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Hi! 👋

👨‍💻 About Me

My name is Tim (he/him).

I'm a cloud-native computational biologist and maker with a passion for problem solving. My mission is to elevate biological intuition and knowledge with a mastery of informatics and systems engineering. As a dynamic technical leader, I'm known for deciphering esoteric technical challenges; flourishing in environments where I can architect systems, craft tools, streamline processes, and mentor and advocate for others to empower an exceptional team around me.

I'm motivated and fascinated by extracting, compiling, and presenting visual meaning from complex information. Scientifically, I'm most comfortable solving mysteries large and small in the world of nucleic acid biology: sequence processing, novel assay development, and algorithmic implementation. Documentation and reproducibility are not just checkboxes; they are the backbone of my analytical work. I find my sweet spot in engineering cloud resources, informatic tools, and robust automated systems to fuel massively parallel computational biology and machine learning.

📝 My GitHub

I host a lot of random repos on GitHub - primarily a combination of bioinformatics, genAI experimentation, personal hardware projects, and home-automation related code and documentation.

Code hosted here is mostly either very old legacy and/or experiments done in spare moments here or there and doesn't represent my current style nor reproducibility/documentation practices when working on production code. The vast bulk of code I write for work is proprietary - for up-to-date code samples please contact me directly.

If you have questions or requests on any repos, please feel free to add an issue and I'll do my best to address it.

GitHub Stats

💬 Ask me about:

  • 🧬 Bioinformatics, especially Next-Generation Sequencing (NGS) informatics
  • ☁️ Cloud solutions architecture (AWS)
  • 🔌 Hobbyist microelectronics and smarthome devices
  • 🔬 Gene Therapies, Cancer Immunotherapy (CAR-T), RNA Editing, Synthetic Biology, etc
  • 🤖 GenAI
  • 🌐 Home networking

📫 How to reach me:

Create an issue here, message me on LinkedIn , or visit my (very out of date) website at www.timothyjohnstone.com

👥 Socials

LinkedIn

💻 Dev Stack includes:

Python R | Visual Studio Code RStudio

AWS

GitHub GitHub Actions Anaconda SonarLint Nginx Git

Raspberry Pi Arduino | Pi-Hole Home Assistant

Ubuntu Windows macOS Firefox

Timothy Johnstone's Projects

auto_rnngine icon auto_rnngine

Snakemake-driven pipeline for creating generative text models with tensorflow-char-rnn. Produces nice reports comparing models with various parameters.

aws-parallelcluster icon aws-parallelcluster

AWS ParallelCluster is an AWS supported Open Source cluster management tool to deploy and manage HPC clusters in the AWS cloud.

bioinformatics_collection icon bioinformatics_collection

A collection of various scripts I've written to accomplish various bioinformatic tasks. Good place to find some more updated code samples.

brewce icon brewce

Automation of Nespresso Essenza coffeemaker using Particle Photon

crush-ping icon crush-ping

A cute little IoT device which receives and prints messages.

deepestracer icon deepestracer

Reward functions for a competitive DeepRacer autonomous 1/18 scale vehicle

discord-calbot icon discord-calbot

A simple discord bot to poll scheduled events on a server/guild, convert them to ics, and push that ics to a consistent place

dna-keyboard icon dna-keyboard

Documentation for building a simple 4-key USB Keyboard that has ACGT to act as the equivalent of a tenkey for bioinformatics

dnd-chargen icon dnd-chargen

d&d character generator frontend written in shiny, uses a model generated via tgjohnst/auto-rnngine

exogene icon exogene

A workflow for identifying viral integrations in both short and long read data

gpt2-outputs icon gpt2-outputs

Outputs from running and training GPT-2 on a variety of sources

ikea-parts-db icon ikea-parts-db

beginnings of a project to scrape and catalog all ikea parts for all ikea furniture

interactive-coding-challenges icon interactive-coding-challenges

April 2017 - Huge Update! Interactive, test-driven Python coding interview challenges (algorithms and data structures). Includes Anki Flashcards.

jackboxlauncher icon jackboxlauncher

Fan made Jackbox game launcher to view all your favorite games in one spot without have to launch each game.

mask_rcnn icon mask_rcnn

Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow

padd icon padd

PADD (formerly Chronometer2) is a more expansive version of the original chronometer.sh that is included with Pi-Hole. PADD provides in-depth information about your Pi-hole.

pihole-guide icon pihole-guide

Guide to creating a Pi-Hole (DNS/DHCP server that blocks ads network-wide!)

playgrounnd icon playgrounnd

Documentation for various experiments with neural networks

r-plotting icon r-plotting

functions, guides, and scripts for various visualizations in R

restaurant-weekr icon restaurant-weekr

Hobby project to create website(s) that provide much-improved restaurant week listings (since city websites inevitably suck), powered by the Yelp API

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