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Brandon Barker
Computational Scientist

Brandon E. Barker

Brandon joined the Cornell Center for Advanced Computing in 2014 as a member of the the Consulting Group. Previously, Brandon completed his doctoral research on method development in metabolic modelling and applications of metabolic modelling to genetic interactions at Cornell. Brandon continues to work in this field, as well contributing to other fields of science and computing.

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Areas of Research or Expertise

  • Containers and reproducibility
  • Cloud computing
  • Scientific software and High Performance Computing (HPC)
  • Web services
  • Software development
  • Safety-critical programming
  • Parallel and concurrent computing
  • Systems programming
  • Computational biology
  • Systems biology
  • Metabolic modeling
  • Convex optimization

Projects

  • Aristotle Federated Cloud - Leading containerization and automation effort for the Aristotle Federated Cloud project, emphasizing portability and reproducibility of scientific workflows. Worked with multiple research groups (1, 2, 3), and in the Metabolic Modeling use case, contributing directly to the core science of the project.
  • Leading a group in software development and research related to integrating mRNA or protein expression data with reaction stoichiometry to infer metabolic fluxes (FALCON).
  • arXiv e-print archive: aiding architecture and implementation of arXiv-NG, ORCiD support, hypothes.is integration, etc.
  • Dairy-farm economics simulation.
  • Consulting and training for Red Cloud.
  • Applied Type System (ATS; a programming language): contributor; packaging and releasing ATS2; also contributed to linear algebra library for ATS2.
  • NCRN / CED2AR: The Comprehensive Extensible Data Documentation and Access Repository (CED2AR) was designed to improve the documentation and discoverability of both public and restricted data - Editor code and associated libraries available at http://github.com/ncrncornell.
  • Cornell Container Runner Service (CCRS) - web service for integrating arbitrary runnable code examples in websites, backed by Singularity or Docker containers.
  • monadic-html (contributor): Tiny DOM binding library for Scala.js.
  • Assorted projects on GitHub.

Past or Inactive Projects

  • Social Media Visualization: developed a web service in Scala and Scala.js to analyze and display emotions from tweets associated with particular events or locations in real time.
  • Microarray database management and programming: MADUK was a harmonious fork and installation of SMD (Stanford Microarray Database) at the University of Kentucky

Publications, Presentations, and Other Writings

Publication listing on Google Scholar.
Works listing on ORCID.
Multiple training topics on the Cornell Virtual Workshop (CVW), oriented for science users and especially HPC users.

Education

B.S., Computer Science and Mathematics, University of Kentucky
Ph.D., Computational Biology and Medicine, Cornell University

Memberships/Professional Affiliations

USENIX

Personal Interests

Fitness, audiobooks, wiki editing, games and game design, local flora.