# Kate Flanagan > Automation Software Engineer at Ginkgo Bioworks, Inc. Location: Cambridge, Massachusetts, United States Profile: https://flows.cv/kateflanagan ## Work Experience ### Software Engineer 2 @ Ginkgo Bioworks, Inc. Jan 2024 – Present | Boston, Massachusetts, United States - Developing the core components of Catalyst ACS, the software running Reconfigurable Automation Carts (RACs) - On-call troubleshooting for internal and customer deployments - Writing drivers for new lab equipment incorporated into RACs - Creating internal tools to speed up hardware setup and deployment ### Automation Operations Engineer 2 @ Ginkgo Bioworks, Inc. Jan 2022 – Jan 2024 | Boston, Massachusetts, United States ### Automation Operations Engineer 1 @ Ginkgo Bioworks, Inc. Jan 2020 – Jan 2022 | Boston, Massachusetts, United States - Troubleshot and root-caused urgent issues with automation in various bioengineering projects via a JIRA Service Management based ticketing system. - Fixed bugs and added features to code for liquid handling and colony picking machines. - Developed a set of bash (and later Ansible) scripts used for code autodeployment on 50+ machines, runnable via Gitlab CI/CD. - Trained biologists on automation equipment, and contributed to documentation for its usage - Trained teammates in use of command-line tools such as git and ssh for remote troubleshooting and code updates ### Mechanical Engineering Intern @ Admetsys Jan 2019 – Jan 2019 | Boston, MA Collaborated with a team of 5-15 others in the development of an automated diabetes treatment system. Determined component specifications, modeled custom brackets and test fixtures, and built prototypes of a moving display and syringe pumps using a Raspberry Pi and Python for control. Became proficient in Autodesk Inventor, including assemblies, design for manufacturability (injection molding, die casting, and CNC machining), and stress analysis (FEA). Calculated tolerance stackup for drive shaft and syringe pump systems, and modified parts to resolve discrepancies. Contributed design inputs, test cases, and SOPs to the company's quality management system. ### Research Assistant @ Mechanics of Slender Structures Lab Jan 2018 – Jan 2019 | Boston University Determined material properties of aggregate rock/fiber structures. Designed construction and testing protocols, built column samples using various string-deposition methods, measured force-displacement data, and analyzed the results in Matlab. Earned a reputation as the "fastest prototyper" of new construction methods and testing rigs. Learned the basics of operating the UR5 arm using ROS (robot operating system) as well as the on-board scripting language. ### Student Worker @ Boston University Graduate Programs Office Jan 2018 – Jan 2018 | Greater Boston Area Processing graduate applications for the 2017-2018 cycle, handling graduate student inquiries. Wrote a small web scraping program in Ruby to speed collection of data. ### Tutor @ Mathnasium - The Math Learning Center Jan 2016 – Jan 2017 ### ORISE Summer Research Intern @ United States Army Institute of Surgical Research Jan 2016 – Jan 2016 Worked under Dr. Greising and Dr. Corona in the department of Extremities Trauma and Regenerative Medicine. Completed a project characterizing motoneuron damage following volumetric muscle loss (VML) injury to the tibialis anterior. Sliced, mounted, and imaged rat spinal cords. Developed a semi-automatic program in MetaMorph for counting neurons in fluorescent Z-stack images of rat spinal cords. Created and presented a poster of this research at an end-of-summer poster session. ### Research Assistant @ University of Texas at Dallas Jan 2013 – Jan 2015 | Texas Biomedical Device Center Worked on projects examining the effect of vagus nerve stimulation (VNS) on traumatic brain injury, Parkinsonism, and hemorrhagic stroke. Monitored rat behavioral tasks, kept track of performance data, performed perfusion fixation, assisted with motor mapping, collagenase infusion and TBI surgeries, and occasionally stained brain sections and made headcaps. ### Peer Tutor @ UTD Student Success Center Jan 2015 – Jan 2015 ### Supplemental Instruction Leader @ UTD Student Success Center Jan 2014 – Jan 2015 ### Research Intern @ Trinity College Institute of Neuroscience Jan 2014 – Jan 2014 | Dublin, Ireland Assisted in research examining the neuroimmunological causes/effects of an Alzheimer’s disease model in mice. Learned how to perform enzyme-linked immunosorbent assays (ELISAs), Western immunoblotting, and on-slide immunostaining with fluorescent secondary antibodies. ## Education ### Master of Science - MS in Mechanical Engineering Boston University ### Bachelor of Science (BS) in Neuroscience, Computer Science minor The University of Texas at Dallas ## Contact & Social - LinkedIn: https://linkedin.com/in/2kate2flanagan --- Source: https://flows.cv/kateflanagan JSON Resume: https://flows.cv/kateflanagan/resume.json Last updated: 2026-03-31