NOTE This was developed/organized for a class at UCSC for the Winter Quarter 2020 (January-March 2020). This is no longer an active class, but material is still up for everyone to see. If you have any questions regarding the material, please submit an issue and we will try to help you out.

The aim of the workshop is to provide the attendants with the jump-start skills necessary to begin using the command line, supercomputers, and the python programing language.

This course is going to be hands-on starting from the basics. We expect every assistant to bring their laptops, and we will go over exercises during class.

If you are a student, enrolling in the seminar is encouraged but not necessary (number 44893). The course is open now.

Starting January 10th, 2020, we will meet Fridays from 2:00-3:00pm (room is booked until 3:30pm just in case) at UCSC/CBB 110.

At the end of the course participants will be comfortable using the bash environment, submitting jobs to the hummingbird supercomputer, and writing basic python scripts.

To pass the course students formally enrrolled are expected to attend at least 70% of the classes and develop a coding project that will be presented in the last class, the project can be developed alone or with a classmate.

W-1 Setting resources necessary, introduction to bash, navigating your computer using bash

W-2 Text editors, basic bash scripts, bash loops

W-3 Introduction to version control, GitHub, Bitbucket

W-4 Connecting to hummingbird, copying data, and submitting jobs

W-5 Introduction to Python, main elements in python, conditionals.

W-6 Project pitching. Complex data types, loops...

W-7 Complex scripts in Python, processing files using loops. Installing brew and python packages.

W-8 Biopython

W-9 Manipulating data frames in Python, pandas, general coding recomendations

W-10 Students’ project presentations

• Work individually or with one classmate.
• Write a python script that solves a problem within your research. Alternatively you can write a python script about a game or something you are passionated about.
• Upload the code to github and write a readme.md file.
• Prepare for a small demostration of the code in the final class.

Merly Escalona ([email protected]): Postdoctoral Scholar in the Paleogenomics lab, experience with bioinformatics, simulation of genomic and high throughput sequencing data, and genome assembly.

Oscar Vargas ([email protected]): Former Postdoctoral Scholar in the Kay lab, experience with bioinformatics and phylogenomics. Now Assistant Professor at Humboldt State University.