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https://github.com/garber-lab/ESAT

Software for the analysis of short reads obtained from end-sequence RNA-seq. ESAT is designed for expression analysis of Digital expression (DGE) libraries that target transcript "ends."

Proper citation: End Sequence Analysis ToolKit (ESAT) (RRID:SCR_015812) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://microbetracker.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone. Software for bacterial microscopy image analysis. It is designed to detect and outline bacterial cells in microscopy images and to analyze fluorescence signal inside them.

Proper citation: MicrobeTracker (RRID:SCR_015939) Copy   

•   Source: SciCrunch Registry

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://github.com/harry-thorpe/piggy

Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary).

Proper citation: Piggy (RRID:SCR_015941) Copy   

•   Source: SciCrunch Registry

https://github.com/KravitzLab/fed/wiki

Flexible open-source device for measuring feeding behavior. FED measures food intake in mice. It is battery powered and designed to be used in rodent colony caging.Home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers alternative to commercial feeders, with convenience of use in tradition colony rack caging.

Proper citation: Feeding Experimentation Device project (RRID:SCR_015942) 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

https://github.com/sanworks

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   

•   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