Skip to content

Latest commit

 

History

History
96 lines (55 loc) · 2.44 KB

Welcome_BIO720.md

File metadata and controls

96 lines (55 loc) · 2.44 KB
title author date output editor_options
WelcomeToBio720
03 Sep 2024
slidy_presentation ioslides_presentation
keep_md highlight fig_retina
true
tango
1
default
chunk_output_type
console

Welcome to BIO720!

Introductions

  • Dr. Ian Dworkin
  • Dr. Brian Golding
  • All y'all

Introduce yourself

  • Name

  • What are you studying? Are you new to McMaster?

  • What skills do you hope to develop during this class?

Why do we use (and need) computers for modern scientific research?

Why do we use (and need) scientific computing skills for modern scientific research?

Learning Objectives for the course

  • develop fundamental computational skills necessary for modern biological research

  • Open the door for you to develop your computational skills for your needs (genomics, bioinformatics, simulations, image analysis..)

  • Organizing your research around principles of reproducibility

What this course is not

  • Genomic analysis course. Covered in BIO722.

  • Bioinformatics class.

  • A computer science course.

  • A statistics course. BIO708.

Course organization and assignments

  • Weekly problem sets

  • Dr. Brian Golding with be sending out an email on how these will be peer evaluated (yes, you are evaluating each other).

Topics

  • Reproducible Research, literate programming and science (ID)

  • Introduction to practical computer programming for science, using R (ID)

  • Introduction to the UNIX command line (shell) and remote computing (BG)

  • Putting it all together (a few examples in bioinformatics, genomics and maybe image analysis?)

Break

What is reproducible research

Literate programming

Literate programming just means combining the computer code with an explanation of what and how you are doing something in a natural language.

The wikipedia page is pretty good for this

R markdown

  • Many ways of achieving this

  • At least while working in R we will use R markdown via Rstudio.

    • R studio also has a newer approach, quatro, which is pretty similar.

R markdown

Let's do a few examples.

  • Combines code snippets (R, python, c++, bash) with a very simple markup language (called markdown) that is human readable, and can be rendered.

link to github page for the class on this

go here