About Me

I am a Bioinformatics Scientist (II) at Somalogic in the Production Bioinformatics group. My work is focused on full stack development of a data analytics pipeline to enable statistical process control of the SomaScan Assay. Applications include:

  • ML-based anomaly detection of highly dimensional data with lead generation utilizing graph networks of process and material data followed by downstream impact analysis
  • Scalable quality reporting powered by seamless traversal between abstractions of data from experiment summary statistics to individual SOMAmer stability
  • Creation of proteomic data lakes wherein data provenance is fully maintained for model development in R and neural network training

The tech stack includes:

  • Python with heavy utilization of the data science libraries
  • Django with Django Rest Framework
  • Celery and RabbitMQ
  • Docker
  • Kubernetes
  • AWS
  • PostgreSQL
  • Neo4j
  • Node.js
  • D3.js and Plotly.js
  • Vue.js with Bootstrap

Before SomaLogic I received my PhD from Colorado State University (CSU) with Dr. Anthony Rappé in computational chemistry where I developed and applied methodologies to elicit enthalpic global minima and reaction pathways. This work was primarily programmed in Fortran 66 and executed on the CRAY at CSU.

I then acquired a bioinformatics post-doctoral position in the Microbiology, Immunology, and Pathology Department with Dr. Mark Stenglein where I focused on the development of metagenomic analysis tools as well as supporting the NGS Core Facility at CSU.

In my spare time I moonlight as an iOS app developer with my father where we have created an organic chemistry reference app called TapOChem. I like to think of it as the best one out there but that might just be my bias talking.

  • Joseph T Allison, PhD