From: Don Armstrong Date: Fri, 7 Mar 2025 02:24:38 +0000 (-0800) Subject: update experience in resume X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=f6c8ff9345cd6b4160a11e44283ef47fd33e7e0a;p=resume.git update experience in resume --- diff --git a/don_armstrong_resume.org b/don_armstrong_resume.org index 3ca387c..8666e77 100644 --- a/don_armstrong_resume.org +++ b/don_armstrong_resume.org @@ -8,15 +8,26 @@ # #+LATEX_CLASS_OPTIONS: [10pt,breaklinks] * Experience -** Team Lead Data Engineering at Ginkgo Bioworks \hfill 2022--Present -+ Lead and manged team of data engineers, system administrators, - statisticians, bioinformaticians, and scientists at the PhD level - working within the AgBio unit of Ginkgo Bioworks. -+ Mentored and coached team members in data science, bioinformatics, - data engineering, and statistics. -+ Key leadership role in successful merger of AgBio unit with Ginkgo, - including all relevant R&D business applications and data-adjacent - systems. +** Director of Data Science and Analytics at Ginkgo Bioworks \hfill 2022--Present ++ Directed a team of managers who lead teams of data engineers, system + administrators, statisticians, bioinformaticians, and scientists at + the PhD level working within the Ag business unit of [[https://www.ginkgobioworks.com][Ginkgo Bioworks]]. ++ Accountable for cost centers totalling $10 M annually, including + budgeting, procurement, vendor relationships, and policy compliance. ++ Hired and developed team members in data science, bioinformatics, + data engineering, and statistics using coaching, mentorship, and + teaching approaches. ++ Accountable (and frequently responsible) for all R&D IT applications + in the Ag BU, including vendor selection, architectural decisions, + deployment, and development where appropriate. ++ Championed the adoption of data governance and data stewardship + principles, including new tools and ways of working. ++ Lead the development of multiple cloud-based serverless and + container-based applications with multiple API and UI interfaces, + including project management as well as contractor and vendor + oversight. ++ Key leadership role in multiple mergers and acquisitions, + specializing in R&D business applications and data-adjacent systems. ** Team Lead Data Engineering at Bayer Crop Science \hfill 2018--2022 + Hired, managed, and developed team of 5+ Data Engineers, Systems Administrators, and Business Analysts working within the Biologics @@ -24,7 +35,7 @@ integration, and operationalization of data analysis pipelines + Developed and supervised implementation of data capture, integration, and analysis strategies to increase the value of - genomics, metabolomics, transcriptomics, spectroscopic, phenotypic + genomics, metabol\-omics, transcript\-omics, spectroscopic, phenotypic (/in vitro/ and /in planta/), and fermentation/formulation process data for discovery and development + Lead the development of multiple systems while coaching, mentoring, @@ -34,8 +45,6 @@ life science collaboration using serverless architecture to provide machine-learning estimates of critical parameters from spectrographic measurements -+ Established and developed network of internal and external contacts - for technical implementation of Bayer program goals. ** Debian Developer \hfill 2004--Present + Maintained, managed configurations, and resolved issues in multiple packages written in R, perl, python, scheme, C++, and C. @@ -61,33 +70,34 @@ scientific research, and modern statistical methodology. + Wrote software and designed relational databases using R, perl, C, SQL, make, and very large computational systems ([[https://bluewaters.ncsa.illinois.edu/][Blue Waters]]) -** Postdoctoral Researcher at USC \hfill 2013--2015 -+ Design, execution, and analysis of an epidemiological study to - identify genomic variants associated with systemic lupus - erythematosus using targeted deep sequencing. -+ Wrote multiple pieces of software to reproducibly analyze and - archive large datasets resulting from genomic sequencing. -+ Coordinated with clinicians, molecular biologists, and biologists to - produce analyses and major reports. -** Postdoctoral Researcher at UCR \hfill 2010--2012 -+ Executed and analyzed an epidemiological study to identify genomic - variants associated with systemic lupus erythematosus using prior - information and array based approaches in a trio and cross sectional - study of individuals from the Los Angeles and greater United States. -+ Wrote and maintained multiple software components to reproducibly - perform the analyses. +# ** Postdoctoral Researcher at USC \hfill 2013--2015 +# + Design, execution, and analysis of an epidemiological study to +# identify genomic variants associated with systemic lupus +# erythematosus using targeted deep sequencing. +# + Wrote multiple pieces of software to reproducibly analyze and +# archive large datasets resulting from genomic sequencing. +# + Coordinated with clinicians, molecular biologists, and biologists to +# produce analyses and major reports. +# ** Postdoctoral Researcher at UCR \hfill 2010--2012 +# + Executed and analyzed an epidemiological study to identify genomic +# variants associated with systemic lupus erythematosus using prior +# information and array based approaches in a trio and cross sectional +# study of individuals from the Los Angeles and greater United States. +# + Wrote and maintained multiple software components to reproducibly +# perform the analyses. * Education -** Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology \hfill UC Riverside -** Batchelor of Science (BS) in Biology \hfill UC Riverside ++ Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology \hfill UC Riverside ++ Batchelor of Science (BS) in Biology \hfill UC Riverside * Skills ** Leadership and Mentoring -+ Lead teams of PhD and MD scientists in multiple scientific and - industrial programs -+ Mentored graduate students and Outreachy and Google Summer of Code - interns -+ Former chair of Debian's Technical Committee -+ Head developer behind https://bugs.debian.org ++ Lead managers and teams of PhD-level scientists in multiple + scientific and industrial programs. ++ Mentorship of multiple employees, graduate students, and + undergraduates throughout career, helping them to fully develop + their potential and thrive. ++ Chair or lead of multiple initiatives and committees, including + aligning highly cross-functional and diverse stakeholders. ** Bioinformatics, Genomics, and Epigenomics + NGS and array-based Genomics and Epigenomics of complex human diseases using RNA-seq, targeted DNA sequencing, RRBS, Illumina @@ -106,12 +116,15 @@ confounders, and batch effects (both Bayesian and frequentist) + Reproducible research ** Software Development -+ Languages: python, R, perl, C, C++, python, groovy, sh (bash, POSIX, ++ Languages: python, R, perl, C, C++, groovy, sh (bash, POSIX, and zsh), make + Collaborative Development: git, Jira, gitlab CI/CD, github actions, Aha!, continuous integration & deployment, automated testing + Web, Mobile: Shiny, jQuery, JavaScript -+ Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL ++ Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL, RDS ++ Cloud: AWS, Azure, GCP, OpenStack ++ Infrastructure as Code: AWS Cloudformation, Terraform, puppet, + etckeeper, hieara ** Big Data + Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure) + Inter-process communication: MPI, OpenMP @@ -124,7 +137,6 @@ + Virtualization: libvirt, KVM, qemu, VMware, docker + VCS: git, mercurial, subversion + Mail: postfix, exim, sendmail, spamassassin -+ Configuration Infrastructure: puppet, hiera, etckeeper, git + Documentation: \LaTeX, confluence, emacs, MarkDown, MediaWiki, ikiwiki, trac + Monitoring: munin, nagios, icinga, prometheus + Issue Tracking: Debbugs, Request Tracker, Trac, JIRA @@ -151,28 +163,28 @@ + *[[http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit][Helical Wheel Projections]]*: Web-based tool to draw helical wheel protein projections. * Publications and Presentations -+ 24 peer-reviewed publications cited over 3000 times: ++ 24 peer-reviewed publications cited over 4000 times: https://dla2.us/pubs + Publication record in GWAS, transcriptomics, SLE, GBM, epigenetics, comparative evolution of mammals, and lipid membranes -+ H index >= 20 ++ H index >= 21 + Multiple presentations on EWAS of PTSD, genetics of SLE, and Open Source: https://dla2.us/pres -* Funding and Awards -** Grants -+ 2017 R Consortium: *[[https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants][Adding Linux Binary Builders to R-Hub]]* Role: - Co-PI -+ 2015 Blue Waters Allocation Grant: *Making ancestral trees using Bayesian - inference to identify disease-causing genetic variants* Role: - Primary Investigator -+ *Tracking placenta and uterine funciton using urinary extracellular vesicles* (R21 - RFA-HD-16-037) Role: Key Personnel -+ *NIAMS* R01-AR045650-04 *Genetics of Childhood Onset SLE* to Chaim O. Jacob. - Role: Key Personnel -** Scholarships and Fellowships -+ 2001--2003: University of California, Riverside Doctoral Fellowship -+ 1997--2001: Regents of the University of California Scholarship. +# * Funding and Awards +# ** Grants +# + 2017 R Consortium: *[[https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants][Adding Linux Binary Builders to R-Hub]]* Role: +# Co-PI +# + 2015 Blue Waters Allocation Grant: *Making ancestral trees using Bayesian +# inference to identify disease-causing genetic variants* Role: +# Primary Investigator +# + *Tracking placenta and uterine funciton using urinary extracellular vesicles* (R21 +# RFA-HD-16-037) Role: Key Personnel +# + *NIAMS* R01-AR045650-04 *Genetics of Childhood Onset SLE* to Chaim O. Jacob. +# Role: Key Personnel +# ** Scholarships and Fellowships +# + 2001--2003: University of California, Riverside Doctoral Fellowship +# + 1997--2001: Regents of the University of California Scholarship.