Ten Quick Tips for Deep Learning in Biology

The Deep Rules project is a community-written educational article aiming to increase the quantity and quality of biological research using deep learning.

DNAvisualization.org

DNAvisualization.org is a high-performance web tool for genome-scale sequence visualization built with a novel entirely serverless architecture.

Squiggle

Squiggle is a user-friendly command line tool and accompanying Python package that turns raw DNA sequence files into interactive browser-based two-dimensional visualizations.

Freqgen

Freqgen is a software package that uses genetic algorithms to create DNA sequences that achieve amino acid, codon, and k-mer bias targets.

Hypothesis-Bio

Hypothesis-Bio is an extension for the popular Hypothesis property-based testing tool that enables the automated generation of unit tests to detect bugs in bioinformatics software. Team leader at hackseq, Vancouver, CA, 10/2019.

MechWolf

MechWolf is a tool for the description, analysis, and automation of continuous-flow chemical synthesizers.

Snacc

Snacc is a novel bioinformatics pipeline that allows for alignment-free genome-scale sequence comparison and phylogeny by means of normalized compression distance analysis.

Python Codon Adaption Index

CAI is a software package that enables the efficient calculation of codon adaptation index, relative synonymous codon usage, and relative adaptedness via both an API and a CLI.

kRTD

kRTD is a Python package that efficiently implements a novel DNA-sequence distance metric based on k-mer return time distributions.

CHERVIL

CHERVIL is a bioinformatics pipeline utilizing machine learning for the detection of endogenous retroviral expression patterns that correspond to a current or previous viral infection. Team leader at Rocky Mountain Genomics HackCon, Boulder, CO, 6/2018.

Mycroft Nutrition

Mycroft is online nutrition tool that generates daily meal plans, intelligently extracts one’s true weight from daily fluctuations, and dynamically calculates macronutrient targets. I have used it to lose over 100 lbs (45 kg) to date and kept it off for over three years.