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http://www.braincode.ca

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   

•   Source: SciCrunch Registry

http://digestivediseasescenters.org/content/ddrc-emory-university-overview

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2023. Center for pathobiology research development.

Proper citation: Emory Epithelial Pathobiology Research Development Center (RRID:SCR_015916) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.metanetx.org/

Web application to perform automated model construction and genome annotation for large-scale metabolic networks. Platform for accessing, analyzing and manipulating genome-scale metabolic networks (GSM) as well as biochemical pathways.

Proper citation: MetaNetX (RRID:SCR_015882) Copy   

•   Source: SciCrunch Registry

https://github.com/marbl/canu

Software for scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Canu is a fork of the Celera Assembler and is designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).

Proper citation: Canu (RRID:SCR_015880) Copy   

•   Source: SciCrunch Registry

http://www.emouseatlas.org/emap/eHistology/kaufman/index.php?plate=38&image=38bb

Image repository that allows researchers to interactively explore a collection of cellular-resolution colour histology images detailing mouse development. The original histological sections have been re-digitised at high resolution, in colour and in collaboration with Elsevier, the eHistology Atlas provides the annotations as presented in the original printed version.

Proper citation: eHistology (RRID:SCR_015887) Copy   

•   Source: SciCrunch Registry

http://autoprotocol.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://ukbec.wordpress.com

Consortium studying the regulation and alternative splicing of gene expression in multiple tissues from human brains. The UKBEC dataset comprises of brains from individuals free of neurodegenerative disorders.

Proper citation: UK Brain Expression Consortium (RRID:SCR_015889) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/4444202

Software for high-throughput gene expression and genotyping analysis for use with the Applied Biosystems® 7900HT Fast Real Time PCR System. It features automation software tools to fully automate high-throughput applications for gene expression and SNP genotyping.

Proper citation: Sequence Detector System (RRID:SCR_015806) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/ND-3300

Fluorospectrometer for broad spectrum fluorescence analysis. It uses as little as 1 μL of sample volume and lowers the mass detection limit more than an order of magnitude.

Proper citation: NanoDrop 3300 Fluorospectrometer (RRID:SCR_015804) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/4376600

Equipment and software system that is a real-time thermal cycler for intuitive data analysis of polymerase chain reactions. It comes with analysis software, instrument control software, and a LED-based 4-color optical recording feature.

Proper citation: Thermo Fisher: StepOnePlus Real-Time PCR System (RRID:SCR_015805) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.norpix.com/products/streampix/streampix.php

Software for digital video camera recording that allows users to control and acquire dadta from multiple cameras simultaneously in a singleuser interface. StreamPix provides a complete management console for cameras, simplifying the setup, control and acquisition from any number and type of camera.

Proper citation: StreamPix (RRID:SCR_015773) Copy   

•   Source: SciCrunch Registry

http://www.syngene.com/genesys-2/

Imaging software that works with G:BOX Chemi and PXi imaging systems to automatically or manually capture images. GeneSys also includes a database containing information about applications such as fluorescence, chemiluminescence and chemifluorescence.

Proper citation: GeneSys (RRID:SCR_015770) Copy   

•   Source: SciCrunch Registry

https://genome.tugraz.at/genesisclient/genesisclient_description.shtml

Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments.

Proper citation: Genesis (RRID:SCR_015775) Copy   

•   Source: SciCrunch Registry

http://boinc.berkeley.edu

Software to orchestrate the distribution of computational work units (data and applications) to volunteers and have results collected back. It supports diverse applications, including those with large storage or communication requirements, and addresses unsolved issues in biology, medicine, physics, astronomy and computer science.

Proper citation: BOINC - Berkeley Open Infrastructure for Network Computing (RRID:SCR_015896) Copy   

•   Source: SciCrunch Registry

https://github.com/DDTBOX/DDTBOX

Software toolkit for multivariate pattern analysis (MVPA) of event-related potentials. This software is written in MATLAB.

Proper citation: Decision Decoding Toolbox (RRID:SCR_015978) Copy   

•   Source: SciCrunch Registry

https://github.com/cmayer/BaitFisher-package

Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments.

Proper citation: Baitfisher (RRID:SCR_015985) Copy   

•   Source: SciCrunch Registry

http://avogadro.cc/

Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

Proper citation: Avogadro (RRID:SCR_015983) Copy   

•   Source: SciCrunch Registry