BM432

Welcome to the BM432 computational biology repository for 2022!

This repository contains materials to support workshop sessions on:

• Project management, including:
  • data management
  • reference management
• Data analysis, including:
  • data formats
  • public data resources
  • introductory statistics
• Data presentation, including
  • visualisation
  • reporting of statistical outputs
  • Open Science

These workshops are presented as part of BM432: Being a Biomolecular Scientist 4, at the University of Strathclyde.

The material you are viewing relates to the 2022-2023 presentation of the course, and was prepared by:

• Dr Leighton Pritchard
• Dr Morgan Feeney

NOTE: The 2022-2023 presentation differs from that in 2021-2022 as that the workshop sessions on data analysis are not being run. However, we continue to make the materials for this session available as they may be a useful and valuable reference for students as they work on their projects.

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How do I use this repository?

If you are a student on BM432, you should not need to use this repository, but we make it available in the spirit of open science.

As tutors, we use the code and materials in this repository to generate:

1. standalone HTML files that can be used with MyPlace
2. Shiny webapps that can be run by students on their own machines, or at rstudio.org

The material is written in R using R Markdown, and to work with or generate all the materials, we recommend that you install and use RStudio.

Using this repository on your own machine

To download and use the materials for this workshop on your own computer, please follow the guidance at the link below.

• Configuring your computer to use this repository

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Notebook HTML (2022-2023)

Notebook HTML pages for the current presentation are linked below, for convenience:

Workshop 3: “Project Management” (Wednesday 5th October 2022, 9-11am) landing page

• 01-Data Analysis in the Research Cycle
• 02-Data and Project Management
• 03-Reproducibility, Replicability, and FAIR Guidelines
• 04-Keeping a Lab Notebook to Document Your Project
• 05-Reference Management
• 06-How to Use Reference Management Software

Slides

• Workshop Slides

Example Lab Notebooks

• File 1
• File 2
• File 3
• File 4

Workshop 8: “Data Presentation” (Wednesday 16th November 2022, 10-12am) landing page

• 01-An Introduction to Data Visualisation
  • 01a-Better Tools Than Barcharts (INTERACTIVE)
• 02-Preparing Your Figures For An Audience

Workshop 9: “Presentation Advice”

• 07-01: Presentations - Intro
• 07-02: Presentations - Content
• 07-03: Presentations - Figures
• 07-04: Presentations - Aesthetics
• 07-05: Presentations - Slide Preparation
• 07-06: Presentations - Delivery

Slides

• Workshop Slides

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Notebook HTML (legacy)

Notebook pages from previous years’ presentations of this material are linked below.

“Data Management”

• 01-What is a Dataset?
• 02-Data Formats and File Formats
• 03-How to Access Data from Public Databases

“An Introduction to Statistical Distributions”

• 01-What is Statistics?
• 02-What Does Statistics Do, Anyway?
  • 02a-Exploring a Statistical Distribution (INTERACTIVE)
  • 02b-Exploring a Statistical Relationship (INTERACTIVE)
• 03-Where Do Statistical Distributions Come From?
  • 03a-Where Does the Normal Distribution Come From? (INTERACTIVE)
• 04-Hypothesis Testing

“Scientific Posters”

• 01-The Anatomy of a Scientific Poster
• 02-Preparing a Scientific Poster

(Scientific posters, for MP507)

• The Anatomy of a Scientific Poster
• Preparing a Scientific Poster

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Workshop Demos

• OpenRefine
• Excel/Minitab/R - data analysis
• Excel/Minitab/R - data visualisation