From: Don Armstrong Date: Sat, 15 Nov 2014 00:23:22 +0000 (-0800) Subject: Merge branch 'master' of ssh://git.donarmstrong.com/sites/git/don X-Git-Url: https://git.donarmstrong.com/?p=don.git;a=commitdiff_plain;h=af664fd4a0083ecd964669024d38bf9d5c4fac69;hp=37dd6bd0b1f5743937b968a54ff9fd5468852907 Merge branch 'master' of ssh://git.donarmstrong.com/sites/git/don --- diff --git a/archives.mdwn b/archives.mdwn index d07b73b..e8ffe32 100644 --- a/archives.mdwn +++ b/archives.mdwn @@ -1,3 +1,4 @@ +[[!meta title="Archives"]] [[!if test="archives/*" then=""" Browse through blog archives by year: [[!map pages="./archives/* and !./archives/*/* and !*/Discussion"]] diff --git a/favicon.ico b/favicon.ico new file mode 100644 index 0000000..c6dfd1a Binary files /dev/null and b/favicon.ico differ diff --git a/images/da_background.jpg b/images/da_background.jpg index 85f42d5..bf2a3c7 100644 Binary files a/images/da_background.jpg and b/images/da_background.jpg differ diff --git a/index.mdwn b/index.mdwn index 220c1b3..62a1027 100644 --- a/index.mdwn +++ b/index.mdwn @@ -1,11 +1,13 @@ +[[!meta description="Don Armstrong's blog and web pages. Don Armstrong is a Bioinformatician and Debian Developer currently a postdoc at the University of Southern California and living in Riverside, CA."]] + +[[!inline pages="./posts/* and !*/Discussion" show="10" +actions=yes rootpage="posts"]] + [[!if test="enabled(sidebar)" then=""" [[!sidebar]] """ else=""" [[!inline pages=sidebar raw=yes]] """]] -[[!inline pages="./posts/* and !*/Discussion" show="10" -actions=yes rootpage="posts"]] - This blog is powered by [ikiwiki](http://ikiwiki.info). diff --git a/local.css b/local.css index ac1ea19..ce5b8e5 100644 --- a/local.css +++ b/local.css @@ -5,6 +5,8 @@ * local.css and use it to override or change settings in this one. */ +@import url("/fonts/liberationserif/stylesheet.css"); + /* html5 compat */ article, header, @@ -385,7 +387,7 @@ input#searchbox { } /* highlight plugin */ -pre.hl { color:#404048; background-color:#ddf; } +pre.hl { color:#404048; background-color:#eef; } .hl.num { color:#2020ff; } .hl.esc { color:#005858; } .hl.str { color:#2020ff; } @@ -395,7 +397,7 @@ pre.hl { color:#404048; background-color:#ddf; } .hl.dir { color:#008200; } .hl.sym { color:#404048; } .hl.line { color:#ff00c0; } -.hl.mark { background-color:#ffffbb; } +.hl.mark { background-color:#ffb; } .hl.kwa { color:#008858; font-weight:bold; } .hl.kwb { color:#7040ff; font-weight:bold;} .hl.kwc { color:#87002f; font-weight:bold; } @@ -548,7 +550,7 @@ pre { body { margin: 0; padding: 0; - font-family: sans-serif; + font-family: "liberation_serifregular",sans-serif; color: black; background: white; } @@ -562,13 +564,18 @@ body { border-color: #999; border-style: none none solid none; border-width: 1px; - background-image: url('/images/da_background.jpg'); - background-repeat: no-repeat; + background-image: url('/images/da_background.jpg'); + background-repeat: no-repeat; + background-size: 100% 100%; } .pageheader .header { float: left; font-size: 120%; + background-color: rgba(255, 255, 255, 0.8); + border-radius: 0.5em; + box-shadow: 4px 4px rgba(0, 0, 0, 0.2); + padding: 0.25em; } .header { @@ -578,7 +585,7 @@ body { .title { display: block; margin-top: .2em; - font: 140% sans-serif; + font: 180% "liberation_serifregular", san-serif; } #searchform { @@ -597,7 +604,9 @@ body { } #content, #comments, #footer { - margin: 1em 2em; + margin: 1em auto; + max-width: 55em; + text-align: justify; } #pageinfo { @@ -615,9 +624,9 @@ body { font-size: 120%; } -h1 { font: 120% sans-serif } -h2 { font: bold 100% sans-serif } -h3, h4, h5, h6 { font: bold 80% sans-serif } +h1 { font: 140% "liberation_serifbold", sans-serif } +h2 { font: 100% "liberation_serifbold",sans-serif } +h3, h4, h5, h6 { font: 80% "liberation_serifbold",sans-serif } /* Smaller headings for inline pages */ .inlinepage h1 { font-size: 110% } @@ -655,10 +664,13 @@ div.recentchanges { } .sidebar { - border-bottom: 0; - border-right: 0; + border-bottom: 0; + border-right: 0; border-top: 0; margin-top: 0.5em; padding: 0 0 0 2ex; border-color: #999; } +.sidebar p { + font-size: 120%; +} diff --git a/posts/dropbox_downloader.mdwn b/posts/dropbox_downloader.mdwn new file mode 100644 index 0000000..90c810b --- /dev/null +++ b/posts/dropbox_downloader.mdwn @@ -0,0 +1,16 @@ +[[!meta title="Dropbox Recursive Downloader"]] + +I'm working on some analyses for the +[Genetic Analysis Workshop #19](http://www.gaworkshop.org/gaw19/index.html), +which has placed it's data on Dropbox. Unfortunately, Dropbox doesn't +allow for people to download zip archives larger than 1GB, and the +data was made available in an unpacked structure with more than a +hundred files. Some searching indicated that no one had written a +recursive downloader for Dropbox, so 30 minutes of hacking with +[WWW::Mechanize](http://search.cpan.org/~ether/WWW-Mechanize-1.73/lib/WWW/Mechanize.pm) +later, I wrote a +[simple recursive downloader for Dropbox](http://git.donarmstrong.com/?p=bin.git;a=blob;f=dropbox_recursive;hb=HEAD). + +Two hours later, all of the files had downloaded. + +[[!tag tech debian genetics]] diff --git a/posts/embedded_raster_in_vector_plot.mdwn b/posts/embedded_raster_in_vector_plot.mdwn new file mode 100644 index 0000000..ed841fb --- /dev/null +++ b/posts/embedded_raster_in_vector_plot.mdwn @@ -0,0 +1,64 @@ +[[!meta title="Plotting Embedded Bitmap in Vector Plot in R"]] + +Recently, one of my collaborators complained that one of my plots took +forever to render on his machine. The particular plot in question had +a few thousand points, many of which were overlapping. Ideally, R +would be able to simplify the vector image which was drawn to avoid +drawing points which were occluded by other points, but this is +difficult to do properly, and R currently doesn't do it. + +However, R is able to plot to a bitmap, and bitmap images have the +nice property of automatically handling this for you. Furthermore, +raster images have recently been made far less clunky in R, so it's +pretty easy to shove an arbitrary bitmap image anywhere. With +`dev.capture` in Cairo coupled with `grid.raster` in grid, we have +everything we need to solve this problem: + +[[!format R """ +require(grid) +require(Cairo) + +start.rasterplot <- function(width=NULL,height=NULL) { + x.y.ratio <- convertX(unit(1,"npc"),"mm",valueOnly=TRUE)/ + convertY(unit(1,"npc"),"mm",valueOnly=TRUE) + width.points <- as.numeric(convertX(unit(1,"npc"),"points")) + dpi <- as.numeric(convertX(unit(1,"inch"),"point")) + if (is.null(width) && is.null(height)) { + width <- 1024 + } + if (is.null(width)) { + width <- height*x.y.ratio + } + if (is.null(height)) { + height <- width/x.y.ratio + } + Cairo(width=width,height=height,dpi=1024/width.points*dpi,file="/dev/null") +} + +stop.rasterplot <- function(plot=TRUE) { + raster.image <- dev.capture(native=TRUE) + dev.off() + if (plot) { + grid.raster(raster.image,width=unit(1,"npc"),height=unit(1,"npc")) + return(invisible()) + } else { + return(raster.image) + } +} +"""]] + +Now we can do the following: + +[[!format R """ +pdf(file="raster.pdf") +start.rasterplot() +print(xyplot(y~x, + data=data.frame(y=rnorm(1E8),x=rnorm(1E8)))) +stop.rasterplot() +dev.off() +"""]] + +and our PDF will contain a raster image, and will load in seconds +instead of taking forever to plot the file. + +[[!tag r genetics biology]] diff --git a/posts/ergodox_keyboard.mdwn b/posts/ergodox_keyboard.mdwn new file mode 100644 index 0000000..080a041 --- /dev/null +++ b/posts/ergodox_keyboard.mdwn @@ -0,0 +1,42 @@ +[[!meta title="ErgoDox keyboard assembly"]] + +[[!agimg don_lab/017_even_more_lab_desk_10232003.jpg]] + +I routinely use a Kinesis Advantage Pro keyboard, which is a split, +ergonomic keyboard with thumb clusters that uses brown cherryMX +switches. Over the thirteen years that I've been using it, I've become +a huge fan of this style of keyboard. However, I have two major +annoyances with the Kinesis. First, while the firmware is good, +remapping the keys is complicated and producing more complicated +keyboard layouts with layers and keycodes that are not present in the +original layout is not possible. Secondly, the interconnect between +the main key wells and the controller board in the middle occasionally +fails, and requires disassembly and occasional re-tinning of the +circuit board interconnect connector. + +[[!agimg 2014/08_August/20140801_ergodox/IMG_20140801_232557.jpg]] +1 +About a year ago, I became aware of the [ErgoDox](http://ergodox.org/) +keyboard, which is a keyboard design which mimics the kinesis to some +degree, but with completely separated key halves (useful, because I'm +substantially bigger than the average human), programmable firmware +(so I can finally have the layers and missing keys) and with slightly +more elegant interconnects (TRRS cables). Unfortunately, at the time I +first heard about it (and other custom keyboards), making it required +sourcing circuit boards, parts, and finding someone to cut a case for +the keyboard. Then, a few months ago, I learned about +[MassDrop](http://www.massdrop.com), a company who puts together +groups of people to do buys of products at near-wholesale level +prices, and their offer of all of the parts to +[build an ErgoDox](https://www.massdrop.com/buy/ergodox). After +waiting for a group buy of the keyboard to become available, I put in +an order, and received the parts two months later. + +Over a few hours yesterday, I learned how to do surface mount +soldering of the 78 diodes (one for each key), and finished assembling +and flashing the firmware. This morning, I fixed up the few key +bindings that I needed to be productive, and viola, my laptop at home +now has a brand new ergonomic keyboard. + + +[[!tag tech debian keyboards]] diff --git a/posts/scale12x.mdwn b/posts/scale12x.mdwn new file mode 100644 index 0000000..2ce24cd --- /dev/null +++ b/posts/scale12x.mdwn @@ -0,0 +1,18 @@ +[[!meta title="Debian Booth at Scale 12x"]] + +I spent the weekend at +[SCALE 12x](http://www.socallinuxexpo.org/blog/scale-12x) running the +[Debian](http://www.debian.org) booth. SCALE is one of the best +conferences that I get to attend every year; it has a great mix of +commercial exhibitors and community groups, and routinely gets great +speakers. As I've done for quite some time, I organized a Debian booth +there, and talked to lots of people about Debian. + +[[!agimg "2014/02_February/scale_12x_debian_booth.jpg"]] + +If you're in the Southern California area, or have a chance to give a +talk for SCALE 13x, you should do so! Thanks again to Matt Kraai and +Paul Hardy for helping out in the Debian booth all weekend! + +[[!tag debian scale tech]] + diff --git a/posts/working_with_org.mdwn b/posts/working_with_org.mdwn index 9f5bbc0..c786300 100644 --- a/posts/working_with_org.mdwn +++ b/posts/working_with_org.mdwn @@ -20,8 +20,8 @@ ORG_GREP='-e .org$ -e .org_archive$ -e .org_done$' if [ "x$1" == "xdoit" ]; then if git status --porcelain -z | grep -z '^ M' | grep -zq $ORG_GREP; then - git status --porcelain -z | grep -z '^ M' | grep -z $ORG_GREP | \ - sed -z 's/^ M//g' | \ + git status --porcelain -z | grep -z '^ M' | grep -z $ORG_GREP | \ + sed -z 's/^ M//g' | \ xargs -0 git commit -m'update org files' git push; fi; diff --git a/projects.mdwn b/projects.mdwn index 14a48c9..9b4c952 100644 --- a/projects.mdwn +++ b/projects.mdwn @@ -1,69 +1,62 @@ -Projects -======== +[[!meta title="Projects"]] - These are some of the more recent publicly available projects that - I've been working on. Most of the code here is available under the - GPL, but check the licences in individual files or e-mail me if it is - unclear. Everything here is primarily used by me, and may not be - suitable for you. Feel free to e-mail me with any questions or - patches, though. As always, Caveat Lector. +Here are some of the many projects I'm working on or have previously +worked on. +[[!toc levels=2]] +Debian +====== -Reference System ----------------- +I use [Debian](http://www.debian.org) on all of my computers and +regularly contribute to it. You can see some of the work I'm doing in +Debian below. -Originally written in PHP, the reference system is being totally -rewritten in perl with mod_perl, postgresql and various other -routines. It was originally designed to track scholarly articles and -hold note and references related to them. However, the new version of -the system will be used to track everything from books to images to -newspapers to songs. Basically, it's a portable memory system that -happens to be web based and accessible from any where in the planet. +* [My Debian packages](http://qa.debian.org/developer.php?login=don) +* [Debbugs](http://wiki.debian.org/Teams/Debbugs) -- the bug tracking + system for Debian +* [Listmaster](http://wiki.debian.org/Teams/Listmaster) -- mailing + list maintainers for [lists.debian.org](http://lists.debian.org) +* [Technical Committee](http://www.debian.org/devel/ctte) -- Debian's + technical decision making board; responsible for resolving technical + disputes between developers - * [PHP CVS](http://rzlab.ucr.edu/cgi-bin/viewcvs.cgi/ref_php/?root=Ref+CVS) - * [New CVS](http://rzlab.ucr.edu/cgi-bin/viewcvs.cgi/ref/?root=Ref+CVS) -Utilities Modules ------------------ -The new reference system has lead me to redesign many of the modules -that I use alot. Most of them now can be plugged into and out of perl -programs at will, decreasing development time of mod_perl based web -projects. More importantly, it makes my code a lot more modular, and -keeps me from going insane tracking it all. - - * Class::Modular is a superclass that allows one to generate a single - class from modules spread throughout multiple files and overload - methods within that class at will. Da::DB inherits from - Class::Modular. [svn repository](http://rzlab.ucr.edu/cgi-bin/viewcvs.cgi/?root=Class+Modular) - * Da::DB is the main Database class. All (or almost all) database - interaction occurs through da_dbh objects or dynamically loaded sub - modules of Da::DB. (The new Template::Provider code is an example - of a loadable sub module.) [svn repository](http://rzlab.ucr.edu/cgi-bin/viewcvs.cgi/?root=Da+DB) +Debbugs +------- -Micro Array Utilities ---------------------- -These R functions and a few perl scripts are used to analyse Gene -Microarray data from affymetrix datafiles. +Debbugs is Debian's Bug Tracking System. I am currently the primary +maintainer of debbugs. You can see what I'm working on in +[my git repositories](http://git.donarmstrong.com/debbugs.git), what I +need to work on in +[Debbug's bug list](https://bugs.debian.org/debbugs), +[read more information](http://wiki.debian.org/Teams/Debbugs) about +contributing to Debbugs yourself, and see all of +[my posts](/tags/debbugs/) about Debbugs. - * [CVS](http://rzlab.ucr.edu/cgi-bin/viewcvs.cgi/ma_utilities/?root=RZ+Lab+CVS) - * [Download](http://rzlab.ucr.edu/cgi-bin/viewcvs.cgi/ma_utilities/ma_utilities.tar.gz?tarball=1&root=RZ+Lab+CVS) -LaTeX Math to PNG +Debian R Packages ----------------- -Converts LaTeX math formula to PNG files. ($$x^2_0+y^2_0=r^2_0$$) -becomes ![rendered equation](http://rzlab.ucr.edu/scripts/latexmath2png/latexmath2png.pl) - * [CVS](http://rzlab.ucr.edu/cgi-bin/viewcvs.cgi/latexmath2png/?root=RZ+Lab+CVS) - * [Source](http://rzlab.ucr.edu/cgi-bin/viewcvs.cgi/latexmath2png/latexmath2png.pl?rev=HEAD&root=RZ+Lab+CVS&content-type=text/vnd.viewcvs-markup) - * [Download](http://rzlab.ucr.edu/cgi-bin/viewcvs.cgi/latexmath2png/latexmath2png.tar.gz?tarball=1&root=RZ+Lab+CVS) +I maintain +[builds of the vast majority of R packages for Debian](/r/debian_r). +You can also see [my posts](/tags/debian-r) about the Debian-r archive. + +Bioinformatics +============== + +Below are some of the bioinformatics and biologically relevant tools I +have built. -Diary Script --------------------- +Postgresql Mirror of dbSNP +-------------------------- + +Being able to query [dbSNP](http://www.ncbi.nlm.nih.gov/SNP/) locally +is very useful for adding annotations to deep sequencing results and +other DNA polymorphism based analyses. See how to set up a +[postgresql mirror of dbsnp](/genetics/dbsnp_mirror/) yourself using +my scripts. - * [Source](diary/diary.html) - * [Download](diary/diary.gz) - Helical Wheel Plots ------------------- Plots alpha helical wheels with hydrophobic moment according to the @@ -74,8 +67,35 @@ wif scale (not woct). * [Download](http://rzlab.ucr.edu/cgi-bin/viewcvs.cgi/wheel/wheel.tar.gz?tarball=1&root=RZ+Lab+CVS) * [CVS](http://rzlab.ucr.edu/cgi-bin/viewcvs.cgi/wheel/?root=RZ+Lab+CVS) -Frog's Leap Website -------------------- -Various Scripts and HTML design for both the flash and html sections of the site using perl and javascript. -* [Link](http://www.frogsleap.com) +Ikiwiki Plugins +=============== + +My entire website is now built using [ikiwiki](http://ikiwiki.info). +Here are some ikiwiki plugins I have written: + +* [Sweavealike](http://git.donarmstrong.com/?p=ikiwiki_plugins.git;a=blob;f=sweavealike.pm;hb=HEAD) + is a plugin for [IkiWiki](http://ikiwiki.info) that tries to do some + of the useful things for IkiWiki that Sweave/Knitr does for R and + LaTeX. See [my blog post](/posts/introducingsweavealike) for more + information. + + +Perl Modules +============ + +* Class::Modular is a superclass that allows one to generate a single + class from modules spread throughout multiple files and overload + methods within that class at will. Da::DB inherits from + Class::Modular. + [svn repository](http://rzlab.ucr.edu/cgi-bin/viewcvs.cgi/?root=Class+Modular) + + +LaTeX Math to PNG +----------------- +Converts LaTeX math formula to PNG files. ($$x^2_0+y^2_0=r^2_0$$) +becomes ![rendered equation](http://rzlab.ucr.edu/scripts/latexmath2png/latexmath2png.pl) + + * [CVS](http://rzlab.ucr.edu/cgi-bin/viewcvs.cgi/latexmath2png/?root=RZ+Lab+CVS) + * [Source](http://rzlab.ucr.edu/cgi-bin/viewcvs.cgi/latexmath2png/latexmath2png.pl?rev=HEAD&root=RZ+Lab+CVS&content-type=text/vnd.viewcvs-markup) + * [Download](http://rzlab.ucr.edu/cgi-bin/viewcvs.cgi/latexmath2png/latexmath2png.tar.gz?tarball=1&root=RZ+Lab+CVS) diff --git a/resume.mdwn b/resume.mdwn index 3f239c5..14d54df 100644 --- a/resume.mdwn +++ b/resume.mdwn @@ -1,55 +1,50 @@ -Resume -====== +[[!meta title="Curriculum Vitæ, Research Statement, and Teaching Statement"]] -[Don Armstrong](http://www.donarmstrong.com/) +Introduction +------------ +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. + +For my contact information or additional references, please e-mail - - -[Phone contact information available via e-mail.] - -I am a practitioner of the art of solving problems as elegantly and -practically as possible. I seek to enhance my abilities to solve -problems in the digital realm by learning (and inventing where -appropriate) new methods and techniques, and to help others achieve -their goals by removing or smoothing over ponderous obstacles in their -path. If you have difficult problems for which a digital approach -seems appropriate, I'm the person to talk to to find a solution. - -Education ----------- -* Doctor of Philosophy in Cell, Molecular and Developmental Biology from [UC Riverside](http://www.ucr.edu), 2008 -* Bachelor of Science in [Biology](http://bio.ucr.edu) from [UC Riverside](http://www.ucr.edu), 2001 -* Graduate, Scholar with Distinction from [Marina High School](http://www.hbuhsd.k12.ca.us/mhs/), 1997 - -Experience ----------- -* July 2002-July 2003: Researcher for Socratech, LLC - * Affymetrix Gene Microarray Analysis using R, and Perl. - * Custom designed cell, tissue and data tracking system in perl - * Analysis of MA results using Gene Ontology - * Literature minining using custom designed Perl scripts to search pubmed. -* Jun. 2000-Jun 2001: Computer Resource Coordinator for [UC Riverside](http://www.ucr.edu) - * Network administration/design of a 2000+ node network - * developed web based registration system using bash, dhcp, perl, php and mysql - * Developed network monitoring system - ([rnm](http://rnm.sourceforge.net)) using php, mysql, perl, and - snmp. - * Supervised a staff of 13 RCCs
  • Administration of 7+ Unix Servers (Apache,ISC DHCP, MySQL, mod_perl, slash) -
  • Computer Lab Administration (NT) -
  • Developed a printer recharge/tracking system using card readers, perl, mysql, and lpr-ng -
  • Developed a customer-tech Help Request System/Billing System using php, mysql, smtp, and perl - -Skills ------- - - -Projects --------- -[Current projects|projects] - -References ----------- -Available Upon Request. +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) + diff --git a/resume/curriculum_vitae.mdwn b/resume/curriculum_vitae.mdwn new file mode 100644 index 0000000..80211df --- /dev/null +++ b/resume/curriculum_vitae.mdwn @@ -0,0 +1,154 @@ +[[!meta title="Curriculum Vitæ"]] +Curriculum Vitæ +=============== + +* [Don Armstrong](http://www.donarmstrong.com/) +* +* + +Education +---------- +* Doctor of Philosophy + * 2001-2008 **Cell, Molecular and Developmental Biology**. + [University of California at Riverside](http://www.ucr.edu). + Dissertation: The Role of membrane Composition in the Activity of + Membrane-Associated Signal Transduction Proteins. +* Bachelor of Science + * 1997-2001 [Biology](http://bio.ucr.edu). + [University of California at Riverside](http://www.ucr.edu). + +Postdoctoral Experience +------------------------- + +### University of Southern California ### + +* 2013--Present. Postdoctoral researcher under Chaim O. Jacob. + Identifying genes and causal alleles associated with Systemic Lupus + Erythematosus using genome-wide association, next-generation + sequencing, computational and biochemical approaches. +* 2009--2010. Postdoctoral researcher under Florence M. Hofman. + Identifying signaling pathways which are responsible for the + functional alteration of endothelial cells in glioblastoma + multiforme and arteriovenous malformations. + +### University of California at Riverside ### +* 2010--2012. Postdoctoral researcher under Raphael Zidovetzki. + Identifying genes which are associated with Systemic Lupus + Erythematosus using prior information and targeted trio-based + studies. + +Teaching +-------- +### Teaching Assistant ### +* 2004--2007. University of California at Riverside. First and second + quarter introduction to biology for majors (BIO 5A and 5B). + Introduction to Genetics (BIO 102), Human Embryology (CBNS 169). + +Work in Industry +---------------- +### Non-Profit ### +* 2004--Present. [Debian Project](http://www.debian.org), Developer; + Technical Committee Member (2010--Present) + +### Employment Experience ### +* 2002-2003. **Socratech** in Rochester, NY. Bioinformatics researcher: + developed new microarray analysis methods for a start-up + biotechnology company working on developing treatments for + Alzheimer's disease + +Publications +------------ +## Refereed Publications ## +1. **Don L. Armstrong**, Raphael Zidovetzki, and Chaim O Jacob. Novel + lupus associated genes discovered in GWAS; two signals explain all + HLA SNPs in European Americans. *Genes Immun*, In press. + +2. Chaim O Jacob, Miriam Eisenstein, Mary C Dinauer, Wenyu Ming, + Qiang Liu, Sutha John, Francesco P Quismorio, Andreas Reiff, Barry + L Myones, Kenneth M Kaufman, Deborah McCurdy, John B Harley, Earl + Silverman, Robert P Kimberly, Timothy J Vyse, Patrick M Gaffney, + Kathy L Moser, Marisa Klein-Gitelman, Linda Wagner-Weiner, Carl D + Langefeld, **Don L Armstrong**, and Raphael Zidovetzki. + Lupus-associated causal mutation in neutrophil cytosolic factor 2 + (NCF2) brings unique insights to the structure and function of + NADPH oxidase. *Proc Natl Acad Sci USA*, 109(2):59--67, Jan 2012. +3. **Don L Armstrong**, Omer Markovitch, Raphael Zidovetzki, and Doron + Lancet. Replication of simulated prebiotic amphiphile vesicles + controlled by experimental lipid physicochemical properties. *Phys + Biol*, 8(6):066001, Dec 2011. + +4. Christopher J Stapleton, **Don L Armstrong**, Raphael Zidovetzki, + Charles Y Liu, Steven L Giannotta, and Florence M Hofman. + Thrombospondin-1 modulates the angiogenic phenotype of human + cerebral arteriovenous malformation endothelial cells. + *Neurosurgery*, 68(5):1342--53, May 2011. + +5. **D L Armstrong**, A Reiff, B L Myones, F P Quismorio, M + Klein-Gitelman, D McCurdy, L Wagner-Weiner, E Silverman, J O + Ojwang, K M Kaufman, J A Kelly, J T Merrill, J B Harley, S-C Bae, T + J Vyse, G S Gilkeson, P M Gaffney, K L Moser, C Putterman, J C + Edberg, E E Brown, J Ziegler, C D Langefeld, R Zidovetzki, and C O + Jacob. Identification of new SLE-associated genes with a two-step + Bayesian study design. *Genes Immun*, 10(5):446--56, Jul 2009. + +6. Chaim O Jacob, Jiankun Zhu, **Don L Armstrong**, *et al.* + Identification of IRAK1 as a risk gene with critical role in the + pathogenesis of systemic lupus erythematosus. *Proc Natl Acad Sci + USA*, 106(15):6256--61, Apr 2009. + +7. Bahram Namjou, Andrea L Sestak, **Don L Armstrong**, Raphael + Zidovetzki, *et al.* High-density genotyping of STAT4 reveals + multiple haplotypic associations with systemic lupus erythematosus + in different racial groups. *Arthritis Rheum*, 60(4):1085--95, Apr 2009. + +8. **Don Armstrong** and Raphael Zidovetzki. Amplification of + diacylglycerol activation of protein kinase c by cholesterol. + *Biophys J*, 94(12):4700--10, Jun 2008. + +9. **Don L Armstrong**, Chaim O Jacob, and Raphael Zidovetzki. + Function2gene: a gene selection tool to increase the power of + genetic association studies by utilizing public databases and + expert knowledge. **BMC Bioinformatics**, 9:311, 2008. + +10. Chaim O Jacob, Andreas Reiff, **Don L Armstrong**, Barry L Myones, + Earl Silverman, Marisa Klein-Gitelman, Deborah McCurdy, Linda + Wagner-Weiner, James J Nocton, Aaron Solomon, and Raphael + Zidovetzki. Identification of novel susceptibility genes in + childhood-onset systemic lupus erythematosus using a uniquely + designed candidate gene pathway platform. *Arthritis Rheum*, + 56(12):4164--73, Dec 2007. + +11. Raphael Zidovetzki, Burkhard Rost, *Don L Armstrong*, and Israel + Pecht. Transmembrane domains in the functions of fc receptors. + *Biophys Chem*, 100(1-3):555--75, 2003. + +12. **Don L Armstrong**, Dan B Borchardt, and Raphael Zidovetzki. + Synergistic perturbation of phosphatidylcholine/sphingomyelin + bilayers by diacylglycerol and cholesterol. *Biochem Biophys Res + Commun*, 296(4):806--12, Aug 2002. + +13. Zhenhua Wu, Huang Guo, Nienwen Chow, Jan Sallstrom, Robert D Bell, Rashid + Deane, Andrew I Brooks, Suhasini Kanagala, Anna Rubio, Abhay Sagare, Dong + Liu, Fang Li, **Don Armstrong**, Thomas Gasiewicz, Raphael Zidovetzki, Xiaomei + Song, Florence Hofman, and Berislav V Zlokovic. Role of the meox2 homeobox gene in neurovascular dysfunction in + alzheimer disease. *Nat Med*, 11(9):959--65, Sep 2005. + +14. Rashid Deane, Shi Du Yan, Ram Kumar Submamaryan, Barbara LaRue, + Suzana Jovanovic, Elizabeth Hogg, Deborah Welch, Lawrence Manness, + Chang Lin, Jin Yu, Hong Zhu, Jorge Ghiso, Blas Frangione, Alan + Stern, Ann Marie Schmidt, **Don L Armstrong**, Bernd Arnold, + Birgit Liliensiek, Peter Nawroth, Florence Hofman, Mark Kindy, + David Stern, and Berislav Zlokovic. Rage mediates amyloid-beta peptide transport across the blood-brain + barrier and accumulation in brain. *Nat Med*, 9(7):907--13, Jul 2003. + +Selected Presentations +---------------------- +### Conference Presentations ### +* 2007-06-07. FOCIS 2007. Uniquely designed candidate gene + identification platform discovers novel genes in childhood-onset + SLE. + +References +---------- +Please e-mail for references + diff --git a/resume/dla-cv.pdf b/resume/dla-cv.pdf new file mode 100644 index 0000000..0b9fde9 Binary files /dev/null and b/resume/dla-cv.pdf differ diff --git a/resume/research_statement.mdwn b/resume/research_statement.mdwn new file mode 100644 index 0000000..a2c382a --- /dev/null +++ b/resume/research_statement.mdwn @@ -0,0 +1,244 @@ + + +# Research Objectives + +## Uncovering genetic causes of diseases using a multidisciplinary bioinformatics-driven approach + + + +My research focuses on designing and using bioinformatics techniques +to identify causes and mechanisms underlying human diseases such as +Systemic Lupus Erythematosus, Glioblastoma Multiforme, and +Arteriovenous Malformations followed be designing appropriate +diagnostics and treatment methods. Once identified, I work with +collaborators to verify the bioinformatics-discovered mechanisms +utilizing *in silico*, *in vitro*, and *in vivo* techniques, and +develop therapeutic and diagnostic techniques to identify and treat +the underlying human disorder. Cell-culture-based methods are utilized +as the first step in designing multi-target treatments, followed by +appropriate animal models.. + +# Unique Qualifications + +## Straddling Biology, Computer Science, and Statistics + +In addition to being a cellular and molecular biologist, I have +extensive experience in algorithm design, computer programming, and +statistics. The combination of these areas enables me to handle +biological problems which involve large numbers of samples and data +and require statistical analysis which can address confounders which +are often present in non-laboratory settings. It also gives me a +unique perspective which enables me to design novel methods to analyze +and interpret large amounts of data. + +## Multidisciplinary approach + +I have published in multiple disciplines, including membrane +biophysics, bioinformatics, genetics, and cellular biology. My +experiences in these fields and my experiences while transitioning +fields has allowed me to apply unique insights garnered from my +previous work to new topics leading to novel approaches and +breakthrough discoveries. + +# Previous Research Projects + + + +## Genetic Basis of System Lupus Erythematosus (SLE) + +I developed novel bioinformatic methods which increase + + +likelihood of identifying reproducible genetic associations using +prior knowledge from publicly available databases and expert +information [^Armstrong2008:function2gene]. Using these methods, I was +able to identify genes previously unassociated with SLE in a +trio-based study [^Jacob2007:ar_lupus]. These genes were then +replicated in a larger case-control study which was funded by the NIH +on the basis of the original findings [^Jacob2009:sle_irak1],[^Armstrong2009:sle_gi]. +Among other findings, this larger study +identified a missense allele in NCF2 (H389Q, rs17849502) which was +associated with SLE. Collaborative work indicated that H389Q altered +the binding energy of NCF2 with VAV1 using docking simulations, and in +vitro experiments confirmed that H389Q altered NADPH oxidase function +[^Jacob2012:sle_ncf2], thus identifying it as a causative SLE +mutation. + +## Cancer Stem Cells in Glioblastoma + +Glioblastoma is a almost invariably fatal form of brain cancer[^survival_rate] which is +diagnosed in \(\approx\) 9,000 people in the US annually. It is typified +by high levels of chemotherapeutic-resistant recurrences, some of +which is likely caused by cancer stem cells which are insensitive to +many chemotherapeutic agents. In collaboration with Florence Hoffman +at USC, I have classified glioblastoma-derived cancer stem cells and +cancer cell lines into distinct classes using gene microarrays and +various clustering approaches, which will enable the design of a +class-specific treatment of this devastating disease. + +## Regulatory pathways underlying cranial arteriovenous malformations + +The mechanisms underlying the formation of arteriovenous +malformations[^avm_definition] (AVMs) which occur in the brain are +unknown. Using gene microarrays, qtPCR, and *in vitro* experiments on +primary human endothelial cells cultured from resected AVMs, I +indentified multiple gene regulation pathways, many of them novel, +including the Id1/Thsb1 inhibitory pathway. Additional experiments +indicated that the *in vitro* pathology of endothelial cells could be +partially rescued using extracellular Thsb1 +[^Stapleton2011:thbs1]. + +# Future research directions + +## Identification of causal mutations in SLE + +While many regions and SNPs which are associated with SLE have been +identified, few of those regions have identified causal alleles with +known function. Furthermore, even for regions with identified causal +alleles, no systematic searches have been performed to identify +additional causal regions. Continuing my existing collaboration with +Chaim O. Jacob, I will rectify this by + +1. Deep sequencing the associated regions in 500 lupus cases and 1000 controls + +2. Identifying which newly found variants are associated with SLE + +3. Selecting variants with a high likelihood of producing functional variants + +4. Verifying biological relevance of variants by *in vitro* study + +5. Verifying functional relevance in human subjects + +## Developing analysis tools for massive amounts of sequencing data + +The ability to cheaply and rapidly sequence large numbers of samples +has massively increased the amount of data processing required by +researchers. Compounding this increase in data, most existing tools +have not been designed to take full advantage of the current advances +in computer architecture, which parallel solutions to problems which +can be run on architectures with vastly differing computational +abilities (such as GPUs). + +To resolve this, I am in the process of actively developing new open +source tools[^extending_note] which are capable of running on +massively parallel architectures using both multiple computers +(openMPI) and multiple GPUs on the same computer (Nvidia's CUDA) to + +1. Develop an open source massively parallel imputation method which + can combine existing GWAS results with new deep sequencing + and genetic profiling results. + +2. Extend same tools to call SNPs both incrementally and in parallel. + +I am currently working on extending samtools (an Open Source SNP +calling suite) to support running on multiple computers. + +## Gut microbiota alteration in SLE + +Many autoimmune disorders are known to be affected by gut microbiota. +Preliminary evidence suggests that mice which develop SLE have +differences in gut microbiota from mice which do not develop SLE, +which suggests that SLE severity may also be affected by differences +in human gut microbiota. I am currently developing novel methods to + +1. Determine which gut microbiota differ between mice with and + without SLE and using 16S sequencing + +2. Determine which gut microbiota differ between humans with and + without SLE using 16S sequencing, given #1. + +## Continuous, incremental analysis + +Just as science requires continuous testing of hypotheses, +bioinformatics is slowly moving towards continuous incremental +analysis of data. Most current tools use iterative analysis, where +analyses must be completely re-run with each new piece of data that is +obtained. When the amount of data remains small relative to the +overall computing power available, this is a feasible approach. +However, as the amount of data increases, it stops being feasible to +completely reanalyze data as new data is obtained, and incremental +analysis approaches are necessary. I will be working to extend +existing analysis pipelines to handle the incremental analysis of +data. + +# Research Funding + +## Funding Opportunities + +I anticipate obtaining funding from the following sources to pursue +the research goals outlined previously: + +1. National Institute of Health + + 1. [Research Project Grant (RO1)](http://grants.nih.gov/grants/guide/pa-files/PA-13-302.html) (NHGRI, NIAID, BISTI) + + 2. [NLM Career Development Award in Biomedical Informatics (K01)](http://grants.nih.gov/grants/guide/pa-files/PAR-13-284.html) + + 3. [Continued Development and Maintenance of Software (R01)](http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html) (extending existing biofinformatics software) + +2. Alliance for Lupus Research + + 1. [Target Identification in Lupus](http://www.lupusresearch.org/news-and-events/press-releases/til.html) + +3. Institution specific funding + +## Track Record of Funding + +The projects that I am proposing have a strong track record of being +funded by both the NIH and the Alliance for Lupus Research. + +# Wider impact of research agenda + + +My research will identify genetic variants and pathways underlying SLE +and other important human diseases, leading to better methodologies +for both the diagnosis and treatment of those diseases, and resulting +in significant decreases is patient morbidity and mortality. +Secondarily, the tools that I develop to effect this work will enable +researchers in other fields to more rapidly and cheaply identify +relevant factors for economically and environmentally important +phenotypes, such as pathogen-resistance in crops or +disease-susceptibility in thylocenes. Furthermore, as all of my tools +will be released under Open Source licenses, external researchers will +be able to build upon and improve my tools without being forced to +reinvent them. + + +[^Armstrong2009:sle_gi]: D L Armstrong et al. “Identification of new SLE-associated genes with a two-step + Bayesian study design”. In: Genes Immun. 10.5 (July 2009), pp. 446–456. doi: + [10.1038/gene.2009.38](http://dx.doi.org/10.1038/gene.2009.38). + +[^Armstrong2008:function2gene]: Don L Armstrong, Chaim O Jacob, and Raphael Zidovetzki. “Function2Gene: a + gene selection tool to increase the power of genetic association studies by utilizing + public databases and expert knowledge”. In: BMC Bioinformatics 9 (2008), p. 311. + doi: [10.1186/1471-2105-9-311](http://dx.doi.org/10.1186/1471-2105-9-311). + +[^Jacob2009:sle_irak1]: Chaim O Jacob et al. “Identification of IRAK1 as a risk gene with critical role + in the pathogenesis of systemic lupus erythematosus”. In: Proc. Natl. Acad. Sci. + U.S.A. 106.15 (Apr. 2009), pp. 6256–6261. doi: [10.1073/pnas.0901181106](http://dx.doi.org/10.1073/pnas.0901181106). + +[^Jacob2007:ar_lupus]: Chaim O Jacob et al. “Identification of novel susceptibility genes in childhood- + onset systemic lupus erythematosus using a uniquely designed candidate gene + pathway platform”. In: Arthritis Rheum. 56.12 (Dec. 2007), pp. 4164–4173. doi: + [10.1002/art.23060](http://dx.doi.org/10.1002/art.23060). + +[^Jacob2012:sle_ncf2]: Chaim O Jacob et al. “Lupus-associated causal mutation in neutrophil cytosolic + factor 2 (NCF2) brings unique insights to the structure and function of NADPH + oxidase”. In: Proc. Natl. Acad. Sci. U.S.A. 109.2 (Jan. 2012), pp. 59–67. doi: + [10.1073/pnas.1113251108](http://dx.doi.org/10.1073/pnas.1113251108). + +[^Stapleton2011:thbs1]: Christopher J Stapleton et al. + “Thrombospondin-1 modulates the angiogenic phe- notype of human + cerebral arteriovenous malformation endothelial cells”. In: + Neurosurgery 68.5 (May 2011), pp. 1342–1353. + doi: [10.1227/NEU.0b013e31820c0a68](http://dx.doi.org/10.1227/NEU.0b013e31820c0a68). + +[^survival_rate]: Only 4% of patients survive to 5 years after diagnosis + +[^avm_definition]: Direct artery to vein connection without an + intervening capilary bed; leads to high pressure arterial flow in + venous tissue and can lead to hemmorrhage and death. + +[^extending_note]: and extending existing open source tools where they + exist + diff --git a/resume/research_statement.pdf b/resume/research_statement.pdf new file mode 100644 index 0000000..862d9bd Binary files /dev/null and b/resume/research_statement.pdf differ diff --git a/resume/teaching_statement.mdwn b/resume/teaching_statement.mdwn new file mode 100644 index 0000000..36c2cd2 --- /dev/null +++ b/resume/teaching_statement.mdwn @@ -0,0 +1,135 @@ +[[!meta title="Teaching Statement"]] + +# Why I teach + +I have always wanted to know how everything works, interconnects, and +evolved. That moment when a flash of insight shines a light on the +underlying structure of nature is an incredible feeling. Like many +researchers in science, I willingly subject myself to experimental +failures, difficult-to-interpret results, funding difficulties, and +long hours in order to receive that momentary feeling. + +I teach because I want to share the excitement of discovery and +knowing, and I want others to be able to experience that excitement +for themselves. It is also quite rewarding to see the glimmer of +insight in my students eyes when they finally reach understanding for +themselves. + +# General Goals for Students + +## Desire and Excitement + +If my students are *only* interested in learning the material I am +teaching to earn credit, then I have failed as a teacher. I want to +covey at least some of my excitement in the subject to them. +Perhaps it's naïve, but I think that once students are excited about +the material, they are more likely to succeed. + +## Informed Skepticism + +While only a small percentage of my students will become scientists, I +want them all to know how science works, how to analyze claims, weigh +evidence, do background research, and come to an independent +understanding of nature. From politics to the latest false claim on +the Internet, an ability to become informed, think critically, and +analyze skeptically will help my students be conscientious members of +our democratic society. + +# How I Teach + +## Task Analysis + + +For each course, I identify course-specific overall goals that I want +all of my students to achieve. Then, I plan a path to these goals, +with a hierarchy of sub-goals along the way. This enables me to +measure the effectiveness of my teaching and the students' progress at +each step during the course. For example, in an introductory +bioinformatics course, an overall goal might be to have students be +able to use common bioinformatic databases to answer biological +questions. A corresponding sub goal would be for students to be able +to use dbSNP to select all genetic variants in a specific gene in a +specific organism. + +## Learn By Doing + +Even though lecturing, demonstrations, and similar passive learning +techniques are important, everyone learns best by doing. Mistakes, +failure, experimentation, and learning from them are important parts +of learning by doing, just as they are in science. To the greatest +extent possible, I want to provide opportunities for students to learn +by doing. I want students to learn by solving problems using the +knowledge and resources they have gained in the course. + +## Individual Engagement + +In large courses it is very difficult to keep individual students +engaged, as they feel they are just one face in a hundred and have +limited opportunities to ask questions. When lecturing, I like to +combat this by asking students questions directly, and getting +students (even those at the back) to participate in demonstrations. I +will also be accessible both in-person on campus, and via e-mail. +Finally, I will encourage my teaching assistants (TAs) to be engaged +with our students by asking TAs about students in their sections in TA +meetings. + +## Students Teaching Others + + +Having every student engaged with a teacher is a laudable goal, and +may be achievable in small in large ones, there will always +be some people who are not reached. Students teaching other students +is one method of extending a teacher's reach. In the past, I have had +online forums or mailing lists for all courses that I have taught. In +these forums, students are able to ask questions, and other students +are able to answer them. In addition, students are able to reinforce +their learning by answering other student's questions. You know a +concept when you can teach others. + +## Technology + +Classroom technology is very useful in increasing the ability of +students to learn, experiment, and measuring outcomes in the +classroom. I plan on using: + +1. Interactive websites to enable student's active learning by doing, + including exercises, experiments, and other activities. + +2. Real-time online feedback using automated grading on a website to + the extent possible on homework so students know whether they + understand the material. + +3. In-lecture questions through clickers or smart phones when the + course is too large to gauge student understanding of material by + asking questions of students or raising hands. + +4. Recording lectures so that students (and I) can refer to them + later. + +5. Forums, mailing lists, and other communication methods so that + students can learn cooperatively. When students explain material to + other students, it answers other student's questions and reinforces + their own knowledge. + +6. Demonstrations in class and online, both real and simulated, when + appropriate to the material being taught. + +# Measuring Outcomes + +## Success and Failure + +I'm continuing to study how to be a more effective teacher by learning +from other teachers and research into teaching techniques, and will +continue to do that as long as I teach. I will measure the outcomes of +my teaching in order to determine how effective I am. By correlating +the teaching methods I use for each sub-goal of my course with student +outcomes, over time I can identify the most effective teaching +strategies for me. + +# Teaching Experiences + +## Teaching Assistant + +While a graduate student at UC Riverside, I was a teaching assistant +for +[Introductory Biology, Introductory Genetics, Molecular Biology, and Developmental Biology.](http://www.biology.ucr.edu/courses/UGcourses.html) diff --git a/resume/teaching_statement.pdf b/resume/teaching_statement.pdf new file mode 100644 index 0000000..7a90fd9 Binary files /dev/null and b/resume/teaching_statement.pdf differ diff --git a/sidebar.mdwn b/sidebar.mdwn index a7b9fd7..2ce6a34 100644 --- a/sidebar.mdwn +++ b/sidebar.mdwn @@ -1,9 +1,3 @@ -[[!if test="enabled(calendar)" then=""" -[[!calendar pages="./posts/* and !*/Discussion"]] -"""]] - - - [[Genetics]] [[Projects]] @@ -14,5 +8,10 @@ [[Archives]] +[[!if test="enabled(calendar)" then=""" +[[!calendar pages="./posts/* and !*/Discussion"]] +"""]] + + [[Tags]]: [[!pagestats style="list" pages="./tags/*" among="./posts/*"]] diff --git a/tags/keyboards.mdwn b/tags/keyboards.mdwn new file mode 100644 index 0000000..68abcb4 --- /dev/null +++ b/tags/keyboards.mdwn @@ -0,0 +1,4 @@ +[[!meta title="pages tagged keyboards"]] + +[[!inline pages="tagged(keyboards)" actions="no" archive="yes" +feedshow=10]] diff --git a/tags/scale.mdwn b/tags/scale.mdwn new file mode 100644 index 0000000..eb57812 --- /dev/null +++ b/tags/scale.mdwn @@ -0,0 +1,4 @@ +[[!meta title="pages tagged scale"]] + +[[!inline pages="tagged(scale)" actions="no" archive="yes" +feedshow=10]] diff --git a/templates/page.tmpl b/templates/page.tmpl new file mode 100644 index 0000000..d042d13 --- /dev/null +++ b/templates/page.tmpl @@ -0,0 +1,226 @@ + + + + + + + + + + + + +<TMPL_VAR TITLE> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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