OCIUW
This is a (growing) collection of course materials and readings for the Okinawa Collaborative International Undergraduate Workshop 2015 at OIST.- Course Software
- General Resources
- Data Analysis and Statistics
- Images in Biology
- Modelling and Simulation
Course Software
-
Download and install R and RStudio. Do this by completing Steps 2.1 and 2.2 in the following guide:
- Download and install COPASI. Installation instructions for various platforms can be found here.
General Resources
-
Workshop facebook group
- Workshop schedule
- Quabinet - collection of quantiative biology resources
Data Analysis and Statistics
Learning Goals
- Thinking
- Critically read and assess a data analysis presented in a paper
- Evaluate scientific claims and understand degrees of belief
- Doing
- Systematically assess data collection, presentation, and analysis using a catalogue of criteria
- Feeling
- Gain confidence in understanding and performing data analyses
- Appreciate the importance of decisions made in design, analysis and presentation of data
- Be wary of commonly made mistakes
(Optional) pre-course reading
-
I Fooled Millions Into Thinking Chocolate Helps Weight Loss. Here's How.
Images in Biology
Learning Goals
- Thinking
- Reflect on the choices made when producing and processing an image
- Understand the relationships between data and images
- Compare and contrast different ways to represent the same data
- Doing
- Produce and process image according to visualisation principles
- Feeling
- Appreciate the beauty of information
- Strive for clarity and truth
(Optional) pre-course reading
-
PLoS Biol, 13(4): e1002128.
Further resources
-
Data visualisation pinterest board
-
Second edition, Graphics Press LLC.
Modelling and Simulation
Learning Goals
- Thinking
- Reproduce the steps in going from a conceptual model to a computational model
- Discuss the assumptions behind a model
- Recognise a situation where simulations are beneficial
- Doing
- Build simple models using the COPASI simulation software
- Navigate BioModels Database
- Feeling
- Appreciate the value of modelling and simulations in biology
- Feel empowered to use simulations in their own work
(Optional) pre-course reading
-
Nature Reviews Genetics, 16, 146-158.
Further resources
-
Modelling success stories from Nicolas Le Novère's blog
- Model of the Month on BioModels database
-
Modelling success stories from Nicolas Le Novère's blog
-
Data visualisation pinterest board