Thursday, 9 June | Bootcamp 2022

Using MATLAB on Oscar | 9:30 - 11:00 EDT

An introduction to using MATLAB on Oscar. Topics covered include: working with MATLAB interactively on Oscar, using the MATLAB GUI, and using MATLAB in batch jobs.

slides | exercises | video

MATLAB: Programming Basics | 11:00 - 12:30 EDT

An introduction to programming using MATLAB. Topics covered include: programs and functions, relational operators, logical operators, and controlling flow with if statements and loops.

video

MATLAB: Improving Performance | 1:30 - 3:00 EDT

This workshop will cover basic performance optimization and parallel computing techniques in MATLAB, including: code profiling, pre-allocation, sequential memory access, vectorization, parallel for-loops and efficient matrix-vector storage and operations. We will assume that participants have a basic understanding of the MATLAB programming language.

slides | video

video (all sessions)

Using Jupyter Notebooks | 9:30 - 10:00 EDT

A quick overview to using Jupyter Notebooks. We will provide some Python-specific functionality and some tips about notebooks in general.

https://github.com/compbiocore/ccv_bootcamp_python/blob/main/notebooks/Using_jupyter.ipynb

Python Programming Basics | 10:00 - 12:00 EDT

An introduction to Python programming. Topics covered will include: the basics of variables, lists, dictionaries and arrays; the logic of control-flow techniques such as if-then statements, for loops, list comprehensions; a basic understanding of writing functions.

https://github.com/compbiocore/ccv_bootcamp_python/blob/main/notebooks/Intro_to_python_programming_draft.ipynb

Data Wrangling in Python | 1:30 - 3:30 EDT

A quick introduction to working with data in Python. We will touch on two ways work with data in general. A prerequisite is that you are at least familiar wiht simnple python programming or attended the previous session.

Using standard Python programming
Using Pandas the Python Data Analysis package

https://github.com/compbiocore/ccv_bootcamp_python/blob/main/notebooks/Data_wrangling_in_Python.ipynb

Using Python on Oscar | 4.00 - 4:30 EDT

A short overview on how to work with Python on OSCAR.

https://github.com/compbiocore/ccv_bootcamp_python/blob/main/notebooks/Using_python_on_OSCAR.ipynb

A Gentle Introduction to R Programming | 9:30 - 12:00 EDT

This session will cover an introduction to R, including data types and data formats, useful R functions, writing your own functions, importing and exporting data, and installing packages.

https://github.com/compbiocore/ccv_bootcamp_R/blob/main/R_Bootcamp_Intro_R.ipynb

video

R/TidyVerse Essentials | 1:30 - 2:30 EDT

This session will cover data wrangling (filtering, reshaping, joining) using Tidyverse.

https://github.com/compbiocore/ccv_bootcamp_R/blob/main/R_Bootcamp_Tidyverse.ipynb

video

Essentials of GGplotting with R | 2:45 - 3:45 EDT

This session will cover data visualization using ggplot.

https://github.com/compbiocore/ccv_bootcamp_R/blob/main/R_ggplot2.ipynb

video

Using R on Oscar | 4:00 - 4:30 EDT

This session will briefly cover different approaches to using R on Oscar.

https://github.com/compbiocore/ccv_bootcamp_R/blob/main/R_on_Oscar.ipynb

video

Introduction to Julia | 9:30 - 11:30 EDT

The Julia programming language has been gaining popularity in the scientific computing and data science communities. The language boasts performance characteristics approaching that of compiled languages like C, C++, and Fortran, while also being as expressive as Python, R, Ruby, or Matlab. This will be an introduction to the Julia language for users without previous experience using Julia. This will be a "hands-on" introduction, and will cover the basics of the language. No prior experience with Julia is required; some familiarity with another programming language will be benficial, but is not necessary.

video