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 schedule below shows an approximation of what is covered in the course.
|Day 1: Introduction to Python||
1.1: UNIX shell and Jupyter notebooks
1.2: The Basics: Hello, World!, Variables, and Printing
|Day 2: Functions and Control Flow||
2.1: Functions and Methods
2.2: Tests, Loops, and Escapes
|Day 3: Data Structures||
3.1: Lists, Dictionaries, Tuples, and Sets
3.2: Fancy Data Structures: Nested Loops
|Day 4: File Manipulations and Modules||
4.1: Reading and Writing from Files
4.2: Modules, Numpy, Scipy
|Day 5: Using External Libraries||
5.1: Introduction to Plotting
5.2: Biopython and System Calls
CCB Bioinformatics Workshops
The Center for Computational Biology offers bioinformatics workshops which follows the "Introduction to Programming for Bioinformatics" bootcamp.
Each workshop focuses on one specific topic, walking participants through a pipeline that starts with raw data and ends with some basic analysis and figure creation. While these workshops are designed to follow the Bioinformatics bootcamp, participation in the bootcamp is not a prerequisite for participation in these workshops.
|Day 1: Phylogenetics||Topic: Construction of phylogenetic trees built on whole genome sequencing data
Instructor: Christopher Hann-Soden
|Day 2: Variant Calling||Topic: Detection and analysis of genetic variants using high-throughput sequencing data
Instructor: James Hart
|Day 3: RNA-sequencing||Topic: Gene expression quantification and analysis using next generation sequencing
Instructor: David DeTomaso
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. Our core skills seminars to date are listed in reverse chronological order.
|Dec 04 2015||Speaker: Marek Kudla
Topic: Parallel Computing with OpenCL and R
|Nov 11 2015||Speaker: Bo Li
Topic: RNA-sequencing quantification with RSEM
|Oct 01 2015||Speaker: Derek Reeve
Topic: Introduction to Git
|May 05 2015||Speaker: Harold Pimentel
Topic: Kallisto/Sleuth and RNA-sequencing Tools
|Apr 27 2015||Speaker: Brooke Rhead
Topic: Navigating the Genome Browser
|Mar 30 2015||Speaker: Robert Tunney
Topic: Concepts and Applications of PCA