Fall 2025
Information for the course, including homework assignments and information about exams, will be posted here as we progress through the semester.
Lecture 01 – Introduction to MSCBIO 2025 and setup [reading] [slides] [notebook]
Lecture 02 – File systems and bash [reading] [slides] [notebook]
Lecture 03 – More on the command line [reading] [slides] [notebook]
Lecture 04 – Introduction to Python [reading] [slides] [notebook]
Lecture 05 – Data visualization [reading] [slides] [notebook]
Lecture 06 – Vectors with numpy [reading] [slides] [notebook]
Lecture 07 – Differential equation modeling [reading (introduction)] [slides] [notebook]
Lecture 08 – Principles of code design and functions [reading 1] [reading 2] [slides] [notebook]
Lecture 09 – Function fitting [reading] [slides] [notebook]
Lecture 10 – Systems biology modeling [reading] [materials]
Lecture 11 – Principles of data analysis and pandas [reading] [slides] [notebook]
Lecture 12 – Tabular data with Pandas [reading] [slides] [notebook]
Lecture 13 – Sequence analysis I [reading] [slides] [notebook]
Lecture 14 – Sequence analysis II [reading] [slides] [notebook]
Lecture 15 – Protein dynamics with ProDy [reading] [slides] [notebook]
Lecture 16 – More protein dynamics [slides] [notebook]
Lecture 17 – Molecular dynamics analysis I [slides] [notebook]
Lecture 18 – Molecular dynamics analysis II [slides] [notebook]
Lecture 19 – Clustering and Dimensionality reduction [slides] [notebook]
Lecture 20 – Clustering and Dimensionality reduction-II [slides] [notebook]
Lecture 21 – RNA Sequencing [slides] [notebook]
Lecture 22 – RNA Sequencing II [slides] [notebook]
Lecture 23 – RNA Sequencing III [slides] [notebook]
Lecture 24 – Deep Learning [slides] [notebook]
Lecture 25 – Tutorial [slides] [notebook]
Follow the assignment links below to work on and submit each homework through GitHub Classroom.
Homework 01 – Bash introduction [assignment]
Homework 02 – Plotting in Python [assignment]
Homework 03 – Differential equations [assignment]
Homework 04 – Function fitting [assignment]
Homework 05 – Systems biology modeling [assignment]
Homework 06 – Data analysis with pandas [assignment]
Homework 07 – Sequence processing [assignment]
Homework 08 – Protein dynamics [assignment]
Homework 09 – Molecular dynamics [assignment]
Homework 10 – Dimensionality reduction [assignment] [Single-cell datafile][Answer template][Figure to analyze]
The materials here draw from previous versions of the course taught by David Koes and friends.
