Justin Vrana

sythetic biologist | software engineer

Currently

Software engineer, Just-Evotec Biotherapeutics, Seattle, WA

Research interests

Synthetic biology | cellular computation | computer-aided design and manufacturing | laboratory automation | democratization of science

Summary

I am a trained researcher with 10 years experience in software engineering and synthetic biology. I believe in the power of using biology as an engineering medium to improve our world. To this end, I am passionate about building genetic and software tools that facilitate rapid prototyping and engineering of new organisms.

During my PhD work, I have built among the largest genetic circuits using CRISPR in Baker’s yeast (2017). Currently, I am working on high-throughput genetic circuit characterization methods in human cells and using deep learning to understand synthetic gene circuits. Additionally, I am working with DAPRA to develop a computer-aided manufacturing system to automate the design-build-test-learn cycle for engineered organisms. I’ve worked on several projects related to lab automation, including an Amazon Catalyst-backed project for developing a mammalian engineering cloud laboratory and a collaborative project to improve reproducibility of clinical laboratory tests in low-resource settings using human-in-the-loop automation.

I am currently finishing up a few projects and related publications before my anticipated graduate in 2019/2020. I am searching for jobs at intersection of software engineering and synthetic biology.

Education

2014-2021 Ph.D, University of Washington-Seattle

Department of Bioengineering

Advisor: Eric Klavins

Dissertation: Automating the design and construction of engineered S. cerevisiae strains using end-to-end computer-aided design, planning, and manufacturing.

2007-2010 BS, University of Wisconsin-Madison

Department of Chemistry (Honors in the Major)
Department of Philosophy
Graduation with Distinction
Dean’s List (2007-2011)

2009-2010 Certificate in Computer Science, University of Wisconsin-Madison

Technical Skills

Computation

Programming Languages: Python, Ruby, JavaScript, Java, C/C++, BASH

Web Development: Flask, Ruby on Rails, React, Jekyll, HTML, CSS, Bootstrap

Software tools: Git, GitHub, Docker, Docker-Compose, SQL, UNIX commands

Modeling and data analysis: TensorFlow, graph neural networks, NumPy, SciPy, dynamical modeling, ODE simulation/modeling

Wetlab

Yeast: cell culture, transformations, genomic integrations, CRISPR multiplex integration

Mammalian: cell culture, plasmid transfections, lentivirus production, microscopy

Molecular biology: gibson assembly, golden gate, HT library cloning

Assay: flow cytometery, cell sorting, Illumina NGS, single-cell RNA Seq

Awards

2018 DLA Piper $2,500 Best Idea with Global Reach For for OLASimple, a start up centered around a drug-resistance detection diagnostic and accompanying lab automation software.

2018 UW Business Plan Competition (Final 16) For business plan for OLASimple.

2017 $100K Amazon Catalyst Grant For UW BIOFAB, a cloud laboratory for genetic engineering to expand to automated mammalian cell work.

2015 Top prize, 2015 CSN Sandbox Competition For VertiGone, an app & hardware that detects the onset of a fall and helps reorient patients using 3D auditory cues.

2010 Phi Beta Kappa

2010 iGEM Gold Award

2008 Sophomore Honors Research Apprentice Grant

2007-2010 William F. Vilas Grant

2007-2011 Anthony Delorenzo Grant

Software Projects

2019-present Terrarium
Terrarium is a dynamic computer-aided process planner (CAPP) for biology designed for agile manufacturing of biological products, such as E Coli & Yeast strains, or Mammalian cell lines. The software automatically plans scientific experiments in Aquarium using historical planning data and current laboratory inventory and solves an MST optimization problem to give optimal and valid operational workflows.

2017-present DASi Automated DNA Assembly
DASi is an automatic DNA cloning plan designer aimed for operating on small budgets by focusing on material re-use and a dead-simple user interface. The software converts a nucleotide sequence, or a library of sequences, to an executable molecular assembly plan while optimizing material cost, assembly efficiency, and assembly time. No molecular biology expertise is required to use DASi. DASi produced plans can be automatically executed using a biofabrication facility (such as the UW-BIOFAB.

2016-present Aquarium/Trident
Aquarium, a open-source human-in-the-loop laboratory automation system that enables rapid, flexible, and reproducible workflow development and execution. Trident (developed by Justin Vrana), is the fully-featured Python interface for Aquarium that allows high-throughput scripted experiment submission, fast data mining, and machine learning on experimental data.

Mini Projects

BenchlingAPI The unofficial Python API for Benchling.

jdna A Python DNA sequence editor that represents sequences as a linked list. It includes basic molecular reaction simulations and a viewer class.

pyblast-bio Python wrapper for installing and using NCBI’s BLAST algorithms.

keats Keats is a Python build, installation, and workflow manager.

Experience

2018-present Researcher for DARPA Synergistic Design and Discovery (SD2) UW-Seattle
I am currently the lead for design and build for yeast construction for the SD2 DARPA program, for which I consult on building genetic circuit and act as software developer. I have developed python-based automation tools for automating the design and build of engineered yeast strains. Borrowing concepts from computer-aided manufacturing, I created the first computer-aided process planner for biology, allowing researchers to design and build new plasmids and yeast strains with no prior knowledge of molecular biology or laboratory operations. Currently, I am working with mathematicians at Duke and Montana State University to implement and test a new dynamic genetic circuit design tool. So far, we have used the automation tools I have developed to automatically design experiments to build and test 350 new yeast strains and plan over 2000 laboratory operations. Using docker and cloud computing tools, I deployed my software to the Texas Advanced Computer Center (TACC) cluster for automated integration with other teams within the program.

2014-present Graduate Researcher UW-Seattle
Lab of Eric Klavins, Deparment of Bioengineering
I designed, built and tested genetic circuits for digital computation using CRISPR/dCas9 in yeast. At the time (2017), built the largest genetic circuit ever constructed in a eukaryote. Performed mathematical modeling of behavior and fitted experimental results using differential evolution optimization. Performed parameter sensitivity analysis. In addition to this research, I have also performed continuous development and testing of Aquarium, a laboratory operating system for reproducible experimental execution. I was the main developer for Aquarium’s Python API and machine learning tools for data mining and experiment design tools, contributing over 350K lines of code.

2017-2019 Software lead, OLA Simple, Seattle, Washington
I was the lead for the automation software that paired with an innovative point of care lab diagnostics. I developed code (Ruby/Ruby-on-Rails/Docker) the provides inventory tracking and highly reproducible protocol instruction for clinical diagnostic assay to detect drug-resistance in HIV patients. I traveled to implemented the diagnostic kit and software in Nairobi, Kenya to simulate low-resource settings. 98% of new users were able successfully complete diagnostic assay using the automation software.

2017-2018 Amazon Catalyst Fellow UW-Seattle
Development of digitally guided protocols and workflows in which users are able to design custom mammalian cell lines, develop experimental workflows to assay them, view and analyze data, and execute experiments, all from the comfort of a coffee shop.

2016-2017 Workflow Developer UW BIOFAB, University of Washington-Seattle
Founding member of the synthetic biology foundry UW-BIOFAB. Developed highly reproducible human-in-the-loop automation workflows for molecular cloning and yeast strain construction. Consulted team on scientific validity of experiments and procedure.

2011-2014 Research Assistant University of Colorado-Denver
Lab of Chandra Tucker. Developed light inducible systems for gene expression, protein targeting, endocytosis, actin polymerizationin both yeast and mammalian cells. Characterized light dependent dimerization of phytochrome and cryptochrome proteins to develop novel red/blue light inducible protein dimerization systems. Analyzed of non-amyloid protein aggregation to understand protein recycling in yeast and mammalian cells. Developed code and hardware for optogenetic light delivery systems.

2008-2011 Research Assistant University of Wisconsin-Madison
Lab of David C Schwartz, Department of Chemistry and Genetics
Developed platform for single molecule dynamic studies and confined 2-dimensional biochemistry. Used lab built genomic optical mapping to construct low-resolution genome maps for bacterial, plant, and human genomes. Used university high-throughput computing cluster to assembly whole genomes.

2010–2011 Research Intern University of Wisconsin International Genetically Engineered Machines Team (iGEM)
Lab of Brian Pfleger, Department of Chemical and Biological Engineering
Developed of recombination based genetic circuit in E. Coli for detection of sequential environmental input Developed of bacterial peptide delivery system for probiotic therapy.

2008-2009 Undergraduate Research Scholar University of Wisconsin-Madison
Lab of Lingjun Li, Department of Chemistry
Used MALDI TOF/TOF mass spectrometry to analyze peptide-level responses to environmental stress in crustaceans.

2007-2008 Undergraduate Researcher University of Wisconsin-Madison
Lab of Mark Brownfield, School of Veterinary Medicine.
Used immunihistochemistry to identify lcoation of serotonin receptor variants in rat brain and adrenal glands.

Publications

Journals

2021 Aquarium: open-source laboratory software for design, execution and data management Justin Vrana, Orlando de Lange, Yaoyu Yang, Garrett Newman, Ayesha Saleem, Abraham Miller, Cameron Cordray, Samer Halabiya, Michelle Parks, Eriberto Lopez, Sarah Goldberg, Benjamin Keller, Devin Strickland, Eric Klavins Oxford University Press Synthetic Biology (accpeted)

2021 Simpler and faster Covid-19 testing: Strategies to streamline SARS-CoV-2 molecular assays Nuttada Panpradist, Qin Wang, Parker S Ruth, Jack H Kotnik, Amy K Oreskovic, Abraham Miller, Samuel WA Stewart, Justin Vrana, Peter D Han, Ingrid A Beck, Lea M Starita, Lisa M Frenkel, Barry R Lutz EBioMedicine 64, 103236

2019 OLA-Simple: A software-guided HIV-1 drug resistance test for low-resource laboratories N Panpradist, IA Beck, J Vrana, N Higa, D McIntyre, PS Ruth, I So, … EBioMedicine 50, 34-44

2017 Digital logic circuits in yeast with CRISPR-dCas9 NOR gates.
MW Gander, JD Vrana, WE Voje, JM Carothers, E Klavins
Nature communications 8, 15459

2016 Benchmarking of optical dimerizer systems.
GP Pathak, D Strickland, JD Vrana, CL Tucker
ACS synthetic biology 3 (11), 832-838

2014 Peripheral nervous system defects in a mouse model for peroxisomal biogenesis disorders
MG Hanson, VL Fregoso, JD Vrana, CL Tucker, LA Niswander
Developmental biology 395 (1), 84-95

2014 An optimized optogenetic clustering tool for probing protein interaction and function
A Taslimi, JD Vrana, D Chen, S Borinskaya, BJ Mayer, MJ Kennedy, CL Tucker
Nature communications 5, 4925

2014 Tools for controlling protein interactions using light
CL Tucker, JD Vrana, MJ Kennedy
Current protocols in cell biology 64 (1), 17.16. 1-17.16. 20

2013 Optical control of protein-protein interactions to modulate cellular function
A Taslimi, G Pathak, JD Vrana, CL Tucker
CLEO: 2013, 1-2

2013 Optogenetic control of cell function using engineered photoreceptors
GP Pathak*, JD Vrana*, CL Tucker
Biology of the Cell 105 (2), 59-72 *co-first author

2012 Rapid profiling of disease alleles using a tunable reporter of protein misfolding
AMC Pittman, MD Lage, V Poltoratsky, JD Vrana, A Paiardini, A Roncador, CL Tucker
Genetics 192 (3), 831-842

2012 Light-dependent, dark-promoted interaction between Arabidopsis cryptochrome 1 and phytochrome B proteins
RM Hughes, JD Vrana, J Song, CL Tucker
Journal of Biological Chemistry 287 (26), 22165-22172

In Preparation
(08/2019)

2019 Development and evaluation of OLA-Simple 1.0: a software-guided test kit for low-resource laboratories to detect drug resistance in HIV
Nuttada Panpradist, Ingrid A. Beck, Justin Vrana, Nikki Higa, David McIntyre, Parker S. Ruth, Isaac So, Enos C. E. Kline, Ross Milne, Ruth Kanthula, Annie Wong-On-Wing, […], Jaime Soria, James Lai, Eric Klavins, Lisa M. Frenkel, Barry R. Lutz
Science Translational Medicine (in review)

2019 Implementation of an interactive mobile application to pilot a same-day HIV drug resistance assay from whole-blood in Kenya.
Justin Vrana, Ingrid A Beck, Nuttada Panpradist, Nikki Hilga, Daisy Ko, Ruth Kanthula, Bhavna Chohan, James Lai, Michael Chung, Eric Klavins, Lisa M Frenkel, Barry Lutz

2019 End-to-end integration of experiment design, execution and analysis for engineered biological systems.
Justin Vrana, Ben Keller, Dany Fu, Andrei Lapets, Douglas Densmore, Eric Klavins

2020 Characterization and design of CRISPR-based cellular information processing systems in mammalian cells using single cell RNA-Seq.
Justin Vrana, Eric Klavins

Invited Talks

2019 Aquarium: a laboratory operating system for reproducible experimental design and execution SIMB (Society for Industrial Microbiology and Biotechnology), Automation session, Washington, D.C.

Poster Presentations

2019 Software-Enable Design and Automated Construction of CRISPR Gene Circuits in S. cerevisiae Poster and lightning talk. SEED (Synthetic Biology: Engineering, Evolution, and Design), New York City, NY

2016 Rational Design of Large Crispr/dCas9 Transcriptional Logic Circuits in Eukaryotic Cells Poster and lightning talk. SEED (Synthetic Biology: Engineering, Evolution, and Design), Chicago, IL

Teaching

2019 Teaching Assistant, UW-Seattle Electrical and computer engineering 590: Advanced Programming for Embedded Systems. Course on C/C++. Embedded device communication using C/C++. Google testing framework. Automated grading scripts.