Thursday, 9 June
Introduction to Programming
Today's tutorials will occur along four tracks, each devoted to a different programming language, running concurrently. Each tab below corresponds to one of these tracks. The tutorials associated with each track are listed on the relevant tab.
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.
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.
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.
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.
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
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
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
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
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
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.
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