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Preclinical Western Blot in the Era of Digital Transformation and Reproducible Research, an Eastern Perspective

Abstract

The current research is an interdisciplinary endeavor to develop a necessary tool in preclinical protein studies of diseases or disorders through western blotting. In the era of digital transformation and open access principles, an interactive cloud-based database called East–West Blot (https://rancs-lab.shinyapps.io/WesternBlots) is designed and developed. The online interactive subject-specific database built on the R shiny platform facilitates a systematic literature search on the specific subject matter, here set to western blot studies of protein regulation in the preclinical model of TBI. The tool summarizes the existing publicly available knowledge through a data visualization technique and easy access to the critical data elements and links to the study itself. The application compiled a relational database of PubMed-indexed western blot studies labeled under HHS public access, reporting downstream protein regulations presented by fluid percussion injury model of traumatic brain injury. The promises of the developed tool include progressing toward implementing the principles of 3Rs (replacement, reduction, and refinement) for humane experiments, cultivating the prerequisites of reproducible research in terms of reporting characteristics, paving the ways for a more collaborative experimental design in basic science, and rendering an up-to-date and summarized perspective of current publicly available knowledge.

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Data Availability

The developed application is hosted in the free tier of shinyapps.io server https://rancs-lab.shinyapps.io/WesternBlots. Correspondences can be made to the corresponding author.

Abbreviations

atm:

Unit of pressure (atmosphere)

g:

Unit of weight (gram)

mm:

Unit of distance (millimeter)

3Rs:

Three principles (replacement, reduction, and refinement), developed for performing more humane animal research

FPI:

Fluid percussion injury

HBA:

Harm-benefit analysis

HHS:

United States Department of Health and Human Services

PRISMA:

A statement guiding the process of systematic review and meta-analysis

R:

Programming language and software environment for statistical computing

SSD:

Subject-specific database

TBI:

Traumatic brain injury

UI:

User interface

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Correspondence to Saman Sargolzaei.

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Sargolzaei, S., Kaushik, A., Soltani, S. et al. Preclinical Western Blot in the Era of Digital Transformation and Reproducible Research, an Eastern Perspective. Interdiscip Sci Comput Life Sci 13, 490–499 (2021). https://doi.org/10.1007/s12539-021-00442-7

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Keywords

  • Computational science
  • Digital transformation
  • Interdisciplinary
  • Online database
  • Reproducible research
  • Western blot