IIBM Bootcamp 2022

Institute for Biological and Medical Engineering (IIBM), Pontificia Universidad Catolica de Chile

Instructors: Carlos Valle ([email protected]) & Gabriela Vargas ([email protected])

Class materials for the IIBM Bootcamp to be held between January 17 and 21 of 2022. During the 5 days, practical excersices in relation to Programming Python, Calculus and Algebra will be teached, been the main objective to equip studens of the postgraduate programs of the Institute for Biological and Medical Engineering (IIBM) with tool that will be necessary to sucdeed in the different courses of the programs.

Jupyter notebooks and additional material for each of the days will be uploaded here.

Learning Objetives

• Adcquire basic programming skills
• Apply programming tools
• Design basic scripts
• Explain chosen methods and obtained results to an interdisciplinary and diverse audience
• Contrast the results critically and respectfully with different people

Description of the Tutorials

The following is a brief description of each tutorial generated in 2022:

Day	Colab tutorial	Description
Day 1 morning		Setting up Tools Google Colab and Github and basics of data types
Day 1 afternoon		Control flow
Day 2 morning		Reading data, arithmetics and functions
Day 2 afternoon		Excersise: 'SARS-Cov-2 sequence'
Day 3 morning - numpy		Numpy: Array and matrix
Day 3 morning - plots		Matplotlib: Figures and plots
Day 3 afternoon		Excersise: 'Chile: COVID data'
Day 4 morning		Derivatives
Day 4 afternoon		Integrals
Day 5 morning		Integrals, Linear equations, Filtering
Day 5 afternoon		Excersise: Integrate all the week content

Remember to send your work!!

In order to give you feedback, don't forget to send your work to the following form

Week Schedule

Speakers presentations

Check out the incredible speaker presentations we had throughout the week

Day	Presentation	Personal lab link
Day 1	-	Francisco Sahli Costalba
Day 2	pdf	Lab PB3
Day 3	pdf	Wenzel Lab
Day 4	-	Quantitative Physiology Lab
Day 5	pdf	Pablo Irarrazaval

Topics

Introduction

1. Overview of the course
   • Course description and objectives
   • Coding in the IIBM
2. Setting up Tools
   • Google Colab
   • Github

Python

3. Basic data types
   • Strings
   • Lists
   • Numbers (int and float)
   • Booleans
4. Control process
   • Loops: for and while
   • Conditions and if statements
   • Control statements: break, continue and pass
5. Arithmetic operators and naming conventions
   • Arithmetics operators (/, //, %, **, + and -)
   • Naming conventions for variables and functions
6. Functions and scripts
7. Data reading
   • Reading from files (.txt and .csv)
   • Reading images
   • Common libraries for data reading
8. Introduction to Numpy and Matplotlib libraries
   • Numpy: Operating with Matrix and vectors
   • Matplotlib: Plots and parameters
9. Debugging

Calculus and Algebra

10. Calculus
    • Derivatives
    • Integrals
11. Algebra
    • Matrix operations
    • Vector operations