Welcome to the course website for 2025 MSTP Bioinformatics Bootcamp!
When: Aug 18—Aug 22; 8AM-12PM PDT
Where: Medical Education and Telemedicine Building (MET) 315
Instructor: Hannah Carter (hkcarter@health.ucsd.edu)
TA: Vicente Fajardo Rosas (vfajardorosas@ucsd.edu)
Questions or concerns? Feel free to send along an email.
| Day | Date | Topic | Links | Homework |
|---|---|---|---|---|
| 0 | BEFORE 08/18/2025 | Setup: "Shall We Begin?" | Day_0 | Pre-Bootcamp Survey Install Ubuntu (only if Windows user) Log in to TSCC Installations |
| 1 | 08/18/2025 | Module 1: Bootcamp prep and genomics overview | Day_1 | Read Hangauer et al. |
| 2 | 08/19/2025 | Module 2: QCing and Aligning sequencing reads | Day_2 | |
| 3 | 08/20/2025 | Module 3: Alignment viz and quantification | Day_3 | |
| 4 | 08/21/2025 | Module 4: Downstream analysis in Python (DEGs, DESeq2) | Day_4 | Prep for GenePattern workshop Post-Bootcamp Survey |
| 5 | 08/22/2025 | Module 5: GenePattern Workshop | Day_5 |
Biology Meets Programming: Bioinformatics for Beginners
Bioinformatics Algorithms: An Active Learning Approach (YouTube)
BIOM262 Quantitative Methods/Genetics - Several notebooks were taken and adapted from this course and we recommend it if you'd like to have a broad introduction to bioinformatics methods.
CSE284 Personal Genomics/Bioinformatics - This is an invaluable course (focusing on personal genomics) that blends theory and application seamlessly. Information from this course also made its way into bootcamp.
CSE258 Recommender Systems & Web Mining - This course is focused on machine learning applications (primarily in Python), while providing some introductory theory. This is a great course to get your feet wet in the ocean of ML.
BNFO286 Network Biology & Biomedicine
MED278 Cancer Genomics Journal Club