From: Don Armstrong Date: Thu, 22 Feb 2018 04:18:50 +0000 (-0800) Subject: Merge branch 'master' into jobs/system_administration X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=a51892a0bfcf04642e52ab5f4e8910635fcf5131;p=resume.git Merge branch 'master' into jobs/system_administration --- a51892a0bfcf04642e52ab5f4e8910635fcf5131 diff --cc don_armstrong_resume.org index c024aae,57c9f5e..456986b --- a/don_armstrong_resume.org +++ b/don_armstrong_resume.org @@@ -7,59 -7,82 +7,103 @@@ # #+LATEX_CLASS_OPTIONS: [10pt,breaklinks] * Experience +** Debian Developer \hfill 2004--Present - + \emph{Debian Project}, Developer; Technical Committee - Member (2010--2016), Technical Committee Chair (2015--2016). +++ 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 - + Developing and designing software and hardware - requirements. Deploying and maintaining enterprise-level systems for - web, email, and data storage backends using MySQL and other - solutions. +++ 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. ** Research Scientist at UIUC \hfill 2015--2017 - + Epigenetic modifications associated with PTSD, the genomic basis of - the development of parturition in mammals, and detecting adverse - pregnancy outcomes using urinary exosomes. + + 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. + + 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. ** Postdoctoral Researcher at USC \hfill 2013--2015 - + Identifying genes and causal alleles associated with Systemic Lupus - Erythematosus using genome-wide association, next-generation - sequencing, computational and biochemical approaches. + + 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. + + 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 - + Identifying genes which are associated with Systemic Lupus - Erythematosus using prior information and targeted trio-based - studies. - + + 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. + + 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 -+ 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. * Education - ** Doctor of Philosophy (PhD) \hfill UC Riverside - + Cell, Molecular and Developmental Biology. + ** Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology \hfill UC Riverside ** Batchelor of Science (BS) in Biology \hfill UC Riverside * Skills +** Programming Languages + + [[http://r-project.org][R]], [[http://www.perl.org][Perl]], sh (bash, POSIX, and zsh), SQL, PL/SQL, C/C++, HTML, CSS, + javascript +** Applications and Daemons + + Web: apache, ngix, varnish, REST, SOAP + + SQL servers: PostgreSQL, MySQL (including failover and replication) + + VCS: git, subversion + + Mail: postfix, exim, sendmail, spamassassin + + Configuration Infrastructure: puppet, etckeeper, git + + Documentation: \LaTeX, emacs, MarkDown, MediaWiki, ikiwiki, trac + + Monitoring: munin, nagios, icinga, prometheus + + Issue Tracking: Debbugs, Request Tracker, Trac + + Statistics: R, SAS + + Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel, + Powerpoint + + Virtualization libvirt, KVM, qemu, VMware +** 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 (5.0-10) + + MacOS (10-10.13) +** Statistics + + Statistical modeling in very large datasets + + Addressing confounders and batch effects + ** 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) -+ Addressing confounders and batch effects -+ Reproducible research ** Big Data + Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure) + Inter-process communication: MPI, OpenMP