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https://edspace.american.edu/openbehavior/project/kinemouse-wheel/
Project is related to Columbia University designed KineMouse Wheel, light weight running wheel for head fixed locomotion that allows for 3D positioning of mice with single camera. System uses single camera and DeepLabCut (or similar) software.
Proper citation: KineMouse Wheel project (RRID:SCR_021425) Copy
https://edspace.american.edu/openbehavior/project/mousecam/
Project related to capturing detailed behavior in freely moving mice. System combines lightweight head mounted camera and head movement sensors to detect behaviors in mice. Used to monitor behaviors including eye position, whisking, and ear movements in unrestrained animals.Can be mounted in combination with neural implants for recording brain activity.Provides software Python package with functions for extracting and analyzing data recorded using camera.
Proper citation: Mousecam project (RRID:SCR_021422) Copy
Software tool used to create summary of findings tables for cochrane systematic reviews. Web application to create, manage and share summaries of research evidence called Evidence Profiles and Summary of Findings Tables.
Proper citation: GRADEpro (RRID:SCR_021308) Copy
Software R package of igraph network analysis library.
Proper citation: igraph for R (RRID:SCR_021238) Copy
https://ggraph.data-imaginist.com/
Software tool as extension of ggplot2 aimed at supporting relational data structures such as networks, graphs, and trees. While it builds upon foundation of ggplot2 and its API it comes with its own self-contained set of geoms, facets, etc., as well as adding concept of layouts to grammar.
Proper citation: ggraph (RRID:SCR_021239) Copy
https://tomopy.readthedocs.io/en/1.5.2/ipynb/tomopy.html
Software tool for tomographic reconstruction.
Proper citation: Gridrec (RRID:SCR_021358) Copy
https://github.com/tseemann/abricate
Software tool for mass screening of contigs for antimicrobial and virulence genes. Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB.
Proper citation: Abricate (RRID:SCR_021093) Copy
https://corybrunson.github.io/ggalluvial/
Software tool as ggplot2 extension for alluvial plots. Used to visualize frequency distributions over time or frequency tables involving several categorical variables. Requires user to specify dimensions, either as separate aesthetics or as key-value pairs, relies on separate layers (stats and geoms) to produce strata, alluvia, and alluvial segments called lodes and flows.
Proper citation: ggalluvial (RRID:SCR_021253) Copy
Software supports QuantStudio12K Flex Real Time PCR System to open and analyze experiments. Enables to set up experiments, send experiments to instrument, control thermal cycling process in instrument, collect data and analyze collected data.
Proper citation: Applied Biosystems QuantStudio 12K Flex RT PCR Software (RRID:SCR_021096) Copy
https://github.com/parkgilbong/Minhee_Analysis_Pack
Software package for detection and measurement of spontaneous synaptic events. Integrated software package for detection and management of spontaneous synaptic events. Used in neurophysiology to detect spontaneous postsynaptic currents, search and visualize them in custom way, and perform hypothesis testing of retrieved data.
Proper citation: Minhee Analysis Package (RRID:SCR_021250) Copy
Software tool to quantify relative gene expression across large number of genes and samples. Allows to analyze gene expression data on any current Applied Biosystems real time PCR instrument.
Proper citation: ExpressionSuite (RRID:SCR_021095) Copy
https://github.com/jpgill86/neurotic
Software Python toolbox for interactive characterization in neuroscience.Users can read in variety of file formats for neural data and video, which they can then process, filter, analyze, annotate and plot.Used to review and annotate signal data synchronized with video, performs simple initial analyses including signal filtering and spike detection, supports variety of file formats.Facilitates collaborations by using portable specification for loading and processing data and retrieving data files from online sources.App for Windows, macOS, and Linux to review and annotate electrophysiology data and simultaneously captured video.
Proper citation: neurotic (RRID:SCR_021406) Copy
Software tool as macro for SPSS, SAS, and R that conducts observed variable mediation, moderation, and conditional process analysis.Observed variable OLS and logistic regression path analysis modeling tool. Used for estimating direct and indirect effects in single and multiple mediator models parallel and serial, two and three way interactions in moderation models along with simple slopes and regions of significance for probing interactions, and conditional indirect effects in moderated mediation models with single or multiple mediators or moderators. Operates on Windows and Mac versions of SPSS and SAS.
Proper citation: PROCESS (RRID:SCR_021369) Copy
http://www.cytobank.org/index.html
A cloud-based platform which allows users to analyze, visualize, and archive multiparamter cytometry data for single-cell biology. Multiple single-cell data sets can be analyzed and visualized simultaneously with a variety of graphics, inlcuding Sunburst, SPADE, and viSNE. Users can store and back up related data such as protocols, microscopy images, and presentations and collaborate and share analysis and data sets with other Cytobank users. Cytobank also provides a variety of services and training sessions to assist with experiment workflow.
Proper citation: Cytobank (RRID:SCR_014043) Copy
A simulation software package which hosts a collection of algorithms used to run bioelectric field simulations inside of SCIRun. The software provided in the package may be used for geometric modeling, simulation, and visualization for solving bioelectric field problems.
Proper citation: BioPSE (RRID:SCR_014044) Copy
A web application which allows users to collect data, perform complex analyses, and generate results. Users can upload data sets from their computer or from the internet for data analysis and graph creation which can be saved, printed, and downloaded. More than 15,000 statistical data sets are available.
Proper citation: StatCrunch (RRID:SCR_013992) Copy
http://actimetrics.com/products/limelight/
A video tracking system designed for high-throughput behavioral experiments. LimeLight can track up to 4 arenas at once and can collect images at up to 30 frames per second for one animal or up to 8 frames per second when tracking 4 arenas at once. The tracking system has 2 different hardware configurations: the 1-camera system can be used to record 1 to 4 animals at once, while for multiple animals, each one is placed in a separate arena in one quadrant of the image. The software contains productivity features such as flexible arena setup, user-defined behavior scoring, stimulus control, and various analytical functions for quantifying behavior. The program is designed for experiments such as Open Field, Plus Maze, Radial Arm Maze, Zero Maze, Novel Object Recognition, Conditioned Place Preference, and Barnes Maze.
Proper citation: Limelight (RRID:SCR_014254) Copy
http://www.lsm.tugraz.at/csim/
Software tool for simulating heterogeneous networks composed of different model neurons and synapses. CSIM simulates networks containing up to a few thousand neurons and up to the order of 1.000.000 synapses. It is capable of supporting different levels of modeling and has an object oriented design. A user manual is available on the site.
Proper citation: CSIM (RRID:SCR_014256) Copy
http://www.cse.unr.edu/brain/ncs
A neural simulator which models integrate-and-fire neurons with conductance-based synapses. NCS supports simulations for larger models and also supports real-time neurorobotics applications. Two versions of NCS are available: NCS 5, which is based on CPU cluster; and NCS 6, a multi-box, multi-GPU version. NCS 5 models integrate-and-fire neurons with conductance-based synapses using two clusters: four SUN 4600 machines and 208 Opteron cores. NCS 6 is a neural simulator for heterogeneous clusters of both CPUs and GPUS.
Proper citation: NeoCortical Simulator (RRID:SCR_014257) Copy
http://www.nitrc.org/projects/neuritetracer
A set of ImageJ plugins for fully automated measurement of neurite outgrowth in fluorescence microscopy images of cultured neurons. The plugin analyzes fluorescence microscopy images of neurites and nuclei of dissociated cultured neurons. Given user-defined thresholds, the plugin counts neuronal nuclei, and traces and measures neurite length. NeuriteTracer accurately measures neurite outgrowth from cerebellar, DRG and hippocampal neurons.
Proper citation: NeuriteTracer (RRID:SCR_014146) Copy
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