Oct 30, 2018

baRcodeR with PyTrackDat: Open-source labelling and tracking of biological samples for repeatable science

BioRxiv : the Preprint Server for Biology
Yihan I WuRobert I. Colautti

Abstract

Repeatable experiments with accurate data collection and reproducible analyses are fundamental to the scientific method but may be difficult to achieve in practice. Several flexible, open-source tools developed for the R and Python coding environments aid the reproducibility of data wrangling and analysis in scientific research. In contrast, analogous tools are generally lacking for earlier stages, such as systematic labelling and processing of field samples with hierarchical structure (e.g. time points of individuals from multiple lines or populations) or curating heterogenous data collected by different researchers over several years. Such tools are critical for modern research given trends toward globally distributed collaborators using higher-throughput technologies. As a step toward improving repeatability of methods for the collection of biological samples, and curation of biological data, we introduce the R package baRcodeR and the PyTrackDat pipeline in Python. The baRcodeR package provides tools for generating biologically informative, hierarchical labels with digitally encoded 2D barcodes that can be printed and scanned using low-cost commercial hardware. The PyTrackDat pipeline integrates with baRcodeR output to buil...Continue Reading

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Mentioned in this Paper

Computer Software
Research
Environment
Research Personnel
Research Project
Dnm1l protein, mouse
Tracking
DNA Barcoding, Taxonomic
Structure
Disease Management

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