Schedule Details
Bootcamp is held in the week prior to the start of Fall classes, from September 16, 2024 to September 20, 2024. Unless specified otherwise, activities are held in MET. Breakfast and lunch are provided each day.
Please note the schedule is actively being developed and is subject to change.
Color Key
Monday, September 16, 2024
BISB Opening Statement from Program Chairs
Welcome to the BISB/BMI graduate program! Our program directors will provide an overview of the Bioinformatics and Systems Biology graduate program.
BISB Administrative Overview
Bootcamp Overview
Module 1: Understanding Computational Environments
In this module we will introduce you to the UCSD Jupyterhub (Data Science) Platform. You will learn how to navigate with Command Line Interfaces (CLI) using a Terminal Application. We will also cover package and environment management with including: how to use the conda package manager, configuring conda channels, creating, saving, and loading new conda environments, and the basics of commonly-used python packages (e.g., jupyterlab, numpy, etc.) We will also go over the 5 basic concepts found in most programming languages. We will also review some examples of common programming tasks in bioinformatics including printing/manipulating text and reading/writing files.
Module 2: Introduction to Next-Generation Sequencing
In this module we will describe the molecular biology foundations of sequencing technologies, from the original sanger method to the current cutting-edge. We will work with sequencing data from the SK-BR-3 breast cancer cell line to learn about sequencing data file formats, compare data from different technologies, and search for cancer mutations.
Breakout: International Student Info / Choosing a PhD Advisor
International Student Info: This section will cover a brief introduction of the first things that international students have to deal with once they arrive in the US, and important points to consider in the BISB program. Also how to connect with other international students on campus!
Choosing a PhD Advisor: What should you consider when deciding on a lab beyond your research interests? Here are tips and questions to ask when identifying your new home for the next few years.
Enjoying San Diego: The BISB Guide to San Diego Sights, Eats, and Drinks
Tuesday, September 17, 2024
BMI Opening Statement from Amy Sitapati
Welcome to the BISB/BMI graduate program! Our program directors will provide an overview of the Bioinformatics and Systems Biology graduate program.
Module 3: Pragmatic Statistics for Modern Biology
In this module we will introduce you to regression analysis and its applications in biology, including multiple regression, generalized linear models, and mixed effects models. We will also touch upon the multiple testing problem, regularization, and bayesian vs frequentist statistics.
Module 4: Introduction to Machine Learning
Wednesday, September 18, 2024
Module 5: Bioinformatics Problem Sets
In this module, you and a partner will be given a relatively simple problem to solve from the Rosalind Bioinformatics Project’s textbook track and bioinformatics stronghold track. By the end of this module, you should: 1. Have a working solution for your problem prepared! 2. Have a short slide (in this presentation) explaining your code along with a fun fact about yourselves!