add start of resume

diff --git a/Makefile b/Makefile
new file mode 100644 (file)
index 0000000..7148a54
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,16 @@
+#!/usr/bin/make
+
+EMACSARGS=--batch  -l ~/.emacs 
+EMACS=emacs
+
+
+all: dla-resume.pdf
+
+# dla-resume.pdf: dla-resume.tex $(wildcard *.bib)
+#      latexmk -pdf -pdflatex="xelatex -interaction=nonstopmode" -bibtex -use-make $<
+
+
+dla-resume.pdf: dla-resume.org
+       $(EMACS) $(EMACSARGS) --visit $^ \
+       --eval "(setq org-latex-remove-logfiles nil)" \
+       --funcall org-latex-export-to-pdf

diff --git a/dla-resume.org b/dla-resume.org
new file mode 100644 (file)
index 0000000..2beb3c9
--- /dev/null
+++ b/dla-resume.org
@@ -0,0 +1,140 @@
+#+OPTIONS: ^:nil
+#+OPTIONS: toc:nil
+#+TITLE: Resume
+#+AUTHOR: Don Armstrong
+#+LATEX_CMD: xelatex
+#+LATEX_CLASS: dlaresume
+#+LATEX_CLASS_OPTIONS: [10pt,breaklinks]
+
+#+BEGIN_EXPORT latex
+  %% Name  
+  \noindent{\Huge {\textsc{\textbf{\myauthor}}}}
+  \hfill
+   \begin{minipage}[t]{0.0in}
+     % dummy (needed here)
+  \end{minipage}
+  \medskip
+  % Address and contact block
+  \hfill
+  \begin{minipage}[t]{1.7in}
+    \flushright {\footnotesize
+      \myphone \\ 
+      \href{mailto:\myemail}{\myemail} \\
+      \href{\myweb}{\myweb}}
+  \end{minipage}
+
+  \medskip
+
+#+END_EXPORT
+
+#+BEGIN_EXPORT latex
+\begin{minipage}[t]{0.33\textwidth}
+#+END_EXPORT
+
+* Education
+** UC Riverside
++ *PhD* in Cell, Molecular and Developmental Biology. July 2008.
++ *BS* in Biology. July 2001.
+* Skills
+** Statistics
+   + Multiple testing and confounders
+   + Genetic epidemiology of human populations
+   + Modeling (GLM, ordered models, etc.)
+** -omics
+   + DNA Methylation analysis in humans and non-model organisms
+   + RNA quantification and differential analysis using RNAseq and
+     arrays in humans and non-model organisms
+   + DNA variant calling and analysis in tens of thousands of samples
+** Software Development
+   + Languages: perl, R, C, C++, assembly, sh
+   + Collaborative Development: git, issue tracking, testing harnesses
+   + Databases: Postgresql (PL/SQL), SQLite, Mysql
+** Parallel and Cloud Computing
+   + Inter-process communication: MPI, OpenMP, Hadoop
+   + Filestorage: Gluster, CEFS, GPFS, Lustre
+   + Cloud based-infrastructure: Azure, AWS, Docker, cloud-init
+   + Debian GNU/Linux system administration
+
+#+BEGIN_EXPORT latex
+\end{minipage}
+\hfill
+\begin{minipage}[t]{0.66\textwidth}
+
+#+END_EXPORT
+* Experience
+** 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.
+** Postdoctoral Researcher at USC
++ 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
++ 2010--2012. Identifying genes which are associated with Systemic
+  Lupus Erythematosus using prior information and targeted trio-based
+  studies.
+** Debian Developer with the Debian Project
++ 2004--Present. \emph{Debian Project}, Developer; Technical Committee
+  Member (2010--Present), Technical Committee Chair (2015--2016).
+* Authored 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]]
+* Publications
++ 20 peer-reviewed refereed publications cited over 1700 times
++ Publication record in GWAS, expression analysis
+
+#+BEGIN_EXPORT latex
+\end{minipage}
+#+END_EXPORT
+
+* Funding and Awards
+** Grants
++ 2017 R Consortium: *[[https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants][Adding Linux Binary Builders to R-Hub]]* Role:
+  Co-PI
++ 2015 Blue Waters Allocation Grant: *Making ancestral trees using Bayesian
+  inference to identify disease-causing genetic variants* Role:
+  Primary Investigator
++ BD2K Mentored Career Development Award: *Predicting individualized*
+  *chemotherapeutic treatment outcomes using large multi-omics and*
+  *clinical datasets* (K01 RFA-ES-16-002) (under review) Role: PI
++ *Mechanism of PR Resistance in Endometriosis* (R01 RFA-HD-16-036)
+  (under review) Role: Co-PI
++ *Tracking placenta and uterine funciton using urinary extracellular vesicles* (R21
+  RFA-HD-16-037) (under review) Role: Key Personnel
++ *Molecular Transducers of Physical Activity Bioinformatics Center*
+  (U24 RFA-RM-15-012) (under review) Role: Key Personnel
++ *NIAMS* R01-AR045650-04 *Genetics of Childhood Onset SLE* to Chaim O. Jacob.
+  Role: Key Personnel
+** Conference Awards
++ 2007 FOCIS Trainee Award
++ 2009 FOCIS Trainee Award
+** Scholarships and Fellowships
++ 2001--2003: University of California, Riverside Doctoral Fellowship
++ 1997--2001: Regents of the University of California Scholarship.
+* Service
+** Consortiums
++ *H3A Bionet*: Generating workflows and cloud resources for
+  bioinformatics analysis as part of the H3 Africa consortium
++ *Psychiatric Genomics Consortium*: Identification of epigenetic
+  variants which are correlated with PTSD.
++ *SLEGEN*: System lupus erythematosus genetics consortium.
+** Mentoring
++ *Laren Riesche*: Differential methylation of marmoset placentas
+  using RRBS. Statistical training and bioinformatics training
+  resulting in PhD in Nursing. 2016-2017.
++ *Christine Y. Chan*: Ancestral trees for disease predictions. 2016
++ *[[https://developers.google.com/open-source/gsoc/2006/][Phillip Kern]]*: GUI for Debian's bug tracking system.
++ *[[https://gnome.org/opw/][Virginia King]]*: Improving documentation of Debian's Bug Tracking system.
+** Reviewing
++ /Ad hoc/ reviewer for PLoS One.
+
+
+

diff --git a/dlaresume.cls b/dlaresume.cls
new file mode 100644 (file)
index 0000000..e152e81
--- /dev/null
+++ b/dlaresume.cls
@@ -0,0 +1,139 @@
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesClass{dlaresume}[2017/01/21 DLA Resume Class]
+
+\RequirePackage{ifthen}
+\RequirePackage{xkeyval}
+
+%\DeclareOptionX*{\PassOptionsToClass{\CurrentOption}}
+\ProcessOptionsX*
+
+% much of this was borrowed from Mako's work: git://projects.mako.cc/bmh-cv
+
+% include data on fonts
+\LoadClass{article}
+
+\RequirePackage{fontspec}
+
+\setmainfont[Ligatures=TeX]{FreeSerif}
+\setsansfont{FreeSans}
+\setmonofont{FreeMono}
+
+\RequirePackage{lastpage}
+\PassOptionsToPackage{letterpaper,margin=1in,left=1in,ignoreall=true}{geometry}
+\RequirePackage{geometry}
+\RequirePackage{url}
+\RequirePackage{fancyhdr}
+\PassOptionsToPackage{final}{graphicx}
+\RequirePackage{graphicx}
+\PassOptionsToPackage{labelfont=bf,font=sl}{caption}
+\RequirePackage{caption}
+\RequirePackage{multirow}
+\PassOptionsToPackage{usenames,dvipsnames}{color}
+\RequirePackage{color}
+\PassOptionsToPackage{x11names,svgnames,table}{xcolor}
+\RequirePackage{xcolor}
+\RequirePackage{hyperref}
+\PassOptionsToPackage{nomargin,inline}{fixme}
+\RequirePackage{fixme}
+\PassOptionsToPackage{capitalize}{cleveref}
+\RequirePackage{cleveref}
+\PassOptionsToPackage{backend=biber,hyperref=true,style=numeric-comp}{biblatex}
+\RequirePackage{biblatex}
+\addbibresource{references.bib}
+
+\hypersetup{colorlinks=true, linkcolor=Black, citecolor=Black, filecolor=Black,
+    urlcolor=Black, unicode=true}
+\urlstyle{same}
+% customize the titles so that they appear in the right margin
+\RequirePackage{titlesec}
+
+%\AtBeginDocument{
+\setlength{\marginparwidth}{0in}
+\setlength{\titlewidth}{0in}
+% set the default indent to nothing
+\setlength{\parindent}{0em}
+%}
+\makeatletter
+% \newif\if@aftersec
+% \newcommand\setsubskip{%
+%     \global\@aftersectrue
+%     \everypar{%
+%         \global\@aftersecfalse
+%         \if@noskipsec
+%             \global\@noskipsecfalse
+%             \clubpenalty\@M
+%             \hskip-\parindent
+%             \begingroup
+%                 \@svsechd\unskip{\hspace{\@tempskipb}}%
+%             \endgroup
+%         \else
+%             \clubpenalty\@clubpenalty\everypar{}%
+%         \fi}}
+
+% \newcommand\subskip{%
+%   \if@aftersec
+%      \removelastskip%         EDIT 2
+%      \vspace{-\baselineskip}% EDIT 2 ??????????????
+%   \else
+%      \removelastskip%
+%      \vspace{0.5em}
+%   \fi
+%   \global\@aftersecfalse}
+\makeatother
+
+\definecolor{date}{HTML}{666666} 
+\definecolor{primary}{HTML}{0b0b0b} 
+\definecolor{headings}{HTML}{1A1A1A}
+\definecolor{subheadings}{HTML}{3A3A3A}
+
+\titleformat{\section}{%
+\color{headings}\fontsize{16pt}{20pt}\selectfont%
+ \raggedright\scshape}{}{0pt}{}
+\titlespacing*{\section}{0pt}{0ex}{0cm}
+\titleformat{\subsection}{%
+\color{subheadings}\fontsize{14pt}{18pt}\selectfont%
+ \raggedright \scshape}{}{0pt}{}
+\titlespacing*{\subsection}{0pt}{0ex}{0ex}
+
+\def\myauthor{Don Armstrong}
+\def\mytitle{Resume}
+\def\mycopyright{\myauthor}
+\def\myaddress{}
+\def\myemail{don@donarmstrong.com}
+\def\myweb{http://www.donarmstrong.com/}
+\def\myphone{+1 714-813-8531}
+
+% create a special cvlist environment to format the items
+\newenvironment{cvlist}{
+\begin{list}{-}{\leftmargin=0em \itemindent=1.0em}
+  \setlength{\itemsep}{0pt}
+  \setlength{\parskip}{0em}
+  \setlength{\parsep}{1em}
+  \setlength{\parindent}{0em}}%
+{\vspace{1em}
+\end{list}}
+
+\renewenvironment{itemize}{\begin{cvlist}}{\end{cvlist}}
+\newcounter{cvlistenumcounter}
+
+\newenvironment{cvlistenum}{
+\begin{list}{\arabic{cvlistenumcounter}. }{\usecounter{cvlistenumcounter}\leftmargin=3.0em \itemindent=-3.0em}
+  \setlength{\itemsep}{0pt}
+  \setlength{\parskip}{0em}
+  \setlength{\parsep}{1em}
+  \setlength{\parindent}{0em}}%
+{\vspace{1em}
+\end{list}}
+
+\renewenvironment{enumerate}{\begin{cvlistenum}}{\end{cvlistenum}}
+% no title
+\renewcommand{\maketitle}{}
+
+% Page layout
+\pagestyle{fancy}
+\renewcommand{\headrulewidth}{0pt}
+\fancyhead{}
+\fancyfoot{}
+\makeatletter
+ \fancyfoot[C]{{\scriptsize \@title \ of \@author \ -- Page \thepage\ of\ \pageref{LastPage}}}
+\makeatother
\ No newline at end of file