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Center for Computational Biology

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Workshops and Bootcamps

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 in June 2023. 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: Introduction to Google Colaboratory and Python basics

Afternoon: Introduction to control flow and logic
Day 2 Morning: Control flow and logic, continued

Afternoon: Introduction to numpy
Day 3 Morning: Review, intro to numpy

Afternoon: Intro to numpy, continued
Day 4 Morning: Review, intro to pandas

Afternoon: Data science with numpy and pandas
Day 5 Morning: Review, plotting with pyplot & mini-project

Afternoon: Office hours, data consultation, & mini-project review

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.

Most seminars will be hybrid & meet in 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 13th, 12:30 – 1:30 PM Speaker: Elise Kerdoncuff (Postdoctoral Researcher,  Moorjani lab)
Topic: Introduction to LaTeX using Overleaf
Thursday, November 10th, 12:30 – 1:30 PM Speaker:  Michael Vinyard (PhD student,  Pinello/Getz labs at Massachusetts General Hospital/Broad Institute)
Topic: Introduction to modelling single-cell dynamics
Thursday, February 2nd, 12:30 – 1:30 PM Speaker:  Sarah Johnson (UC Berkeley)
Topic: Leveraging R’s ggplot for biological data analysis and visualization
Thursday, March 9th, 12:30 – 1:30 PM Speaker:  Tim Wood (Broad Institute, MIT/Harvard)
Topic: Clustering and dimensionality reduction in biology
Thursday, April 13th, 12:30 – 1:30 PM Speaker:  Kiran Kumar (University of Michigan)
Topic: Building an imputation pipeline for low coverage ancient genomes
Thursday, May 11th, 12:30 – 1:30 PM Speaker:  Martin Kim (UC Berkeley)
Topic: Introduction to Jax from the lens of Computational Biology

 

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/

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Outreach

  • Overview
  • Workshops and Bootcamps
  • Seminars and Symposia
  • Annual Retreat
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