Huck Life Sciences Bldg 005 | Tuesday, Thursday 10:35am - 11:50am EST

¹Notify the instructor in advance if you are unable to attend a lecture for whatever reason.

Anton Nekrutenko aun1@psu.edu Wartik 505 Office hours by appointment only

This course does not use Canvas. Canvas is a convoluted system with too many features and undefined purpose. Instead, this course is served from GitHub.

Attendance (33.3%) + Quizzes (33.3%) + Final Project (33.3%) ≈ 100%

The will be divided into several blocks:

1. Fundamentals of data science
2. Datatypes and major analyses in modern biology
3. Specific applications

Links to individual lectures will be posted below. We will be using Galaxy Training Network infrastructure for this course. Specifically, we will be using a dedicated"learning pathway".

• Lecture 1 - Introduction and History
• Lecture 2 - Shell I
• Lecture 3 - Shell II
• Lecture 4 - Intermission + History of Sequencing
• Lecture 5 - Python 1 - Variables, expressions, statements, functions
• Lecture 6 - Python 2 - Strings and lists and FASTQ
• Lecture 7 - Python 3 - A more careful look at lists and dictionaries
• Lecture 8 - Python 4 - Processing files
• Lecture 9 - Python 5 - Recap (If you feel bored, do this)
• Lecture 10 - Pandas - A set of tools for data wrangling
• Lecture 11 - What is Machine Learning: A CNN example
• Lecture 12 - Git/GitHub 1 - Git logic
• Lecture 13 - How to create your own web-site using GitHub and Markdown + Project discussion
• Lecture 14 - How Illumina works + Introduction to Galaxy
• Lecture 15 - QCing and algorithmic foundation of mapping
• Lecture 16 - Element Biosciences Sequencing + Adding yourself to BMMB554 queue + Mapping and postprocessing of mapped data
• Lecture 17 - PacBio + Creating a mapping workflow + Understanding BAM files
• Lecture 18 - Calling variants in non-diploid systems
• Lecture 18 - ONT + First look at MEGA trajectories: Is there anything?
• Lecture 19 - Rerunning based on custom reference, Alignment: What are the differences between strains?
• Lecture 20 - Why genome alignments are difficult
• Lecture 21 - How Genomes are assembled

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