From be889c5853906eedd383d4e0b1e014a286767603 Mon Sep 17 00:00:00 2001 From: Don Armstrong Date: Sat, 26 Feb 2022 14:46:18 -0800 Subject: [PATCH] add what I've done at bayer --- don_armstrong_resume.org | 123 +++++++++++++++++++++++++-------------- 1 file changed, 80 insertions(+), 43 deletions(-) diff --git a/don_armstrong_resume.org b/don_armstrong_resume.org index 475e3fb..e22a140 100644 --- a/don_armstrong_resume.org +++ b/don_armstrong_resume.org @@ -7,6 +7,33 @@ # #+LATEX_CLASS_OPTIONS: [10pt,breaklinks] * Experience +** Team Lead Data Engineering at Bayer Crop Science \hfill 2018--Present ++ 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 + 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 + (/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 ++ 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 +** Debian Developer \hfill 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 + provided leadership as the elected chair of the Technical Committee. ++ Developer of [[https://bugs.debian.org][Debbugs]], a perl and SQL-based issue-tracker with ≥ 100 + 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 + Primarily responsible for the planning, design, organization, execution, and analysis of multiple complex epidemiological studies @@ -22,7 +49,7 @@ maintain abreast of current scientific literature, principles of scientific research, and modern statistical methodology. + Wrote software and designed relational databases using R, perl, C, - SQL, make, and very large computational systems. + 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 @@ -42,20 +69,11 @@ the Los Angeles and greater United States. + Wrote and maintained multiple software components to reproducibly perform the analyses. -** Debian Developer \hfill 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 - provided leadership as the elected chair of the Technical Committee. -+ Developer of [[https://bugs.debian.org][Debbugs]], a perl and SQL-based issue-tracker with ≥ 100 - million entries with web, REST, and SOAP interfaces. -** Independent Systems Administrator \hfill 2004--Present +** 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. -+ Provided vendor-level support for complex systems integration issues - on Debian GNU/Linux systems. + Full life-cycle support of medium and small business networking infrastructure, including VPN, network security, wireless networks, routing, DNS, DHCP, and authentication. @@ -64,6 +82,53 @@ ** Batchelor of Science (BS) in Biology \hfill UC Riverside * Skills +** Leadership and Mentoring ++ Lead ++ 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 +** 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 ++ 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 ++ 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 ++ Documentation: \LaTeX, confluence, emacs, MarkDown, MediaWiki, ikiwiki, trac ++ Monitoring: munin, nagios, icinga, prometheus ++ 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 + 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 @@ -83,49 +148,21 @@ learning in very large (> 1TB) datasets) using R and SAS. + Addressing confounders and batch effects + Reproducible research -** Big Data -+ Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure) -+ Inter-process communication: MPI, OpenMP -+ Filestorage: Gluster, CEFS, GPFS, Lustre -+ Linux system administration -** Mentoring and Leadership -+ 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 -** Software Development -+ Languages: perl, R, C, C++, python, groovy, sh, make -+ Collaborative Development: git, travis, continuous integration, - automated testing -+ Web, Mobile: Shiny, jQuery, JavaScript -+ Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL -+ Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel, - Powerpoint -** Communication -+ Strong written communication skills as evidenced by publication - record -+ Strong verbal and presentation skills as evidenced by presentation - and teaching record -# ** Consortia Involvement -# + *H3A Bionet*: Generating workflows and cloud resources for H3 Africa -# + *Psychiatric Genomics Consortium*: Identification of epigenetic -# variants which are correlated with PTSD. -# + *SLEGEN*: System lupus erythematosus genetics consortium. -* Authored Software +* Authored Open Source Software + *[[http://bugs.debian.org][Debbugs]]*: Bug tracking software for the Debian GNU/Linux distribution. [[https://bugs.debian.org]] + *[[http://git.donarmstrong.com/r/CairoHacks.git][CairoHacks]]*: Bookmarks and Raster images for large PDF plots in R. + *[[http://rzlab.ucr.edu/function2gene/][Function2Gene]]*: Gene selection tool based on literature mining which enables Bayesian approaches to significance testing. + *[[http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit][Helical Wheel Projections]]*: Web-based tool to draw helical wheel - protein projections. [[http://rzlab.ucr.edu/scripts/wheel]] + protein projections. * Publications and Presentations -+ 24 peer-reviewed publications cited over 1800 times: ++ 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 -+ H index of 11 ++ H index >= 20 + Multiple presentations on EWAS of PTSD, genetics of SLE, and Open Source: https://dla2.us/pres -- 2.39.2