Curriculum Vitae

Gavin Duggan

Systems Analyst



  1. Doctorate, Biochemistry
    Supervisors: Hans Vogel, Aalim Weljie
    University of Calgary, 2013
  2. Bachelor of Mathematics, Honours Computer Science
    University of Waterloo, 2002
  3. Bachelor of Science, Honours Science
    University of Waterloo, 2002

Research publication links (abrv. titles)

Chest Radiograph Interpretation with Deep Learning Models , Radiology, 2019
Scalable and accurate deep learning with electronic health records , NJP Digital Medicine, 2018
NMR metabolomics characterization of antibiotic method of action , BMC Microbiology, 2016
Metabolomics of Serum Samples by 1H NMR as a Diagnostic Approach for Septic Shock, Critical care medicine, 2014
Effect of Aluminium and Copper on biofilm development of Pseudomonas in different media. Metallomics, Apr 2013
Differentiating short and long-term effects of diet manipulation in mice, Diabetes Obes Metab., Sep 2011
Metabolomic response to exercise training in lean and diet-induced obese mice, J Appl Physiol, May 2011
Metabolic profiling of vitamin C deficiency in mice, J biomol NMR, Apr 2011
Metabolomic profiling of serum and urine in ulcerative colitis of mice, J Proteome Res, Dec 2010
Metabolomic profiling of dietary-induced insulin resistance in the fat-fed mouse, Diabetes, Obesity and Metabolism, 2007
HMDB: The Human Metabolite Database, Nucleic Acids Research, Jan 2007
Resources for display and analysis of DNA structural variants, Cytogenetic Genome Research, 2006
Human Chromosome 7: DNA sequence and biology, Science, May 2003

Guest Speaker, Parallel Computation as a Tool for in silico biology. UofT Bioinformatics Developers Network, 2004
Guest Speaker, Grid Computing and Sytems Biology. Business of Science Symposium, 2003

Life science skills and knowledge

  • Etiological, system-oriented biology. Pathway disruption analysis and modeling.
  • Metabolomics: Mass spectrometric and NMR based analysis of biofluids
  • Genomic sequence analysis using online, local, and hybrid (Taverna, BioMoby) tools
  • Protein structure/folding, molecular dynamics. Transcription and expression analysis
  • Multisource, cross-field data integration
  • Human molecular genetics, animal and plant biotechnology, virology, microbiology
  • Thermodynamics, polymer chemistry, fundamental quantum chemistry
  • Sample preparation, culturing and associated biotechnology procedures and implications

Informatics skills and knowledge

  • Statistical, algebraic, or numeric modeling of multivariate and megavariate datasets.
  • Simulation and analysis in R, Matlab, SIMCA
  • Data visualization using standard or bespoke presentations
  • Large dataset computation on strong or weakly coupled parallel architechtures
  • Optimization of map/reduce and graph-based parallel analysis
  • System performance evaluation, queueing and pipeline simulation theory.
  • Software design in Java, C, C++, R, Perl, Python and PHP
  • RDBMS development using integrated SQL and GUI methodologies
  • Heuristic search development (NP complexity, LISP, Scheme)
  • Multithreaded hardware control programming
  • Cross-platform client/server development using high or low level libraries
  • Hardware level graphics software design and development

Professional skills and knowledge

  • Written and verbal communication expertise. Clear reporting, summary, and presentation
  • Team management and participation with 3-40 team members. Direct and tiered reports
  • Agile development using Scrum methodology for software or scientific projects
  • Cloud based collaboration, scheduling, and project management

Professional Experience

GoogleSoftware Engineer - Analytics2013-
University of CalgaryPostdoctoral Fellow2013
University of CalgaryHMDB, Doctoral Student2006-2013
TCAG: Sick Kids TorontoGenomic analysis, Software development2002-2005
Hughson Lab, UWaterlooCo-op: CSA Physiological signal modeling2001, Palo AltoCo-op: Mobile device development2000
VMI Medical Software, Inc Co-op: MRI software QA1999
Alias|Wavefront, SGICo-op: Studiopaint/Maya UI1998
Blake, Cassels & Graydon, LLPCo-op: Systems administration1997
Ferranti-Packard, Rolls RoyceCo-op: Numerical software conversion1996

Personal and professional references available upon request