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https://github.com/cihga39871/Atria

Open source software tool as adapter and quality trimmer for Next-Generation Sequence data.

Proper citation: Atria (RRID:SCR_021313) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/openeyetrack/

Project related to measurement of fast eye movement dynamics.Tracking eye position in head fixed applications system created by scientists from Boston University. Includes software tool as part of multithreaded eye tracker and Teledyne DALSA Camera with GigE-V framework APIs for Linux.

Proper citation: openEyeTrack project (RRID:SCR_021399) Copy   

•   Source: SciCrunch Registry

https://satijalab.org/signac/index.html

Software framework for analysis of single cell chromatin data. Used for analysis, interpretation, and exploration of single cell chromatin datasets including datasets that co-assay DNA accessibility with gene expression, protein abundance, and mitochondrial genotype. Analysis of single-cell chromatin data including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA motif analysis, and interactive visualization.

Proper citation: Signac (RRID:SCR_021158) Copy   

•   Source: SciCrunch Registry

https://github.com/HeardLibrary/linked-data/tree/master/vanderbot

Software Python tool as Vanderbilt University curation tool.Used for exporting public profiles of university faculty from Vanderbilt University database into Wikidata.Used to create or update items in Wikidata using data from CSV spreadsheet data.

Proper citation: VanderBot (RRID:SCR_021298) Copy   

•   Source: SciCrunch Registry

https://github.com/aidenlab/Juicebox

Visualization and analysis software for Hi-C data.

Proper citation: Juicebox (RRID:SCR_021172) Copy   

•   Source: SciCrunch Registry

https://emea.support.illumina.com/sequencing/sequencing_software/experiment_manager/downloads.html

Software to create and edit sample sheet in order to perform next generation sequencing on Illumina paltforms. Used for MiniSeq, MiSeq, NextSeq 500/550, HiSeq, and NovaSeq 6000 Systems.

Proper citation: Illumina Experiment Manager (RRID:SCR_021202) Copy   

•   Source: SciCrunch Registry

https://github.com/gordonberman/MotionMapper

Software tool to work on videos (not poses).Uses image analysis and multivariate statistical methods to find stereotyped behaviors in flies, mice, and other species.

Proper citation: MotionMapper (RRID:SCR_021384) Copy   

•   Source: SciCrunch Registry

https://github.com/YttriLab/B-SOID

Software pipeline that pairs unsupervised pattern recognition with supervised classification to achieve fast predictions of behaviors that are not predefined by users.Unsupervised learning algorithm that discovers and classifies actions based on inherent statistics of data points provided.

Proper citation: Behavioral Segmentation of Open-field in DeepLabCut (RRID:SCR_021385) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/stytra/

Project related to involvement in larval zebrafish behavioral experiments.Provides integrated system for stimulation, tracking and closed loop behavioral experiments. Provides timed stimulus presentation, interfacing with external devices and simultaneous real time tracking of behavioral parameters such as position, orientation, tail and eye motion in both freely swimming and head restrained preparations.

Proper citation: Stytra project (RRID:SCR_021416) Copy   

•   Source: SciCrunch Registry

https://github.com/jonnew/Oat

Software tool as real time position tracker for behavioral research. Used for processing images, extracting object position information, and streaming data to disk and/or the network in real time.

Proper citation: Online Animal Tracker (RRID:SCR_021412) Copy   

•   Source: SciCrunch Registry

https://github.com/ngaggion/ChronoRoot

System which combines 3D printed open hardware with deep segmentation networks for high temporal resolution phenotyping of plant roots in agarized medium. Deep learning based root extraction method which leverages the latest advances in convolutional neural networks for image segmentation, and incorporates temporal consistency into the root system architecture reconstruction process.

Proper citation: ChronoRoot (RRID:SCR_021259) Copy   

•   Source: SciCrunch Registry

https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification

Software package as collection template and associated materials for SARS-CoV-2 metadata. Contains metadata collection template based on data standard designed to harmonize genomic surveillance contextual data (sample metadata, epidemiological/clinical/laboratory data, methods information) across datasets, laboratories and databases during pandemic, and beyond. Template contains standardized fields, terms and formats for structuring information, and is accompanied by field level reference guide which provides definitions, guidance and examples for populating fields. Fields have been prioritized using colour coding system as required (yellow), recommended (purple), and optional (white). Users can use as much or as little of specification as they wish, according to their needs, and need not share information unless permitted to do so. SOP and protocols for submitting to public repositories are also included.

Proper citation: Public Health Alliance for Genomic Epidemiology SARS-CoV-2 Contextual Data Specification (RRID:SCR_021378) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/locowhisk/

Portable behavioural set up that incorporates both gait analysis (using pedobarograph) and whisker movements (using high speed video camera and infrared light source).Automatically records both whisker and gait information and provides added statistical tools to analyse data. LocoWhisk system includes ARTv2 software for simultaneous measurement of locomotion behaviours and whisker movements.

Proper citation: LocoWhisk project (RRID:SCR_021430) Copy   

•   Source: SciCrunch Registry

https://github.com/bahanonu/ciatah

Software package for analyzing one and two photon calcium imaging datasets.Can be used to create GUI-less, command line ready analysis pipelines. Supports Neurodata Without Borders data standard for reading/writing cell-extraction (e.g. outputs of PCA-ICA, CELLMax, CNMF, CNMF-E, EXTRACT, etc.). Supports reading and writing NWB movie files with continued integration planned. Supports most major imaging movie file formats: HDF5, NWB, AVI, ISXD [Inscopix], and TIFF.

Proper citation: calciumImagingAnalysis (RRID:SCR_021153) Copy   

•   Source: SciCrunch Registry

http://www.kintekexplorer.com

Software tool for fitting kinetic and equilibrium data based on numerical integration of rate equation from any model input user. Simulation and data-fitting software for research and education designed specifically for the field of chemical kinetics.

Proper citation: KinTek Explorer (RRID:SCR_021274) Copy   

•   Source: SciCrunch Registry

https://disk.yandex.ru/d/SItlrfgmZeKhrQ

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 23, 2022.

Proper citation: Software for generation of GB-speckles (RRID:SCR_021272) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/facesync/, https://bio.tools/FaceSync

Project related to emotions and facial expressions. Includes open source guide to building affordable head mount for camera to maintain high temporal and spatial resolution of face throughout duration of experiment. Device is paired with FaceSync, Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions.

Proper citation: FaceSync project (RRID:SCR_021393) Copy   

•   Source: SciCrunch Registry

https://caiman.readthedocs.io/

Software Python toolbox for large scale calcium imaging data analysis and behavioral analysis.Used for motion correction, source extraction, spike deconvolution, and component registration across multiple days. It is suitable for both two-photon and one-photon fluorescence microscopy data, and can be run in both batch and online modes. Contains some routines for analysis of behavior from video cameras.

Proper citation: CaImAn (RRID:SCR_021152) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/head-fixed-setup-combined-behavior-electrophysiology-optogenetics/

Project related to temporally controlled rodent behavior. Provides system which utilizes optimal open source setup of hardware and software through behavioral setup for temporally controlled rodent behavior. Used for combined behavior, electrophysiology and optogenetics experiments. System allows for training of head fixed animals with calibrated sound stimuli, precisely timed fluid and air puff presentations as reinforcers.Combines microcontroller based behavior control with sound delivery system for acoustic stimuli, fast solenoid valves for reinforcement delivery and custom built sound attenuated chamber.

Proper citation: Head-Fixed Setup for Combined Behavior, Electrophysiology, and Optogenetics project (RRID:SCR_021427) Copy   

•   Source: SciCrunch Registry

http://www.lcqb.upmc.fr/COVTree/

Web server providing online analysis of coevolving amino acid pairs in overlapping genes, where residues might be located inside or outside overlapping region.

Proper citation: COVTree (RRID:SCR_021307) Copy   

•   Source: SciCrunch Registry