About

Alex holds a BSc in Computer Science and Biology from the University of British Columbia. At UBC's Michael Smith Laboratories, he was an embedded collaborator in the Brumer Lab — working directly with wet-lab researchers from experimental design through published figures, on metagenomics, RNA-seq, and CAZyme analysis. That work contributed to publications in Science, Applied and Environmental Microbiology, and the Journal of Biological Chemistry.

Alex is the lead developer of SACCHARIS 2, a bioinformatics pipeline for phylogenetic prediction of CAZyme substrate specificity. It is a full rewrite of the original Perl pipeline in Python, with Bioconda distribution and a GUI designed and built from scratch. SACCHARIS 2 is published in Methods in Molecular Biology (Springer Nature, 2024).

Earlier work included analytical chemistry research at Langara College (operating HPLC and GC/MS instrumentation, designing acquisition methods, and analysing plant compound extractions), which grounded a bench-level understanding of where experimental data comes from.

Later work at UBC involved building image analysis automation for a developmental biology lab: implementing a convolutional neural network for tooth detection and, because no existing tool handled the geometric alignment correctly, a custom algorithm using a matrix representation of conic sections to register microscopy image time series. The same instinct — formalise the problem properly rather than approximate it — is what he brings to analysis work that has no clean off-the-shelf answer.

Cordillera Labs exists because every research lab is constantly reinventing the same wheels, often under time pressure and without software engineering training. Alex's long-term goal is a world where biologists can do their work quickly, accurately, and reproducibly, sharing and building on each other's tools, without having to become programmers to get there.