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Python scripting for biochemistry and molecular biology in Jupyter Notebooks.

Paul A Craig1,2, Jessica A Nash2, T Daniel Crawford2,3

  • 1School of Chemistry &amp; Materials Science, Rochester Institute of Technology, Rochester, New York, USA.

Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology
|September 12, 2022
PubMed
Summary
This summary is machine-generated.

This workshop teaches Python programming to biochemists and molecular biologists, enabling them to move beyond basic tools. Participants will learn to write scripts for data analysis and dynamic calculations in scientific research.

Keywords:
Jupyter NotebookMolSSIPythonlive-codingworkshop

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Computational Science

Background:

  • Many biochemists and molecular biologists rely on spreadsheet and web applications for research and teaching.
  • These "plug-and-play" methods can limit the ability to handle large datasets and perform complex calculations.
  • A gap exists in accessible programming training tailored to the needs of these scientific disciplines.

Purpose of the Study:

  • To introduce Python programming to biochemists and molecular biologists.
  • To empower researchers to transition from basic tools to script-based data analysis and computation.
  • To highlight the utility of open-access scientific computing resources.

Main Methods:

  • A live-coding workshop format was developed.
  • The curriculum focuses on practical Python scripting for data parsing and dynamic calculations.
  • Emphasis is placed on utilizing open-access scientific libraries and resources.

Main Results:

  • Participants gain foundational Python programming skills relevant to biological sciences.
  • The workshop facilitates a shift towards more sophisticated data analysis techniques.
  • Awareness of and access to open-source scientific computing tools are increased.

Conclusions:

  • Python programming offers a powerful and flexible approach for biochemical and molecular biology research.
  • Training in scripting enhances researchers' capabilities in data handling and computational analysis.
  • Accessible workshops can effectively bridge the gap in computational skills for life scientists.