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https://edspace.american.edu/openbehavior/project/offline-behavior-video-analysis/
Project related to visualizing and quantifying movement from pre-recorded videos. Provides software toolbox for visualizing and quantifying movement.Used for summarizing animal movement data as single image ( spectral time lapse algorithm) as well as automate analysis of animal movement data.
Proper citation: Quantifying Animal Movement from Pre-recorded Videos project (RRID:SCR_021436) Copy
https://github.com/caleblareau/mgatk
Software python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. This package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays.
Proper citation: mgatk (RRID:SCR_021159) Copy
https://edspace.american.edu/openbehavior/project/boris/
Project related to computer based review of previously recorded videos or live observations. Related to study of animal and human behavior. Provides open source, multiplatform standalone program that allows user specific coding environment for computer based review of previously recorded videos or live observations.Developed by scientists from University of Turin.
Proper citation: Behavioral Observation Research Interactive Software project (RRID:SCR_021434) Copy
Open source designs for customizable, MRI compatible microdrive capable of positioning probes including stimulating electrodes, recording electrodes, drug cannulae, or optogenetic fibers within brain. Design integrates cranial implant, penetration grid for guiding probes, and microdrive body assembly with actuators. Used by neuroscience community related to electrical microstimulation, neuronal recording, and local drug delivery.
Proper citation: MRI Compatible and Customizable Microdrive Design for Neuroscience Research (RRID:SCR_019247) Copy
Software pipeline for single-nucleus RNAseq data generated by Smart-seq2 assays.Used to simultaneously process multiple libraries of single nuclei Smart-seq2 and Smart-seq4 data. For each library (nucleus), the pipeline trims paired FASTQ files, aligns trimmed reads to the genome, counts intronic and exonic reads, and calculates quality control metrics. Counts and metrics for all libraries are combined into merged Loom formatted count matrix.
Proper citation: Smart-seq2 Single Nucleus Multi Sample Pipeline (RRID:SCR_021312) Copy
https://edspace.american.edu/openbehavior/project/m-track/
Project related to tracking movement of labelled paws in grooming and freely behaving mice. Provides software toolbox for automated detection of forepaw trajectories in mice.
Proper citation: M-Track project (RRID:SCR_021433) Copy
Matchmaking platform for clinicians and scientists to facilitate collaborative research on rare and undiagnosed diseases. Used for collaborative projects that advance scientific knowledge and patient care. Currently supports Mouse, Rat, Frog, Zebrafish, Fruit Fly, Nematode Worm, Budding Yeast, Fission Yeast, and E. coli. Used to identify human ortholog of genes in these model organisms and vice versa. Scientists who register in ModelMatcher are asked to classify their genes of interest into Public or Restricted categories.The Match feature will allow Clinicians to obtain information on genes that Scientists classify as both Public and Restricted.
Proper citation: ModelMatcher (RRID:SCR_021208) Copy
https://edspace.american.edu/openbehavior/project/pathfinder/
Project to detect spatial navigation behavior in animals.Provides open source software for analyzing spatial navigation search strategies developed by University of British Columbia scientists.
Proper citation: Pathfinder project (RRID:SCR_021447) Copy
https://edspace.american.edu/openbehavior/project/autopilot/
Project related to behavioral experiments.Provides software Python framework for running behavioral experiments designed by University of Oregon scientists.
Proper citation: AutoPilot project (RRID:SCR_021448) Copy
https://edspace.american.edu/openbehavior/project/bonsai/
Project related to composing reactive and asynchronous data streams coming from video cameras, microphones, electrophysiology systems or data acquisition boards. Provides open source software tool as visual language for reactive programming.
Proper citation: Bonsai project (RRID:SCR_021443) Copy
https://github.com/ENCODE-DCC/chip-seq-pipeline2/
Software tool as ChIP-seq pipeline for processing ChIP-seq reads, aligning to reference genome, peak calling, and IDR analysis of replicate data according to ENCODE standards.
Proper citation: ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline (RRID:SCR_021323) Copy
https://www.southernbiotech.com/
Commercial antibody company that focuses on the development, production, purification, conjugation, and commercialization of antibodies.
Proper citation: SouthernBiotech (RRID:SCR_019250) Copy
A manufacturer of early discovery research products including antibodies, recombinant proteins, ELISA kits, second step reagents and other life sciences products.
Proper citation: Leinco Technologies (RRID:SCR_019252) Copy
https://edspace.american.edu/openbehavior/project/deepbehavior/
Project related to behavior tracking and analysis. Provides deep learning toolbox that automates taking high speed quality video to track behavior in rodents and humans.
Proper citation: DeepBehavior project (RRID:SCR_021387) Copy
https://edspace.american.edu/openbehavior/project/worm-behavior-platform/
Project related to sharing worm tracking data and analysis routines.Open access repository for storing, accessing, filtering data and analysis.
Proper citation: Worm Behavior Platform project (RRID:SCR_021420) Copy
https://edspace.american.edu/openbehavior/project/sleap/
Collection of tools to do video analysis in behavioral neuroscience applications.Offers open source software tools including SLEAP, LEAP and MotionMapper.
Proper citation: SLEAP, LEAP and MotionMapper project (RRID:SCR_021383) Copy
Project related to tracking individual animals in large collective groups.Provides algorithm and software for tracking individuals in large collectives of unmarked animals.Tracks animal identification and tracks when animals touch or cross paths in front of one another.
Proper citation: idtracker.ai project (RRID:SCR_021417) Copy
https://edspace.american.edu/openbehavior/project/cave/
Project related to calcium imaging.Provide open source tool for combined analysis of head mounted calcium imaging and behavior. Used to analyze imaging data from head mounted microscopes simultaneously with behavioral data.
Proper citation: Calcium ActiVity Explorer project (RRID:SCR_021419) Copy
Open source software Java tool for working with data. Used for loading data, cleaning up data, transforming data from one format into another and extending it with web services and external data.
Proper citation: OpenRefine (RRID:SCR_021305) Copy
Open source software Python package for working with hierarchical data. Provides APIs for specifying data models, reading and writing data to different storage backends, and representing data with Python object.Used for working with standardizing, reading, and writing hierarchical object data.
Proper citation: Hierarchical Data Modeling Framework (RRID:SCR_021303) Copy
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