About

Work Experience

• Research Software Engineer, Oregon Health & Science University

  Jan, 2023 - Jan, 20263 years

  Led development of workflow engine and orchestrators. Led development and DevOps for high-throughput computational biology platforms and data commons infrastructure.

  • Developed and maintained Funnel, a GA4GH Task Execution Service (TES) implementation; contributed features including TES v1.1 support, a new MongoDB driver, Slurm/Exacloud integration, and custom plugins.

  • Architected and managed cloud infrastructure using Terraform and Helm; automated deployments, backup/restore, and compliance for Gen3 data commons instances (ACED-IDP, CBDS) on AWS and OpenStack.

  • Developed the DRS Downloader (Go/Python) for secure, cross-cloud DRS data transfer (e.g. AnVIL/Terra) and maintained the data client for simplified data management/ETL.

  • Contributed to FHIR data modeling and the OMOPonFHIR utility for clinical data validation and aggregation.

• Full Stack Software Developer, Saltire Softare Inc.

  Jun, 2022 - Aug, 20222 months

  Contributed to the fullstack development of e-commerce and math & music educational sites.

  • Integrated RESTful APIs for use in authenticating clients during online checkouts.

  • Set up and managed hosting and SSL certification for On the Sensations of Tone.

• Research Software Developer, OHSU, Department of Medical Informatics and Clinical Epidemiology

  Jan, 2019 - Jan, 20201 year

  Furthered development of the Swing desktop application used to curate data for Reactome — an open-source database and visualizer of biological pathways used for research.

  • Implemented a custom class to flag pathway and reaction revisions between varying data sets.

  • Added new UI/UX features based upon communication with users and research database curators.

  • Updated API calls and data processing of a remote NLP document parser (REACH).

• Ski and Snowboard Technician and Shop Hand, Next Adventure

  Jan, 2021 - Jan, 20221 year

  • Assisted 50+ customers a day in fitting, renting, and tuning mountaineering and snowsports equipment.

• Lab Prep Assistant, University of Oregon Honors Biology Lab

  Jan, 2014 - Jan, 20151 year

  • Prepped and sterilized materials for undergraduate biology lab courses.

  • Set up personal computers for use with lab-focused programs.

• Student Researcher - Botanical Genetics, University of Minnesota

  Jan, 2014 - Present

  • Conducted research involving botanical DNA isolation, purification, sequencing, and analysis.

  • Presented results and conclusions at three scientific conferences.

• Student Researcher - Ecology and Restoration, H.J. Andrews Experimental Forest

  Jan, 2013 - Present

  • Analyzed forest networks and plant response to fire disturbances.

  • Surveyed plant communities in experimental sub-alpine meadows as part of ongoing research.

Projects Experience

• convida

  Jan, 2019 - Present

  A Conway's Game of Life simulation with a high performance WebAssembly compilation target.

  • A demonstration is available at convida.liambeckman.com.

• demonic

  Jan, 2018 - Present

  A suite of applications that allows users to try out programs and programming languages by accessing a web terminal or running code snippets.

  • Processes are communicated via WebSockets and run in a lightweight Linux sandbox (Debian chroot secured with Firejail).

• withfeathers

  Jan, 2018 - Present

  A web app and CLI that fetches, parses, and selects a random poem by Emily Dickinson from Project Gutenberg.

  • A Flask-powered web interface at withfeathers.liambeckman.com displays a new poem every day.

• devilish*

  - Present

  A minimalistic shell for Unix-like operating systems.

  • Allows for standard input/output redirection, foreground/background processes, and SIGTSTP/SIGINT signal handling.

• prime*

  - Present

  A program that uses the Sieve of Eratosthenes to compute a given prime number selected by the user.

• RemoveMyWaste

  Jan, 2018 - Jan, 20191 year

  Lead development of RemoveMyWaste, an application for the safe disposal of hazardous household and industrial materials.

  • Users can locate disposal centers and read information on the materials they wish to dispose of.

  • Personally developed Android application and web interface and set up hosting of web and database components.

• mdbook-latex

  Jan, 2019 - Present

  A backend for the mdBook documentation program that converts Markdown sources to LaTeX and PDF.

• matriz*

  - Present

  A shell script for managing matrix operations including multiplication, addition, and transposition.

  • A matrix generator is included in the available functions.

• liambeckman.com*

  - Present

  A personal website and collection of software development tools, including a Git server and a Jenkins instance.

  • The website and all projects are hosted on personal servers (Raspbian on RPi3 Model B and FreeBSD on Thinkpad x230).

• Voyager Index

  Jan, 2019 - Present

  A world map of over 7,000 cities ranked by user-selected filters.

  • Personally spearheaded the development of the server and CLI for the Voyager Index project.

  • Specific contributions included standardizing server interactions with the database, hosting the PostgreSQL database on a personal Raspberry Pi, and presenting the final product.

Skills

Education

Publications