Schedule¶
We start with bioinformatics to learn fundamentals of genomics and transcriptomics. Afterwards, we will cover structure prediction, molecular simulations, and computer-aided drug design in our computational structural biology module. Our third module in scientific python will introduce how we can use Python in computational biology.
Module 01 - Bioinformatics¶
Week 1¶
Tuesday (Aug 27) Lecture 01
- Topics: Introduction to computational biology.
Thursday (Aug 29) Lecture 02
- Topics: DNA sequencing technologies.
Week 2¶
Tuesday (Sep 3) Lecture 03
- Topics: Quality control.
Thursday (Sep 5) Lecture 04
- Topics: De novo genome assembly.
Week 3¶
Tuesday (Sep 10) Lecture 05
- Topics: Gene annotation.
Thursday (Sep 12) Lecture 06
- Topics: Sequence alignment.
Week 4¶
Tuesday (Sep 17) Lecture 07
- Topics: Introduction to transcriptomics.
Thursday (Sep 19) Lecture 08
- Topics: Read mapping.
Week 5¶
Tuesday (Sep 24) Lecture 09
- Topics: Gene expression quantification.
Thursday (Sep 26) Lecture 10
- Topics: Differential gene expression.
Week 6¶
Tuesday (Oct 1)
- Topics: Review
Thursday (Oct 3)
- Topics: Exam 1
Module 02 - Computational structural biology¶
Week 7¶
Tuesday (Oct 8) Lecture 11
- Topics: Structural biology and determination.
Thursday (Oct 10) Lecture 12
- Topics: Protein structure prediction.
Week 8¶
Tuesday (Oct 15) Fall break (no class)
Thursday (Oct 17) Lecture 13
- Topics: Molecular simulation principles.
Week 9¶
Tuesday (Oct 22) Lecture 14
- Topics: Molecular system representations.
Thursday (Oct 24) Lecture 15
- Topics: Gaining atomistic insights.
Week 10¶
Tuesday (Oct 29) Lecture 16
- Topics: Structure-based drug design.
Thursday (Oct 31) Lecture 17
- Topics: Docking and virtual screening.
Week 11¶
Tuesday (Nov 5) Election day: Go vote (no class)
Thursday (Nov 7) Lecture 18
- Topics: Ligand-based drug design.
Week 12¶
Tuesday (Nov 12) Review
Thursday (Nov 14): Exam 2
Module 03 - Scientific python¶
These are optional lectures that will not negatively affect your final grade.
Week 13¶
Tuesday (Nov 19) Lecture 19
- Topics: NumPy
Thursday (Nov 21) Lecture 20
- Topics: Polars
Thanksgiving break¶
No class on Nov 26 and 28.
Week 15¶
Tuesday (Dec 3) Lecture 21
- Topics: Matplotlib
Thursday (Dec 5) Lecture 22
- Topics: SciPy
Week 16¶
Tuesday (Dec 10) Lecture 23
- Topics: Scikit-learn
Final¶
Monday (Dec 16) Final exam
- An optional, cumulative final exam will be offered to replace lowest exam grade.