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https://github.com/yorambenshaul/optimouse

Software tool for analysis of mouse position data.Open source software to analyze positions of individual mice, specifically their nose positions, in behavioral arena with the goal of minimizing error.

Proper citation: Optimouse (RRID:SCR_021527) Copy   

•   Source: SciCrunch Registry

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

Project is related to measurement of complex phenotypes in homecage. Homecage automated open source behavioral testing sytem to enable high throughput 24h testing of many standard operant paradigms. Using Arduino platform and easily sourced inexpensive components system can display light cues and dispense liquid rewards and has nosepoke receptacles with infrared detectors for operant responses, within homecage.Method provided by Dartmouth College scientists.

Proper citation: DIY-NAMIC project (RRID:SCR_021489) Copy   

•   Source: SciCrunch Registry

https://github.com/pascalkieslich/mousetrap-os

Integrated, open source mouse tracking software package.Software plugin to record and analyze mouse movements in computerized lab experiments.Software plugin provides two items that implement mouse tracking in OpenSesame.

Proper citation: Mousetrap (RRID:SCR_021523) Copy   

•   Source: SciCrunch Registry

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

Project related to study learning and memory in preclinical research.Included tracking system for object recognition tasks provides standardization across experiments and labs.Automates scoring process using capacitive sensors, while providing validated 3D-printed objects in order to standardize object recognition to study learning and memory in preclinical research.Used for accurate measurement of interaction time during object recognition tasks.

Proper citation: CapTouch project (RRID:SCR_021488) Copy   

•   Source: SciCrunch Registry

https://hpap.pmacs.upenn.edu/about-pancdb

Portal to make all Human Pancreas Analysis Program data available to anyone in research community and to interact with and connect scientific community. Stores clinical, molecular, cellular, immunology, imaging, and pathology data from pancreatic tissue and cell samples from organ donors with and without type 1 or type 2 diabetes.

Proper citation: PANC-DB (RRID:SCR_021860) Copy   

•   Source: SciCrunch Registry

http://imj.com.au/sgs/

Software tool as biophysical simulation model for livestock systems. It has flexible interface for setting up and running simulations with extensive graphical and data output.

Proper citation: Sustainable Grazing System Pasture Model (RRID:SCR_021854) Copy   

•   Source: SciCrunch Registry

https://www.research.va.gov/mvp/

National research program to learn how genes, lifestyle, and military exposures affect health and illness.

Proper citation: Million Veteran Program (RRID:SCR_021731) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/fuzzywuzzy/

Software pacakge that uses Levenshtein Distance to calculate differences between sequences for string matching.

Proper citation: FuzzyWuzzy (RRID:SCR_021699) Copy   

•   Source: SciCrunch Registry

https://www.nature.com/articles/srep16171#Sec20

Open source program for semi automated analysis of movement and cognitive testing in rodents. Accurately quantifies numerous parameters of movement including travel distance, speed, turning, stationary fraction and laterality. Part of MouseMove system.

Proper citation: MouseMove (RRID:SCR_021618) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/trio-platform/

Portal provides low profile in vivo imaging support and restraint system for mice. System is compact and provides sturdy head fixation, gas anesthesia mask, and warm water bed. Compact design allows to work with variety of microscope stages and use of 3D printed components makes this design customizable.

Proper citation: TRIO Platform (RRID:SCR_021596) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/ipad-visual-discrim/

Portal provides touchscreen platform developed by Texas Christian University scientists. iPad apparatus set up consists of four wall operant chamber, remote desktop program, Visual Basic 6 software, and single wireless iPad. Wireless iPad allows for flexibility in setups during performing visual discrimination behavioral experiments.

Proper citation: Visual Discrimination with an iPad (RRID:SCR_021593) Copy   

•   Source: SciCrunch Registry

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

Portal provides Arduino controlled stimulus isolator that allows for highly accurate, reproducible automated setting of stimulation currents. Automatic stimulation patterns are software controlled and parameters are set from Matlab coded simple, intuitive and user friendly graphical user interface.

Proper citation: StimDuino (RRID:SCR_021594) Copy   

•   Source: SciCrunch Registry

https://simulabeta.sourceforge.io/

Software tool as simulation program for insulin glucose feedback control. Based on nonlinear MiMe-NoCoDI model.

Proper citation: SimulaBeta (RRID:SCR_021900) Copy   

•   Source: SciCrunch Registry

https://samplesizeshop.org

Platform for multilevel and longitudinal data.Provide researchers such as behavioral and social scientists with tools and education related to study design including Calculating power and sample size for any univariate or multivariate test for general linear multivariate model, assuming fixed predictors;Producing confidence intervals on power estimates for designs with fixed predictors;Producing power calculations for designs with single Gaussian covariate;Supporting designs with unequal group sizes, and complicated covariance structures;Creating basic power curves.

Proper citation: Sample Size Shop (RRID:SCR_021747) Copy   

•   Source: SciCrunch Registry

https://github.com/ANGSD/angsd

Software tool fo analysis of next generation sequencing data. Calculates various summary statistics, and performs association mapping and population genetic analyses utilizing full information in next generation sequencing data by working directly on raw sequencing data or by using genotype likelihoods.

Proper citation: ANGSD (RRID:SCR_021865) Copy   

•   Source: SciCrunch Registry

https://evofunvm.dcsr.unil.ch/

Database of metadata and assembly quality metrics for all Arthropod assemblies on NCBI.

Proper citation: Arthropoda Assembly Assessment Catalog (RRID:SCR_021864) Copy   

•   Source: SciCrunch Registry

https://github.com/abyzovlab/CNVpytor

Software Python package and command line tool for CNV/CNA analysis from depth of coverage by mapped reads. Software tool for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing.

Proper citation: CNVpytor (RRID:SCR_021627) Copy   

•   Source: SciCrunch Registry

https://github.com/vlink/marge

Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation.

Proper citation: Motif Mutation Analysis for Regulatory Genomic Elements (RRID:SCR_021902) Copy   

•   Source: SciCrunch Registry

https://trialdesign.org/

Integrated platform for designing clinical trials.

Proper citation: Trialdesign (RRID:SCR_021749) Copy   

•   Source: SciCrunch Registry

https://github.com/mourisl/Rcorrector

Software tool as kmer based error correction method for RNAseq data. Can also be applied to other types of sequencing data where read coverage is nonuniform, such as single cell sequencing. Used for error correction for Illumina RNAseq reads.

Proper citation: Rcorrector (RRID:SCR_022011) Copy   

•   Source: SciCrunch Registry