Name: John Vivian
Type: User
Company: Ideaya Biosciences
Bio: Bioinformatics Ph.D.
Principal Bioinformatics Scientist. Ideaya Biosciences.
Python, Bayesian inference, Rust, technical metal, drumming, machine learning
Location: United States
Blog: http://jvivian.github.io/
John Vivian's Projects
Notebook, data, and methods repository
A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.
Advent of Code challenges
2018 Advent of Code challenges done in Rust
Calculate probability distributions for the game Aristeia
A quick lightning talk on using arrow and dplyr together
Averse is a recipe store and meal planner written in Rust as an exercise
Identify gene outliers from RNA-seq expression
Teaching the fundamentals of bioinformatics and data science. BD2K Summer Workshop 2016
Finds LatTeX citations in HTML documents and replaces with links.
Repository for posts / code that don't need their own repo
Class lectures for BME-230B
Identify relationships between cancer drivers
Lazy kids abusing machines
Repository for CWL Specfications
Ipython Notebooks detailing homework and notes from Andrew Ng's Machine Learning Course
Crossword generator engine in Python
deep learning of TCGA data
Dev
Dockerfiles and assets for building Docker containers
Collection of docker tools
My dotfiles synced form localhost and remote machines
Collects metrics from running EC2 instances. Can shut down workers when they go idle
The fastai book, published as Jupyter Notebooks
FASTQ pairing algorithms written in Rust
A microframework based on Werkzeug, Jinja2 and good intentions
A Bayesian model for identifying gene expression outliers for individual single samples (N-of-1) when compared to a cohort of background datasets.
Repository for learning about Attention/Transformer architecture by building one from scratch