1 [[!meta title="Resumé"]]
4 ## Team Lead Data Engineering at Ginkgo Bioworks 2022--Present
5 + Lead and manged team of data engineers, system administrators,
6 statisticians, bioinformaticians, and scientists at the PhD level
7 working within the AgBio unit of Ginkgo Bioworks.
8 + Mentored and coached team members in data science, bioinformatics,
9 data engineering, and statistics.
10 + Key leadership role in successful merger of AgBio unit with Ginkgo,
11 including all relevant R&D business applications and data-adjacent
13 ## Team Lead Data Engineering at Bayer Crop Science 2018--2022
14 + Hired, managed, and developed team of 5+ Data Engineers, Systems
15 Administrators, and Business Analysts working within the Biologics
16 R&D unit of Bayer Crop Science enabling data capture, data
17 integration, and operationalization of data analysis pipelines
18 + Developed and supervised implementation of data capture,
19 integration, and analysis strategies to increase the value of
20 genomics, metabolomics, transcriptomics, spectroscopic, phenotypic
21 (/in vitro/ and /in planta/), and fermentation/formulation process
22 data for discovery and development
23 + Lead the development of multiple systems while coaching, mentoring,
24 and developing developers and engineers
25 + Served as a key collaborator on multiple cross-function and
26 cross-divisional projects, including leading the architecture of a
27 life science collaboration using serverless architecture to provide
28 machine-learning estimates of critical parameters from
29 spectrographic measurements
30 + Established and developed network of internal and external contacts
31 for technical implementation of Bayer program goals.
32 ## Debian Developer 2004--Present
33 + Maintained, managed configurations, and resolved issues in multiple
34 packages written in R, perl, python, scheme, C++, and C.
35 + Resolved technical conflicts, developed technical standards, and
36 provided leadership as the elected chair of the Technical Committee.
37 + Developer of [Debbugs](https://bugs.debian.org), a perl and SQL-based issue-tracker with ≥ 100
38 million entries with web, REST, and SOAP interfaces.
39 + Provided vendor-level support for complex systems integration issues
40 on Debian GNU/Linux systems.
41 ## Research Scientist at UIUC \hfill 2015--2017
42 + Planning, design, organization, execution, and analysis of multiple
43 complex epidemiological studies involving epigenomics,
44 transcriptomics, and genomics of diseases of pregnancy and
45 post-traumatic stress disorder.
46 + Published results in scientific publications and presented results
47 orally at major scientific conferences.
48 + Wrote and completed grants, including budgeting, scientific
49 direction, project management, and reporting.
50 + Mentored graduate students and collaborated with internal and
52 + Performed literature review, training, and applied new techniques to
53 maintain abreast of current scientific literature, principles of
54 scientific research, and modern statistical methodology.
55 + Wrote software and designed relational databases using R, perl, C,
56 SQL, make, and very large computational systems ([Blue Waters](https://bluewaters.ncsa.illinois.edu/))
57 ## Postdoctoral Researcher at USC 2013--2015
58 + Design, execution, and analysis of an epidemiological study to
59 identify genomic variants associated with systemic lupus
60 erythematosus using targeted deep sequencing.
61 + Wrote multiple pieces of software to reproducibly analyze and
62 archive large datasets resulting from genomic sequencing.
63 + Coordinated with clinicians, molecular biologists, and biologists to
64 produce analyses and major reports.
65 ## Postdoctoral Researcher at UCR 2010--2012
66 + Executed and analyzed an epidemiological study to identify genomic
67 variants associated with systemic lupus erythematosus using prior
68 information and array based approaches in a trio and cross sectional
69 study of individuals from the Los Angeles and greater United States.
70 + Wrote and maintained multiple software components to reproducibly
73 + Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology at UC Riverside
74 + Batchelor of Science (BS) in Biology at UC Riverside
77 ## Leadership and Mentoring
78 + Lead teams of PhD and MD scientists in multiple scientific and
80 + Mentored graduate students and Outreachy and Google Summer of Code
82 + Former chair of Debian's Technical Committee
83 + Head developer behind https://bugs.debian.org
84 ## Bioinformatics, Genomics, and Epigenomics
85 + NGS and array-based Genomics and Epigenomics of complex human
86 diseases using RNA-seq, targeted DNA sequencing, RRBS, Illumina
87 bead arrays, and Affymetrix microarrays from sample collection to
89 + Reproducible, scalable bioinformatics analysis using make,
90 nextflow, and cwl based workflows on cloud- and cluster-based
91 systems on terabyte-scale datasets
92 + Alignment, annotation, and variant calling using existing and custom
93 software, including GATK, bwa, STAR, and kallisto
94 + Using evolutionary genomics to identify causal human variants
96 + Statistical modeling (regression, inference, prediction, and machine
97 learning in very large (> 1TB) datasets) using R and python.
98 + Correcting & experimental design to overcome multiple testing,
99 confounders, and batch effects (both Bayesian and frequentist)
100 + Reproducible research
101 ## Software Development
102 + Languages: python, R, perl, C, C++, python, groovy, sh (bash, POSIX,
104 + Collaborative Development: git, Jira, gitlab CI/CD, github actions,
105 Aha!, continuous integration & deployment, automated testing
106 + Web, Mobile: Shiny, jQuery, JavaScript
107 + Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL
109 + Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure)
110 + Inter-process communication: MPI, OpenMP
111 + Filestorage: Gluster, CEFS, GPFS, Lustre
112 + Linux system administration
113 ## Applications and Daemons
114 + Web: apache, ngix, varnish (load balancing/caching), REST, SOAP,
116 + Build Tools: GNU make, cmake
117 + Virtualization: libvirt, KVM, qemu, VMware, docker
118 + VCS: git, mercurial, subversion
119 + Mail: postfix, exim, sendmail, spamassassin
120 + Configuration Infrastructure: puppet, hiera, etckeeper, git
121 + Documentation: \LaTeX, confluence, emacs, MarkDown, MediaWiki, ikiwiki, trac
122 + Monitoring: munin, nagios, icinga, prometheus
123 + Issue Tracking: Debbugs, Request Tracker, Trac, JIRA
124 + Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel,
127 + Hardware, Linux routing and firewall experience, ferm, DHCP,
128 openvpn, bonding, NAT, DNHS, SNMP, IPv4, and IPv6.
130 + GNU/Linux (Debian, Ubuntu, Red Hat)
134 + Strong written communication skills as evidenced by publication
136 + Strong verbal and presentation skills as evidenced by presentation,
137 leadership, and teaching record
138 # Authored Open Source Software
139 + *[Debbugs](http://bugs.debian.org)*: Bug tracking software for the Debian GNU/Linux
141 + *[CairoHacks](http://git.donarmstrong.com/r/CairoHacks.git)*: Bookmarks and Raster images for large PDF plots in R.
142 * Publications and Presentations
143 + 24 peer-reviewed publications cited over 3000 times:
145 + Publication record in GWAS, transcriptomics, SLE, GBM, epigenetics,
146 comparative evolution of mammals, and lipid membranes
148 + Multiple presentations on EWAS of PTSD, genetics of SLE, and Open
149 Source: https://dla2.us/pres
153 + 2017 R Consortium: *[Adding Linux Binary Builders to R-Hub](https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants)* Role:
155 + 2015 Blue Waters Allocation Grant: *Making ancestral trees using Bayesian
156 inference to identify disease-causing genetic variants* Role:
158 + *Tracking placenta and uterine funciton using urinary extracellular vesicles* (R21
159 RFA-HD-16-037) Role: Key Personnel
160 + *NIAMS* R01-AR045650-04 *Genetics of Childhood Onset SLE* to Chaim O. Jacob.
163 ## Scholarships and Fellowships
164 + 2001--2003: University of California, Riverside Doctoral Fellowship
165 + 1997--2001: Regents of the University of California Scholarship.
167 # Academic Information
169 You can also read my [Curriculum Vitæ](curriculum_vitae)
170 ([pdf](dla-cv.pdf)), [Research Statement](research_statement)
171 ([pdf](research_statement.pdf)),
172 and [Teaching Statement](teaching_statement)
173 ([pdf](teaching_statement.pdf)).
175 For my contact information or additional references, please e-mail
176 <don@donarmstrong.com>