-[[!meta title="Curriculum Vitæ, Research Statement, and Teaching Statement"]]
+[[!meta title="Resumé"]]
-Introduction
-------------
+# Experience
+## 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.
++ 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.
-A brief statement of my research interests and teaching mission
-follows, and my [Curriculum Vitæ](curriculum_vitae)
-([pdf](dla-cv.pdf)),
-[Research Statement](research_statement)
-([pdf](research_statement.pdf)), and
-[Teaching Statement](teaching_statement)
-([pdf](teaching_statement.pdf)) are also available.
+## 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
+ 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 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.
-For my contact information or additional references, please e-mail
-<don@donarmstrong.com>
+## 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
+ provided leadership as the elected chair of the Technical Committee.
++ Developer of [Debbugs](https://bugs.debian.org), 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 2015–2017
++ 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
+ direction, project management, and reporting.
++ Mentored graduate students and collaborated with internal and
+ external scientists.
++ Performed literature review, training, and applied new techniques to
+ 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 ([Blue Waters](https://bluewaters.ncsa.illinois.edu/))
+
+## 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.
++ 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 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
+
+# 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
+
+## 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, 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
++ Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure)
++ Inter-process communication: MPI, OpenMP
++ Filestorage: Gluster, CEFS, GPFS, Lustre
++ Linux system administration
-Research Focus
---------------
-
-My primary research focus is developing and using bioinformatics
-techniques to identify causes and mechanisms underlying human
-diseases, such as Systemic Lupus Erythematosus (SLE). I have
-identified multiple novel genes associated with SLE using both
-genome-wide association studies and trio-based studies in targeted
-regions. In collaborative work, I have identified a causal variant in
-NCF2
-([rs17849502](http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs17849502))
-using both *in silico* and *in vitro* approaches. I am currently
-working on identifying causal variants in additional associated genes
-using targeted deep sequencing using high-throughput variant analysis
-pipelines to prioritize variants for additional *in silico* and *in
-vitro* experiments. In the future, utilizing my extensive
-bioinformatic and software development experience, I will head a
-development group working on techniques for the storage, alignment,
-and analysis of terabytes (eventually petabytes) of next-generation
-sequencing data from collaborations studying human-relevant diseases
-and biological systems.
-
-
-Teaching Mission
-----------------
-
-While teaching, my primary mission is to have my students experience
-the excitement of scientific discovery for themselves. Secondarily, I
-use that excitement to keep them engaged and interested in the
-material. While a graduate student at UC Riverside, I was a teaching
-assistant for [Introductory Biology, Genetics, Molecular Biology, and
-Developmental Biology](http://www.biology.ucr.edu/courses/UGcourses.html)
+## Applications and Daemons
++ Web: apache, ngix, varnish (load balancing/caching), REST, SOAP,
+ Tomcat
++ Build Tools: GNU make, cmake
++ 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
++ 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.
++ *[CairoHacks](http://git.donarmstrong.com/r/CairoHacks.git)*: Bookmarks and Raster images for large PDF plots in R.
+* Publications and Presentations
++ 24 peer-reviewed publications cited over 3000 times:
+ https://dla2.us/pubs
++ 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
+
+# Funding and Awards
+## Grants
++ 2017 R Consortium: *[Adding Linux Binary Builders to R-Hub](https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants)* 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.
+
+# Academic Information
+
+You can also read my [Curriculum Vitæ](curriculum_vitae)
+([pdf](dla-cv.pdf)), [Research Statement](research_statement)
+([pdf](research_statement.pdf)),
+and [Teaching Statement](teaching_statement)
+([pdf](teaching_statement.pdf)).
+
+For my contact information or additional references, please e-mail
+<don@donarmstrong.com>
projects / don.git / blobdiff