CCB Bioinformatics Bootcamp
The Center for Computational Biology offers a 5-day condensed “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 summer “Introduction to Programming for Bioinformatics” bootcamp will be held in June, 2021. The bootcamp will most likely be held online this summer.
Please email ccbadmin@berkeley.edu if you would like to be added to the bootcamp mailing list and be informed when registration is open for the summer bootcamp.
The schedule below shows an approximation of what is covered in the course.
| Day 1 | Morning: The Very Basics: Hello, World! Variables, and Printing
Afternoon: Functions and Methods
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| Day 2 | Morning: Control flow – conditional statements and loops
Afternoon: Data structures – Lists and Tuples
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| Day 3 | Morning: Data structures – Dictionaries
Afternoon: Reading and Writing from Files
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| Day 4 | Morning: Modules, Numpy, Scipy
Afternoon: Visualizing data with Matplotlib
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| Day 5 | Morning: Pandas and Data Manipulation
Afternoon: Applications and Next Steps
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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.
For Spring 2021, the core skills seminars are listed below and all seminars will be held remotely on the second Thursday of each month from 11am – 12pm. Please contact ccbadmin@berkeley.edu for a zoom invite.
To view the recordings of the previous Computational Biology skills seminars and tutorials, please click here.
| February 11, 2021 | Speaker: Giulia Guidi, Computer Science, UCB
Topic: High Performance Computing with AWS
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| March 11, 2021 | Speaker: Galen Xing, Research Assistant, UCB
Topic: Building your first Variational Autoencoder with PyTorch
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| April 8, 2021 | Speaker: Sebastian Prillo, Computer Science, UCB
Topic: Getting started with Github
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| May 13, 2021 | Speaker: Jonathan King, Computational Biology, CMU-Pitt
Topic: Deep learning for protein structure prediction with SidechainNet
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| 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/ |
