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.
Topic: Writing Extensible and Maintainable Code in an Academic Setting: Tools, Tradeoffs, and Methodologies
Details: Wednesday, March 13, 12 - 1pm
Presenter: Matthew Giammar, CCB, UC Berkeley
Materials: Slides, Video
Topic: Leveraging Object-Oriented Programming (OOP) in Python for Bioinformatics
Details: Wednesday, February 14, 12 - 1pm
Presenter: Carmelle Catamura, Lareau Lab, UC Berkeley
Materials: Slides, Video
Topic: Estimating and visualizing population genetic structure for landscape genomics
Details: Thursday, December 14, 12 - 1pm
Presenter: George Zaragoza, Fitak Lab, University of Central Florida
Materials: GitHub Repo/Slides, Video
Topic: An introduction to snakemake: a tool for automating and streamlining your analyses
Details: Thursday, October 12, 12:00 - 1:00pm
Presenter: Stacy Li, Sudmant Lab, UC Berkeley
Materials: GitHub Repo/Slides, Video
Topic: An overview of skills and pipelines for A-Z reproducible manuscripts
Details: Wednesday, November 8, 12:00 - 1:00pm
Presenter: Juan Manuel "Manny" Vazquez, Sudmant Lab, UC Berkeley
Materials: Reproducible manuscript, Reproducible CV, Video, Slides
Topic: Leveraging R's ggplot for biological data analysis and visualization
Details: Thursday, February 2, 12:30 - 1:30pm
Presenter: Sarah Johnson, Moorjani Lab, UC Berkeley
Materials: Slides, Colab Notebook, Video
Topic: Unix tools, scripting, and parallel computing
Details: Thursday, April 6, 12:30 - 1:30pm
Presenter: Lenore Pipes, Nielsen Lab, UC Berkeley
Materials: GitHub Repo/Slides, Video
Topic: Building an imputation pipeline for low coverage ancient genomes
Details: Thursday, April 13, 12:30 - 1:30pm
Presenter: Kiran Kumar, Zoellner Lab, University of Michigan
Materials: Slides, Video
Topic: Introduction to Jax from the lens of Computational Biology
Details: Thursday, May 11, 12:30 - 1:30pm
Presenter: Martin Kim, Yosef Lab, UC Berkeley
Materials: Slides, Colab Notebook
Topic: Introduction to LaTeX using Overleaf
Details: Thursday, October 13, 12:30 - 1:30pm
Presenter: Elise Kerdoncuff, UC Berkeley
Materials: Slides, Video
Topic: Introduction to modelling single-cell dynamics
Details: Thursday, November 10, 12:30 - 1:30pm
Presenter: Michael Vinyard, Massachusetts General Hospital/Broad Institute
Materials: Video
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
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
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
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