CompBio Skills Seminar


These seminars are taught by graduate students and focus on software tools, techniques, and libraries that are useful for researchers performing computation and data analysis. There is an emphasis on subjects related to the biological sciences, but many of the techniques are general and the seminar is open to researchers in all disciplines.

Spring 2022

Topic: Introduction to R's tidyverse for data science
Details: Wednesday, Feb 9, 12 - 1pm
Presenter: Monica Arniella, CCB, UC Berkeley
Materials: Slides, Tutorial, Additional Materials, Video

Topic: Introduction to computational population genetics
Details: Wednesday, March 9, 12 - 1pm
Presenter: Yun Deng, CCB, UC Berkeley
Materials: Static notebook, Interactive notebook, Video, Slides

Topic: Using Github Actions for collaborative development projects
Details: Wednesday, April 13, 12 - 1pm
Presenter: Valeh Valiollah Pour Amiri, Research Engineer, UC Berkeley
Materials: Slides pdf, Slides link, Video

Topic: Introduction to scikit-image for 3D image analysis
Details: Wednesday, May 11, 12 - 1pm
Presenter: Alexandre de Siqueira, BIDS Postdoctoral Fellow, UC Berkeley
Materials: Tutorial, Video

Fall 2021

Topic: Fast and efficient preprocessing of single-cell RNA-seq with kallisto | bustools
Details: Wednesday, Sept 15, 12 - 1pm
Presenter: Joseph Min, EECS, MIT
Materials: Slides/Tutorials, Video

Topic: Making and hosting your personal website using Jekyll and Github pages
Details: Wednesday, Oct 13, 12 - 1pm
Presenter: Graham Northrup, Computational Biology, UCB
Materials: Slides, Repository, Video

Topic: Single-cell and spatial transcriptomics data analysis with Seurat in R
Details: Wednesday, Nov 10, 12 - 1pm
Presenter: Yutong Wang, Biostatistics, UCB
Materials: Tutorial, Video

Topic: Intro to Pyro: a probabilistic programming language for Python
Details: Wednesday, Dec 15, 12 - 1pm
Presenter: Justin Hong
Materials: Tutorial, Slides, Video

Spring 2021

Topic: High Performance Computing with AWS
Details: Thursday, Feb 11, 11am - 12pm
Presenter: Giulia Guidi, EECS, UCB
Materials: Tutorial, Video

Topic: Building your first Variational Autoencoder with PyTorch
Details: Thursday, March 11, 11am - 12pm
Presenter: Galen Xing, Research Assistant, UCB
Materials: Tutorial, Video

Topic: Getting started with Github
Details: Thursday, April 8, 11am - 12pm
Presenter: Sebastian Prillo, EECS, UCB
Materials: Slides, Video

Topic: Deep learning for protein structure prediction with SidechainNet
Details: Thursday, May 13, 11am - 12pm
Presenter: Jonathan King, Computational Biology, CMU-Pitt
Materials: Slides, Notebook, Video

Fall 2020

Topic: Getting Started with Tensorflow
Details: Thursday, Sept 10, 11am - 12pm
Presenter: Matt Jones, Bioinformatics UCSF
Materials: Tutorial, Video

Topic: Leveraging Julia for data science
Details: Thursday, Oct 1, 11am - 12pm
Presenter: Tamas Nagy, Bioinformatics UCSF
Materials: Video, Slides

Topic: Building reproducible software packages with Python, pip, and conda
Details: Thursday, Nov 5, 11am - 12pm
Presenter: Alyssa Morrow, Computer Science, UCB
Materials: Prerequisites, Tutorial, Poll, Video

Topic: Single-cell data analysis with Scanpy and scvi-tools
Details: Thursday, Dec 3, 11am - 12pm
Presenter: Adam Gayoso, Computational Biology, UCB
Materials: Tutorial, Video