Welcome to the course website for the 2024 PSTP Bioinformatics Bootcamp!
When: April 1-12 ; 3PM-5PM PDT
Where: Stein Building rooms SCRB 247AB and SCRB 344AB
Instructor: Hannah Carter ([email protected])
TAs:
Sherlyn Weng ([email protected])
Alex Monell ([email protected])
Lia Gale ([email protected])
Questions or concerns? Please reach out by email.
| Day | Date | Topic | Links | Instructors |
|---|---|---|---|---|
| Week 1 | Basics: Tools and environments for bioinformatics | |||
| 1 | 04/01/2024 | Module 1: Commandline, accessing HPC and running 3rd party tools | Day_1 | TAs |
| 2 | 04/02/2024 | Module 2: Jupyter Notebooks / Basic coding and visualization | Day_2 | TAs |
| 3 | 04/03/2024 | Module 3: Coding and analysis with GPT | Day_3 | TAs |
| Week 2 | Resources and Advanced Workflows: Introduction to campus resources for computational research | |||
| 4 | 04/08/2024 | Module 4: Intro to SDSC / Cloud Computing | Day_6 | Subhashini Sivagnanam / Cyd Burroughs Schilling |
| 5 | 04/09/2024 | Module 5: NDex and Cytoscape / AllofUs Workbench | Day_7 | Dexter Pratt / Sally Baxter |
| 6 | 04/10/2024 | Module 6: Center for Computational Biology and Bioinformatics | Day_8 | Brin Rosenthal |
| 7 | 04/11/2024 | Module 7: Gene Pattern and the Integrative Genomics Viewer | Day_9 | Michael Reich |
Extra time will be used for the submitted projects.
Biology Meets Programming: Bioinformatics for Beginners
Bioinformatics Algorithms: An Active Learning Approach (YouTube)
BIOM262 Quantitative Methods/Genetics - Several notebooks were taken/adapted from this course and I recommend it if you want an 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 also providing some introductory theory. This is a great course to get your feet wet in the ocean of ML.
BNFO286 Network Biology & Biomedicine