From 3e7144e04c61b3de47e7c342a035f0f441b545f5 Mon Sep 17 00:00:00 2001
From: "W. Trevor King" <wking@drexel.edu>
Date: Sat, 23 Oct 2010 14:03:10 -0400
Subject: [PATCH] Add sawsim post.

---
 Makefile              |  4 ++--
 ikiwiki.setup         |  2 +-
 posts/sawsim.mdwn     | 50 +++++++++++++++++++++++++++++++++++++++++++
 posts/sawsim/Makefile | 26 ++++++++++++++++++++++
 tags/papers.mdwn      |  3 +++
 5 files changed, 82 insertions(+), 3 deletions(-)
 create mode 100644 posts/sawsim.mdwn
 create mode 100644 posts/sawsim/Makefile
 create mode 100644 tags/papers.mdwn

diff --git a/Makefile b/Makefile
index 8068493..69e4efa 100644
--- a/Makefile
+++ b/Makefile
@@ -1,7 +1,7 @@
 # Build everything necessary to compile the wiki.
 
-SUBDIRS = posts/problempack posts/rel-vcs posts/yacc2dot posts/Xmodmap \
-	posts/XSLT/chapter posts/XSLT/code
+SUBDIRS = posts/problempack posts/rel-vcs posts/sawsim posts/yacc2dot \
+	posts/Xmodmap posts/XSLT/chapter posts/XSLT/code
 TARGETS = all clean
 
 all :
diff --git a/ikiwiki.setup b/ikiwiki.setup
index 8f9dcb3..96e805f 100644
--- a/ikiwiki.setup
+++ b/ikiwiki.setup
@@ -29,7 +29,7 @@ use IkiWiki::Setup::Standard {
 	# rcs backend to use
 	rcs => 'git',
 	# plugins to add to the default configuration
-	add_plugins => [qw{goodstuff linktoimgonly lockedit mdwn_itex org sidebar rawhtml}],
+	add_plugins => [qw{goodstuff linktoimgonly lockedit mdwn_itex org sidebar rawhtml rst}],
 	# plugins to disable
 	disable_plugins => [qw{editpage passwordauth smiley}],
 	# location of template files
diff --git a/posts/sawsim.mdwn b/posts/sawsim.mdwn
new file mode 100644
index 0000000..cc06c9a
--- /dev/null
+++ b/posts/sawsim.mdwn
@@ -0,0 +1,50 @@
+[[!template id=gitrepo repo=sawsim]]
+
+Introduction
+============
+
+My [[thesis]] project investigates protein unfolding via the
+experimental technique of [force spectroscopy][fs].  In force
+spectroscopy, we mechanically stretch chains of proteins, usually by
+pulling one end of the chain away from a surface with an [AFM][].
+
+For velocity clamp experiments (the simplest to carry out
+experimentally), the experiments produce "sawtooth" force-displacement
+curves.  As the protein stretches, the tension increases.  At some
+point, a protein domain unfolds, increasing the total length of the
+chain and relaxing the tension.  As we continue to stretch the
+protein, we see a series of unfolding peaks.  The [[GPLed|GPL]]
+program [[Hooke]] analyzes the sawtooth curves and extracts lists of
+unfolding forces.
+
+Lists of unfolding forces are not particularly interesting by
+themselves.  The most common approach for extracting some physical
+insights from the unfolding curves is to take a guess at an
+explanatory model and check the predicted behavior of the model
+against the measured behavior of the protein.  If the model does a
+good job of explaining the protein behavior, it might be what's
+actually going on behind the scenes.  Sawsim is my ([published][]!)
+tool for simulating force spectroscopy experiments and matching the
+simulations to experimental results.
+
+[fs]: http://en.wikipedia.org/wiki/Force_spectroscopy
+[AFM]: http://en.wikipedia.org/wiki/Atomic_force_microscopy
+[published]: http://dx.doi.org/10.1016/j.ijbiomac.2009.12.001
+
+
+Getting started
+===============
+
+Sawsim should run anywhere you have a C compiler and Python 2.5+.
+I've tested it on Gentoo and Debian, and I'll write up a Gentoo ebuild
+soon.  It should also run fine on Windows, etc., but I don't have
+access to any Windows boxes with a C compiler, so I haven't tested
+that ([email me][/~wking/contact.shtml] if you have access to such
+a machine and want to try installing Sawsim).
+
+See the [[README]] for more details.
+
+[[!tag tags/papers]]
+[[!tag tags/programming]]
+[[!tag tags/sawsim]]
+[[!tag tags/theory]]
diff --git a/posts/sawsim/Makefile b/posts/sawsim/Makefile
new file mode 100644
index 0000000..b9842f7
--- /dev/null
+++ b/posts/sawsim/Makefile
@@ -0,0 +1,26 @@
+REPO = http://www.physics.drexel.edu/~wking/code/git/sawsim.git/
+PACKAGE = sawsim
+
+.PHONY : all checkout clean
+
+all : README.rst sawsim.pdf
+
+clean :
+	rm -rf $(PACKAGE) README.rst sawsim.pdf
+
+$(PACKAGE) :
+	git clone $(REPO) $@
+
+checkout : $(PACKAGE)
+	git --git-dir $(<:%=%/.git) --work-tree ../ pull
+
+README.rst : checkout
+	cp $(PACKAGE:%=%/README) $@
+
+$(PACKAGE:%=%/Makefile) : checkout
+	notangle -Rmakefile $(PACKAGE:%=%/src/sawsim.nw) \
+	  | sed 's/        /\t/' > $@
+
+sawsim.pdf : $(PACKAGE:%=%/Makefile)
+	$(MAKE) -C $(PACKAGE) doc/$@
+	cp $(PACKAGE:%=%/doc/$@) $@
diff --git a/tags/papers.mdwn b/tags/papers.mdwn
new file mode 100644
index 0000000..9243eaf
--- /dev/null
+++ b/tags/papers.mdwn
@@ -0,0 +1,3 @@
+My publications.
+
+[[!inline pages="link(tags/papers)" show=10 actions=yes]]
-- 
2.26.2