Merge branch 'master' into jobs/system_administration

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--- 1/dla-resume.org
--- 2/dla-resume.org
+++ b/dla-resume.org
@@@ -1,69 -1,53 +1,65 @@@
  #+OPTIONS: ^:nil
  #+OPTIONS: toc:nil
  #+TITLE: Resume
- #+AUTHOR: Don Armstrong
+ #+AUTHOR: Don L. Armstrong
  #+LATEX_CMD: xelatex
  #+LATEX_CLASS: dlaresume
- #+LATEX_CLASS_OPTIONS: [breaklinks]
- 
- #+BEGIN_EXPORT latex
- \begin{minipage}[t]{0.4\textwidth}
-   \begin{minipage}[c][0.6in]{2.3in}
-   {\color{headings}\fontsize{24pt}{24pt}\selectfont {\textsc{\textbf{\myauthor}}}}
-   {\footnotesize
-   \href{mailto:\myemail}{\myemail} \hfill
-   +1~714-813-8531 \\
-   {\centering  \href{\myweb}{\myweb} 
-   \href{https://github.com/dondelelcaro}{https://github.com/dondelelcaro}
-   }
-   }
-   \vfill
-   \end{minipage}
-   \hfill
-    \begin{minipage}[t]{0.0in}
-      % dummy (needed here)
-   \end{minipage}
- %  \medskip
-   % Address and contact block
-   \hfill
-   \begin{minipage}[c][0.6in]{0.6in}
-   \href{https://dla2.us/res}{\qrcode[tight,level=L,nolink,height=0.6in]{https://dla2.us/res}}
-   \end{minipage}
-   \vspace{1em}
- #+END_EXPORT
+ # #+LATEX_CLASS_OPTIONS: [10pt,breaklinks]
  
 -** Debian Developer \hfill 2004--Present
 -+ \emph{Debian Project}, Developer; Technical Committee Member
 -  (2010--2016), Technical Committee Chair (2015--2016).
+ * Experience
++** Debian Developer \hfill 2004--Present
+++ \emph{Debian Project}, Developer; Technical Committee
++  Member (2010--2016), Technical Committee Chair (2015--2016).
++** 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.
+ ** 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.
+ ** 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.
+ ** Postdoctoral Researcher at UCR \hfill 2010--2012
+ + Identifying genes which are associated with Systemic Lupus
+   Erythematosus using prior information and targeted trio-based
+   studies.
  
  * Education
- ** University of California, Riverside
- + *PhD* in Cell, Molecular and Developmental Biology
- + *BS* in Biology
+ ** Doctor of Philosophy (PhD) \hfill UC Riverside
+  + Cell, Molecular and Developmental Biology.
+ ** Batchelor of Science (BS) in Biology \hfill UC Riverside
+ 
  * Skills
 -** 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
 +** 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 (regression, inference, prediction, and
 -  learning in very large (> 1TB) datasets)
 -+ Addressing confounders and batch effects
 -# + Reproducible research
 + + Statistical modeling in very large datasets
 + + Addressing confounders and batch effects
  ** Big Data
  + Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure)
  + Inter-process communication: MPI, OpenMP
@@@ -78,41 -71,11 +74,12 @@@
    record
  + Strong verbal and presentation skills as evidenced by presentation
    and teaching record
- #+BEGIN_EXPORT latex
- \end{minipage}
-   \hfill
-    \begin{minipage}[t]{0.0in}
-      % dummy (needed here)
-   \end{minipage}
-   \medskip
- \hfill
- \begin{minipage}[t]{0.55\textwidth}
- 
- #+END_EXPORT
- * Experience
- ** Debian Developer
- + 2004--Present. \emph{Debian Project}, Developer; Technical Committee
-   Member (2010--2016), Technical Committee Chair (2015--2016).
- ** Independent Systems Administrator
- + 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.
- ** Research Scientist at UIUC
- + 2015--Present. University of Illinois at Urbana-Champaign. Epigenetic
-   modifications associated with PTSD, the genomic basis of the
-   development of parturition in mammals, and detecting adverse
-   pregnancy outcomes using urinary exosomes.
- ** Postdoctoral Researcher at USC
- + 2013--2015. Developing and deploying systems to identify clinically
-   relevant genes and causal alleles associated with Systemic Lupus
-   Erythematosus using genome-wide association, next-generation
-   sequencing, computational and biochemical approaches.
- ** Postdoctoral Researcher at UCR
- + 2010--2012. Identifying genes which are associated with Systemic
-   Lupus Erythematosus using prior information and targeted trio-based
-   studies.
 +
+ # ** 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
  + *[[http://bugs.debian.org][Debbugs]]*: Bug tracking software for the Debian GNU/Linux
     distribution. [[https://bugs.debian.org]]