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https://github.com/larvalign/larvalign

Software package including computational methods for aligning gene expression patterns from the larval brain of Drosophila melanogaster. Its method includes evaluation of the registration framework involved in template generation and mapping.

Proper citation: larvalign (RRID:SCR_015815) Copy   

•   Source: SciCrunch Registry

http://apps.cytoscape.org/apps/cluepedia

Data analysis software and search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data and investigates interrelations within each pathway to reveal associations through gene/protein/miRNA enrichments.

Proper citation: CluePedia Cytoscape plugin (RRID:SCR_015784) Copy   

•   Source: SciCrunch Registry

https://en.freedownloadmanager.org/Windows-PC/Flowing-Software-FREE.html

Software for flow cytometry data analysis. Flowing Software has many common analysis tools, such as dot plots, histograms, quadrants, statistics, overlay histograms etc.

Proper citation: Flowing Software 2.5.1 (RRID:SCR_015781) Copy   

•   Source: SciCrunch Registry

https://biccn.org

Consortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains.

Proper citation: BICCN (RRID:SCR_015820) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.biovoxxel.de/

Software toolkit for analyzing tool for microscopic images. It contains plugins and some macros dealing with image filtering, image segmentation and binary image processing and analysis.

Proper citation: BioVoxxel Toolbox (RRID:SCR_015825) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.sigmaaldrich.com/US/en/products/labware/cell-culture-and-cryogenics/millicell-cell-culture-inserts-and-plates

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://robotica.unileon.es/index.php/Benchmark_dataset_for_analysis_of_cyber-attacks_to_an_indoor_real_time_localization_system_for_autonomous_robots

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   

•   Source: SciCrunch Registry

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