Yang Choo

Hi, I'm a full stack engineer currently obsessed with solving the reproducibility crisis in biology with robotics and machine learning.

I'm leading a team at automated cloud laboratory, working with roboticists, scientists and engineers.

Previously, I studied Chemical Engineering, Biomedical Engineering, and Computational Biology at Carnegie Mellon. At CMU, I was heavily involved in academic research and founded and led multiple organizations to success.

I create software to advance science

Primary architect of Transcriptic Python Library

Developing a SDK for scientists to send runs, fetch data, visualize and analyze results

Curator of Autoprotocol

Maintaining an open-source standard for describing automated biological protocols

Core developer of Autoprotocol-Python

Enabling scientists to programmatically generate validated Autoprotocol

Proponent and developer of CLIs and libraries

Facilitating access to execution contexts for debugging and providing an audit trial

The traditional methods for designing and debugging experiments are inefficient and I believe software development tools can greatly accelerate scientific progress

Jupyter interface (Transcriptic Python Library)

I build automation infrastructure

Full-stack device integrator

Evaluating devices, abstracting instruction interface to coding device API

Liquid handling expert

Developing automatic workflows for liquid-handling calibration and optimization

Data Scientist

Designing algorithms and building pipelines for image and time-series classification

Quality Control Engineer

Building statistical models to capture robot performance and flag anamolies

The standard data generation process of biology is unreliable and I believe automation is a necessary and sufficient condition for predictive biology

Tecan Cavro Omni robot

Master of Science in Computational Biology

Carnegie Mellon University, May 2015

MCSB Merit Fellowship
Accelerated completion

Automation and Machine Learning
Machine Learning with Large Datasets
Cell and Systems Modeling
Computational Bio. Modeling and Simulation
Computational Mol. Bio and Genomics
Bioimage Informatics

Bachelor of Science in Chemical Engineering

Double Major in Biomedical Engineering

Carnegie Mellon University, May 2014

College Honors
University Honors
Mortarboard Honors

Chemical Process and System Design
Chemical Process Control
Cellular and Molecular Biotechnology
Biomedical Engineering Design
Optimization Methods and Algorithms
Introduction to Computer Systems

Staff Software Engineer

Strateos

Menlo Park, May 2019 to Present

Technical Leadership. Leading efforts to migrate all services to a cloud-native approach, utilizing Kubernetes and Docker for scalable deployments. Led multiple major language and framework upgrades, ensuring that technical stack remains cutting-edge. Leading proof-of-concepts such as implementing microfrontends using module federation to allow incremental delivery of frontend features.
Product management. Led technical delivery of a bleeding-edge Chemistry and Biology robotic laboratory. Involved in all aspects: from experimental refinement, to design and coordinating implementation of new compiler, coordination and execution services. Built execution layer in Scala backend using reactive streams (Akka + RabbitMQ) to handle concurrent execution of worklows spanning multiple physical hubs with IO, storage, execution and analytical submodules.

Computational Bioengineering Technical Lead

Transcriptic

Menlo Park, May 2015 to May 2019

Product management. Coordinated mechanical and software engineers, biologists and operators for integrating new devices into the automation stack. Led deployment and integration of software platform with external partners for end-to-end automation of biological workflows.
Devtools engineer. Empowered scientists by architecting and building devtools for decreasing development and debugging time. Built Python libraries for experimental design, data querying and automated analysis.
Full-stack data scientist. Built colony picking and liquid-handling anamoly detection pipelines using open-source Python libraries. Deployed flask-based classification microservice, created annotation service on Ruby backend calling Slack and Google Sheets API.
Infrastructure reliability. Built end-to-end integration testing pipeline for production experiments using Docker, Jenkins pipeline, custom pytest plugins and various APIs. Developed automated QC workflows and analysis tools for ensuring robotic platform reliability.
Backend engineer. Contributed to a Scala backend for device automation and coordination. Ranging from inter-device communication using Akka and RabbitMQ frameworks to driver-level interaction over RS-232 and ethernet to scheduling with a constrained optimization framework.
Statistician and modeler. Created mathematical and statistical models for all forms of data, from liquid handling calibration workflow to geometric well-shape models.

Molecular Technician

Emerald Therapeutics

Menlo Park, Summer 2013

Optimized synthesis process and analysis aspects of peptide synthesis project
Programmed protocols for various automated instruments and parse instrument logs

Peer Tutor

Carnegie Mellon University

Spring 2011 to Fall 2014

Tutored fellow students in an individual and group setting on various courses (included Chemical Engineering, CS, Math and Biomedical Engineering courses)
Teaching assistant for Computational Biology gateway course (for undergrad and graduate students)

Closed-loop Biological Optimization

Transcriptic, Summer 2018

Designed and built a fully automated closed-loop workflow for learning optimal fluorophore spectra
Enabled a 1000-fold improvement in time to solution

Deciphering of Mutational Signatures from exomic and genomic data

Duke-NUS Center for Computational Biology, Summer 2014

Developed Python/R pipeline for analyzing mutational signatures from pre-processing, analysis to visualization
Published paper using results from applying pipeline to cancer data

Application of Machine Learning techniques to clinical asthma data

Masters Research, Fall 2014 to Spring 2015

Built probablistic graphical models of regulatory networks from gene expression and clinical data
Determined shared mechanisms across disease subtypes and predict effective drug targets

Simultaneous quantification of RNA and Protein levels via fluoromodules

CMU iGEM Team Founder, 2012

Won the Best Foundational Advance Project, placed top 16 world-wide out of 190 teams
Designed and submitted BioBricks which are part of a novel characterization system

Python
Scala
Ruby
JS (Vue, React)
R
Java
Matlab
C++

Docker
Kubernetes
Terraform
Jenkins
Ansible

TensorFlow
Scikit-Learn
Spark
Hadoop

Github
Unix
AWS
GCP

Flask
Ruby on Rails
Django
Play
SpringBoot

Akka
RabbitMQ
Kinesis

PostgreSQL
InfluxDB
Redis

Hamilton
Labcyte
Tecan
Agilent
Thermo-Scientific
Gilson

Plate Reader
Centrifuge
Sealer/Peeler
Robotic Arm
Thermocycler
Mass Spectrotometer

Culture (including E. Coli, Yeast, HEK293, MEFs, hESCs)
Cloning
Transfection
Flow Cytometry
Cytotoxicity

Next-Generation Sequencing
PCR
qPCR
Microarrays

ELISA
Western Blot
Immunofluorescence

Solid Phase Peptide synthesis (FMOC)

MADLI
HPLC
GC
UV-Vis

President

Led chapter to Gold Award, exceeding all service and organization requirements
Initiated the highly successful `Life Lessons` series which packed the campus auditorium

Founder, Petition Chair, Philanthropy Chair, Judicial Board Chair

Led and drove all phases of the petitioning process, ensuring that the colony met all requirements to become a fully-fledged chapter
Led creation of chapter bylaws and initiated Gentlemen Sig Program, a holistic skills development program

President, Treasurer

Organized numerous social, networking and acclimatization events; liasing between government, school and company officials
Balanced budget and ensured successful deployment of a complex 6-month booth construction project

Institute of Bioengineering and Nanotechnology, Singapore

Proposed and started project which led to a paper

Characterized delivery efficacy of various cationic bolaamphiphiles

Laboratory for Computational and Engineering Cell Biology

Designed and fabricated masks for controling axonal transport geometry

Optimized multi-layer mold fabrication process

Yang Choo

I create software to advance science

I build automation infrastructure

Curriculum Vitae