From: Don Armstrong Date: Tue, 28 Feb 2023 00:16:54 +0000 (-0800) Subject: update resume to include ginkgo bioworks pieces X-Git-Url: https://git.donarmstrong.com/?p=resume.git;a=commitdiff_plain update resume to include ginkgo bioworks pieces --- diff --git a/don_armstrong_resume.org b/don_armstrong_resume.org index e22a140..3ca387c 100644 --- a/don_armstrong_resume.org +++ b/don_armstrong_resume.org @@ -1,5 +1,6 @@ #+OPTIONS: ^:nil #+OPTIONS: toc:nil +#+OPTIONS: auto-id:f #+TITLE: Resume #+AUTHOR: Don L. Armstrong #+LATEX_CMD: xelatex @@ -7,7 +8,16 @@ # #+LATEX_CLASS_OPTIONS: [10pt,breaklinks] * Experience -** Team Lead Data Engineering at Bayer Crop Science \hfill 2018--Present +** 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. +** 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 R&D unit of Bayer Crop Science enabling data capture, data @@ -17,14 +27,15 @@ genomics, metabolomics, transcriptomics, spectroscopic, phenotypic (/in vitro/ and /in planta/), and fermentation/formulation process data for discovery and development -+ Lead the development of multiple tools in python and R while - coaching, mentoring, and developing multiple developers and - engineers ++ Lead the development of multiple systems while coaching, mentoring, + and developing developers and engineers + Served as a key collaborator on multiple cross-function and cross-divisional projects, including leading the architecture of a 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. @@ -35,10 +46,10 @@ + Provided vendor-level support for complex systems integration issues on Debian GNU/Linux systems. ** Research Scientist at UIUC \hfill 2015--2017 -+ Primarily responsible for the planning, design, organization, - execution, and analysis of multiple complex epidemiological studies - involving epigenomics, transcriptomics, and genomics of diseases of - pregnancy and post-traumatic stress disorder. ++ Planning, design, organization, execution, and analysis of multiple + complex epidemiological studies involving epigenomics, + transcriptomics, and genomics of diseases of pregnancy and + post-traumatic stress disorder. + Published results in scientific publications and presented results orally at major scientific conferences. + Wrote and completed grants, including budgeting, scientific @@ -51,48 +62,54 @@ + 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 -+ Primarily responsible for the design, execution, and analysis of an - epidemiological study to identify genomic variants associated with - systemic lupus erythematosus using targeted deep sequencing. -+ Designed, budgeted, configured, maintained, and supported a secure - linux analysis cluster (MPI/torque) with a shared filesystem (NFS - over gluster) for statistical analyses. ++ 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 -+ Primarily responsible for the execution and analysis of 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. ++ 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. -** Independent Systems Administrator \hfill 2004--2018 -+ Researched, recommended, budgeted, designed, deployed, configured, - operated, and monitored highly-available high-performance enterprise - hardware and software for web applications, authentication, backup, - email, and databases. -+ Full life-cycle support of medium and small business networking - infrastructure, including VPN, network security, wireless networks, - routing, DNS, DHCP, and authentication. * Education ** 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 ++ 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 +** Bioinformatics, Genomics, and Epigenomics ++ NGS and array-based Genomics and Epigenomics of complex human + diseases using RNA-seq, targeted DNA sequencing, RRBS, Illumina + bead arrays, and Affymetrix microarrays from sample collection to + publication ++ Reproducible, scalable bioinformatics analysis using make, + nextflow, and cwl based workflows on cloud- and cluster-based + systems on terabyte-scale datasets ++ Alignment, annotation, and variant calling using existing and custom + software, including GATK, bwa, STAR, and kallisto ++ Using evolutionary genomics to identify causal human variants +** Statistics ++ Statistical modeling (regression, inference, prediction, and machine + learning in very large (> 1TB) datasets) using R and python. ++ Correcting & experimental design to overcome multiple testing, + confounders, and batch effects (both Bayesian and frequentist) ++ Reproducible research ** Software Development + Languages: python, R, perl, C, C++, python, groovy, sh (bash, POSIX, and zsh), make -+ Collaborative Development: git, Jira, github actions, Aha!, travis, - continuous integration, automated testing, continuous deployment ++ 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 ** Big Data @@ -103,12 +120,8 @@ ** Applications and Daemons + Web: apache, ngix, varnish (load balancing/caching), REST, SOAP, Tomcat -+ SQL servers: PostgreSQL, MySQL, SQLite, oracle + Build Tools: GNU make, cmake -+ Continuous Integration/Deployment: codebuild, travis, jenkins, - github actions + Virtualization: libvirt, KVM, qemu, VMware, docker -+ Statistics: R, SAS + VCS: git, mercurial, subversion + Mail: postfix, exim, sendmail, spamassassin + Configuration Infrastructure: puppet, hiera, etckeeper, git @@ -118,36 +131,17 @@ + Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel, Powerpoint ** Networking - + Hardware, Linux routing and firewall experience, ferm, DHCP, - openvpn, bonding, NAT, DNHS, SNMP, IPv4, and IPv6. ++ Hardware, Linux routing and firewall experience, ferm, DHCP, + openvpn, bonding, NAT, DNHS, SNMP, IPv4, and IPv6. ** Operating systems - + GNU/Linux (Debian, Ubuntu, Red Hat) - + Windows - + MacOS ++ GNU/Linux (Debian, Ubuntu, Red Hat) ++ Windows ++ MacOS ** Communication + Strong written communication skills as evidenced by publication record -+ Strong verbal and presentation skills as evidenced by presentation - and teaching record -** Genomics and Epigenomics -+ NGS and array-based Genomics and Epigenomics of complex human - diseases using RNA-seq, targeted DNA sequencing, RRBS, Illumina - bead arrays, and Affymetrix microarrays from sample collection to - publication. -+ Reproducible, scalable bioinformatics analysis using make, - nextflow, and cwl based workflows on cloud- and cluster-based - systems on terabyte-scale datasets -+ Alignment, annotation, and variant calling using existing and custom - software, including GATK, bwa, STAR, and kallisto. -+ Correcting for and experimental design to overcome multiple - testing, confounders, and batch effects using Bayesian and - frequentist methods approaches -+ Using evolutionary genomics to identify causal human variants -** Statistics -+ Statistical modeling (regression, inference, prediction, and - learning in very large (> 1TB) datasets) using R and SAS. -+ Addressing confounders and batch effects -+ Reproducible research ++ Strong verbal and presentation skills as evidenced by presentation, + leadership, and teaching record * Authored Open Source Software + *[[http://bugs.debian.org][Debbugs]]*: Bug tracking software for the Debian GNU/Linux distribution. [[https://bugs.debian.org]] @@ -159,9 +153,8 @@ * Publications and Presentations + 24 peer-reviewed publications cited over 3000 times: https://dla2.us/pubs -+ Publication record in GWAS, expression analysis of microarrays, SLE, - GBM, epigenetics, comparative evolution of mammals, and lipid - membranes ++ Publication record in GWAS, transcriptomics, SLE, GBM, epigenetics, + comparative evolution of mammals, and lipid membranes + H index >= 20 + Multiple presentations on EWAS of PTSD, genetics of SLE, and Open Source: https://dla2.us/pres