From 79142d89ac1f4130365eecbe5785efc119c517db Mon Sep 17 00:00:00 2001 From: Don Armstrong Date: Sun, 16 Feb 2014 14:09:04 -0800 Subject: [PATCH] totally revamp projects section --- projects.mdwn | 123 +++++++++++++++++++++++++++----------------------- 1 file changed, 66 insertions(+), 57 deletions(-) diff --git a/projects.mdwn b/projects.mdwn index eac3480..13be045 100644 --- a/projects.mdwn +++ b/projects.mdwn @@ -2,67 +2,61 @@ 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. - -Reference System ----------------- - -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. - - * [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. +Here are some of the many projects I'm working on or have previously +worked on. - * 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) +Debian +====== -Micro Array Utilities ---------------------- -These R functions and a few perl scripts are used to analyse Gene -Microarray data from affymetrix datafiles. +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. - * [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) +* [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 -LaTeX Math to PNG + +Debbugs +------- + +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. + + +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. + +Postgresql Mirror of dbSNP +-------------------------- -Diary Script --------------------- +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 @@ -73,8 +67,23 @@ 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) + +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) -- 2.39.2