CCB Bioinformatics Bootcamp
The Center for Computational Biology offers a 5-day “Introduction to Programming for Bioinformatics” bootcamp. The goals of this course are to introduce students to Python, a simple and powerful programming language that is used for many applications, and to expose them to the practical bioinformatic utility of Python and programming in general.
The course will allow students to apply programming to the problems that they face in the lab and to leave this course with a sufficiently generalized knowledge of programming (and the confidence to read the manuals) that they will be able to apply their skills to whatever projects they happen to be working on. The course assumes no programming experience, and there are no prerequisites for the course.
The next “Introduction to Programming for Bioinformatics” bootcamp will be offered from January 8-12, 2024. Please email ccbadmin@berkeley.edu if you would like to be added to the bootcamp mailing list or to receive info on how to register.
Please check our FAQ page for any questions you might have.
The schedule below shows an approximation of what is covered in the course.
| Day 1 |
Morning: Intro to Google Colab; Python basics – data types, built-in functions Afternoon: Simple data structures, built-in functions & methods, basic logic & control flow |
| Day 2 |
Morning: Review control flow & data structures; intro to NumPy arrays Afternoon: Continuation of NumPy methods & functions: shapeshifting, masking, filtering, etc. |
| Day 3 |
Morning: Review NumPy; intro to data exploration: importing, cleaning  Afternoon: Continuation of data exploration: summarizing, visualizing; mini-project |
| Day 4 |
Morning: Intro to Pandas: compare/contrast with NumPy, parsing data frames Afternoon: Continuation of Pandas: parsing, basic data science, intro to wrap-up project |
| Day 5 |
Morning: Review Pandas; continue work on wrap-up project Afternoon: Closing: more ways to interact with Python; research application office hours |
Computational Biology Core Skills Seminars
The aim of the Computational Biology Core Skills seminars is to strengthen bioinformatics training on campus by providing a setting to disseminate knowledge and experience among the student community.
These peer-taught seminars are organized by and for graduate students, but are open to other UC Berkeley researchers and affiliates.
All seminars will be in person at Stanley Hall 177.
To view the recordings of the previous Computational Biology skills seminars and tutorials, please click here.
| Dates/Times |
Speakers and Topics
|
| Thursday, October 12th, 12 – 1 PM | Speaker: Stacy Li (Graduate Student in Sudmant Lab, UC Berkeley) Topic: An introduction to snakemake: a tool for automating and streamlining your analyses |
| Wednesday, November 8th, 12 – 1 PM | Speaker: Juan Manuel “Manny” Vazquez (Postdoctoral Scholar in Sudmant Lab, UC Berkeley) Topic: An overview of skills and pipelines for A-Z reproducible manuscripts |
| Thursday, December 14th, 12 – 1 PM | Speaker: George Zaragoza (Graduate Student in Fitak Lab, University of Central Florida) Topic: Estimating and visualizing population genetic structure for landscape genomics |
| Depts/Centers | Courses | Links |
| Berkeley Institute For Data Science (BIDS) | Machine learning, data science, statistics | https://bids.berkeley.edu/events |
| Berkeley Research Computing (BRC) – Research IT | Varies | http://research-it.berkeley.edu/events |
| D-Lab | Python, Excel, and more | https://dlab.berkeley.edu/training |
| R, Python | https://dlab.berkeley.edu/people/drew-hart | |
| Tutorials in R | https://github.com/dlab-berkeley | |
| Department of Statistics | R- Bootcamp | http://statistics.berkeley.edu/computing/r-bootcamp |
| Berkeley Electrical Engineering and Computer Sciences | Varies | https://eecs.berkeley.edu/academics/courses |
| Simons Institute for the Theory of Computing | Data analysis, deep learning, and more | https://simons.berkeley.edu/workshops |
| Computational Genomics Resource Laboratory | Next generation sequencing data analysis | http://qb3.berkeley.edu/cgrl/ |
| Carpentries Club | Python, R, Shell, Git, and more | https://bids.github.io/carpentries-club/who.html |
| Berkeley Center for Cosmological Physics | Varies | http://bccp.berkeley.edu/workshops/ |
| Berkeley Nanosciences and Nanoengineering Institute | Varies | https://nano.berkeley.edu/news/conferences.html |
| UCSF Bakar Computational Health Sciences Insittute | Biomedical informatics, molecular study, systems biology, systems pharmacology | http://bakarinstitute.ucsf.edu/ |
| UC Davis Bioinformatics Core Facility | Data analysis | https://bioinformatics.ucdavis.edu/ |
