 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
https://github.com/hpardoe/napr/
Cloud-based framework that allows users to estimate the age of individual subjects using cortical thickness maps derived from their own locally processed T1-weighted whole brain MRI scans. The provided age prediction models were trained using (i) relevance vector machines and (ii) Gaussian processes machine learning methods applied to cortical thickness surfaces obtained using Freesurfer v5.3.
Proper citation: NAPR: Neuroanatomical Age Prediction using R (RRID:SCR_015759) 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
Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders.
Proper citation: Brain-CODE (RRID:SCR_015877) 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
https://github.com/cerebis/sim3C/tree/0.1
Software for read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC). Sim3C's potential applications include addressing questions directed at the spatial organization of DNA in samples of eukaryotic tissue, single cells, and microbial communities.
Proper citation: Sim3C (RRID:SCR_015772) 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
Simulation software for experimental evolution of microorganisms. Aevol is a digital genetics model for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences).
Proper citation: Aevol (RRID:SCR_015966) 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
https://github.com/hyattpd/Prodigal
Software tool for protein coding gene prediction for prokaryotic genomes.
Proper citation: Prodigal (RRID:SCR_011936) 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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