From: Don Armstrong Date: Tue, 28 Feb 2023 00:36:38 +0000 (-0800) Subject: add missing spaces, replace -- with – X-Git-Url: https://git.donarmstrong.com/?p=don.git;a=commitdiff_plain;h=c7acf9567b7a478134dd6379cba9c3575a9f1873 add missing spaces, replace -- with – --- diff --git a/resume.mdwn b/resume.mdwn index 0258b2c..43e34c0 100644 --- a/resume.mdwn +++ b/resume.mdwn @@ -1,7 +1,7 @@ [[!meta title="Resumé"]] # Experience -## Team Lead Data Engineering at Ginkgo Bioworks 2022--Present +## Team Lead Data Engineering at Ginkgo Bioworks 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. @@ -10,7 +10,8 @@ + 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 2018--2022 + +## Team Lead Data Engineering at Bayer Crop Science 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 @@ -29,7 +30,8 @@ spectrographic measurements + Established and developed network of internal and external contacts for technical implementation of Bayer program goals. -## Debian Developer 2004--Present + +## Debian Developer 2004–Present + Maintained, managed configurations, and resolved issues in multiple packages written in R, perl, python, scheme, C++, and C. + Resolved technical conflicts, developed technical standards, and @@ -38,7 +40,8 @@ million entries with web, REST, and SOAP interfaces. + Provided vendor-level support for complex systems integration issues on Debian GNU/Linux systems. -## Research Scientist at UIUC \hfill 2015--2017 + +## Research Scientist at UIUC 2015–2017 + Planning, design, organization, execution, and analysis of multiple complex epidemiological studies involving epigenomics, transcriptomics, and genomics of diseases of pregnancy and @@ -54,7 +57,8 @@ scientific research, and modern statistical methodology. + Wrote software and designed relational databases using R, perl, C, SQL, make, and very large computational systems ([Blue Waters](https://bluewaters.ncsa.illinois.edu/)) -## Postdoctoral Researcher at USC 2013--2015 + +## Postdoctoral Researcher at USC 2013–2015 + Design, execution, and analysis of an epidemiological study to identify genomic variants associated with systemic lupus erythematosus using targeted deep sequencing. @@ -62,13 +66,15 @@ archive large datasets resulting from genomic sequencing. + Coordinated with clinicians, molecular biologists, and biologists to produce analyses and major reports. -## Postdoctoral Researcher at UCR 2010--2012 + +## Postdoctoral Researcher at UCR 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 at UC Riverside + Batchelor of Science (BS) in Biology at UC Riverside @@ -81,6 +87,7 @@ 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 @@ -92,12 +99,14 @@ + 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 @@ -105,11 +114,13 @@ Aha!, continuous integration & deployment, automated testing + Web, Mobile: Shiny, jQuery, JavaScript + Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL + ## Big Data + Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure) + Inter-process communication: MPI, OpenMP + Filestorage: Gluster, CEFS, GPFS, Lustre + Linux system administration + ## Applications and Daemons + Web: apache, ngix, varnish (load balancing/caching), REST, SOAP, Tomcat @@ -123,18 +134,22 @@ + Issue Tracking: Debbugs, Request Tracker, Trac, JIRA + 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. + ## Operating systems + 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, leadership, and teaching record + # Authored Open Source Software + *[Debbugs](http://bugs.debian.org)*: Bug tracking software for the Debian GNU/Linux distribution. @@ -161,8 +176,8 @@ Role: Key Personnel ## Scholarships and Fellowships -+ 2001--2003: University of California, Riverside Doctoral Fellowship -+ 1997--2001: Regents of the University of California Scholarship. ++ 2001–2003: University of California, Riverside Doctoral Fellowship ++ 1997–2001: Regents of the University of California Scholarship. # Academic Information