Computer Workbench Setting

How my computers are set up with reproducibility in mind.

Introduction

For the purpose of practicing computational biology and my passionate for epigenome analysis, I’m trying to follow Prof. Xiaole Shirley Liu’s course (STAT115 from Harvard University). In the course, they use the Unix command line, R, and Python language. Therefore, I am building the necessary skills from scratch though practice and randomly learning from online courses. I would like to acknowledge Ming (Tommy) Tang for his suggestions and role model.

This project is a big challenge for me as a pharmacist. Without good friends and great suggestions, I would not have been able to develop myself to this point. I would like to acknowledge them for their support in setting up this computer workbench.

Contents

  1. Operating System using Linux
    💡 Unix Trick: Screen to Maintain Terminal Screen
  2. Containerization using Docker
  3. Reproducible Computational Biology Workflow by nf-core
  4. Popular Computational Biology Language with R and R Studio
  5. Tracking versions of code with Git Version Control

Acknowledgment

  • I would like to acknowledge Ming (Tommy) Tang for his encouragement and the valuable knowledge he provided through various online platforms.

  • I would like to thank my software engineer friends (Bui Vinyunavan ang Guy Tongsan) who kindly supported my learning in Unix and answered my funny questions. My very first questions were, “What is this black screen🖥 from a computational biology course ?” and “How to understand those alien syntax” It’s a terminal and unix command line. 🤣🤣

  • I would like to thank all my colleagues for their comments, suggestions, and assistance.

  • Lastly, I would like to thank my Ph.D. advisor. Without him, I would not have discovered the exciting world of cancer biology. 🌞🌞 From that point, I expanded my interest to the -omic fields for a deeper understanding. 🤩🤩

I’m very happy 🥰 that you are visiting my computational biology portfolio and would be even happier if you could provide suggestions or feedback 🤩.

You can contact me through various online platforms here 📬 or leave a comment below using GitHub account. 👇🏼