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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://alleninstitute.github.io/dipde/
Simulation platform for numerically solving the time evolution of coupled networks of neuronal populations. DiPDE can facilitate the fast exploration of mesoscale (population-level) network topologies, where large populations of neurons are treated as homogeneous with random fine-scale connectivity.
Proper citation: DiPDE (RRID:SCR_015822) Copy
http://www.fsm.ethz.ch/publications-list/software.html
Software for tracking and analysis based on algorithms describing structural and topological features of fiber-like objects. The program operates on images from any microscopic source (atomic force or transmission electron microscopy, optical, fluorescence, confocal, etc.), acquiring the spatial coordinates of objects.
Proper citation: FiberApp (RRID:SCR_015826) Copy
https://www.licor.com/bio/image-studio/
Image analysis software that acquires, analyzes, and archives research data without altering raw findings. It integrates data and changes how pixels are mapped to the screen for clearer display, rather than altering the pixels of the image data itself.
Proper citation: LI-COR Image Studio Software (RRID:SCR_015795) 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
http://www.adobe.com/products/audition.html
Software for sound analysis, audio editing, and audio recording. It features multitrack, waveform, and spectral display for creating, mixing, editing, and restoring audio content for research or non-research purposes.
Proper citation: Adobe Audition (RRID:SCR_015796) 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
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
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
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
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
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
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
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
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
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
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
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
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