profile picture

Spencer Bliven

Data, Code, and Open Science

Languages

  • English (Native)
  • German (B2)
  • American Sign Language (Beginner)

Interests

  • Climbing
  • 3D Printing
  • Science Fiction
  • Horology
  • Music & Choir

Career Profile

Senior research data expert and bioinformatician with 18+ years of experience in open science, both as a computational biologist and a service provider for scientific computing infrastructure. Passionate about accellerating research through open science practices and robust data management, with experience in software architecture and programming, large-scale computing, big data, leadership, and strategic planning. Strong communicator, able to translate the needs of researchers into technical solutions.

Competencies

Project Management

Project coordination, agile development, kanban, Jira, distributed teams

Top Programming Languages

Python, Java, Go, Javascript, Typescript, HTML, CSS, C++, Bash, R, SQL

Frameworks & Technologies

Numpy/Pandas, NodeJS, Angular 2, OpenAPI, LinkML, JSON Schema, JSON-LD, REST APIs, Jekyll, MongoDB, Jupyter

Devops

Docker, Kubernetes, Ansible, Helm, CI/CD

Scientific expertise

Electron microscopy, structural biology, bioinformatics, statistics, machine learning, AI, phylogenetics, semantic ontologies

Education

PhD in Bioinformatics

2009-2015
University of California, San Diego

Advisor: Prof. Philip Bourne. Thesis: Structure-Preserving Rearrangements: Algorithms for Structural Comparison and Protein Analysis

BS in Computer Science, BS in Biochemistry (with Distinction)

2004 - 2009
University of Washington

Advisor: Prof. David Baker. Thesis: Efficient Modeling of Disulfide Bonds with Rosetta

Experiences

Scientific Computing Engineer

2018 - Present
Scientific Data Curation, Paul Scherrer Institute, Switzerland
  • Project coordinator for OpenEM (openem.ch). Created an open research data (ORD) infrastructure for Swiss electron microscopy facilities. Wrote ETH and swissuniversities grants leading to 2.4 million CHF, then led a distributed team of 7 developers implementing the infrastructure.
  • Represented PSI in ORD committees and consortiums (ETH-ORD Expert Group for Services and Infrastructure, 2021-Present; ETH Research Data Services Explorer Steering Committee, 2024-Present)
  • Scientific software projects, including full-stack web apps, high-performance computing, and devops deployment. (Typescript, Angular 2, Python, Go, C++, ansible, kubernetes)
  • Created data collection and processing pipelines for the PSI electron microscopy facility. (Slurm, relion, cryoSPARC, hardware purchasing and installation, network configuration)

Postdoctoral Researcher

2017 - 2018
Zurich University of Applied Science, Switzerland

Advisor: Prof. Maria Anisimova. Focused on phylogenetic methods for tandem repeat proteins, including software development and benchmarking. Developed novel methods for the Tandem Repeat and applied these systematically to the Armadillo Repeat protein family. (Python, slurm, Apache spark)

NIH Postdoctoral Fellow

2015 - 2017
National Institutes of Health, Bethesda, MD

Advisors: Prof. Philip Bourne (NIH) and Dr. Guido Capitani (PSI).

  • Analysis of protein-protein interactions in crystal structures as part of the EPPIC, the Evolutionary Protein Protein Interface Classifier. (Java, Javascript, NGL, vis.js)
  • Assessor for the Critical Assessment of Structure-based Prediction (CASP12) community-wide experiment. (Python, web development)

PhD in Bioinformatics

2009-2015
University of California, San Diego

Advisor: Prof. Philip Bourne. Thesis: Structure-Preserving Rearrangements: Algorithms for Structural Comparison and Protein Analysis

  • Structural comparison algorithms for proteins, including CE-Symm for detecting internal pseudosymmetry.
  • Deployment of structural analysis tools on the RCSB Protein Data Bank, as well as large-scale systematic analyses. (Java, Open Science Cloud, BioJava core developer, Open Bioinformatics Foundation member)

Lab Intern, Prof. Donald Hilvert

2008
ETH Zürich

Undergraduate Researcher, Dr. Eugene Kolker

2007
Seattle Children's Hospital/U. Washington Dept. Biomedical and Health Informatics

Software Intern

2006 - 2007
Exbiblio

Certifications

Project Management Methodology and Leadership

2023
Jürg Kuster

Deutsch B2 (results pending)

2026
TELC

Deutsch A2

2019
TELC

Publications
https://orcid.org/0000-0002-1200-1698