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[blog.git] / posts / sawsim.mdwn

diff --git a/posts/sawsim.mdwn b/posts/sawsim.mdwn
index 969bdfce9887e81debd5b01fc5a97cf836a8947b..524a1e943cb0b0633588ca41645a0c63673005e3 100644 (file)
--- a/posts/sawsim.mdwn
+++ b/posts/sawsim.mdwn
@@ -4,7 +4,7 @@ Introduction
 ============
 
 My [[thesis]] project investigates protein unfolding via the
-experimental technique of [force spectroscopy][fs].  In force
+experimental technique of [[force spectroscopy]].  In force
 spectroscopy, we mechanically stretch chains of proteins, usually by
 pulling one end of the chain away from a surface with an [AFM][].
 
@@ -27,29 +27,38 @@ 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
+The main benefits of sawsim are its ability to simulate systems with
+arbitrary numbers of states (see the [[manual|sawsim.pdf]]) and to
+easily compare the simulated data with experimental values.  The
+following figure shows a long valley of reasonable fits to some
+ubiquitin unfolding data.  See the IJBM paper (linked above) for more
+details.
+
+[[!img fit-space.png alt="Fit space Surface bump for photodiode sensitivity"
+  title="Surface bump for photodiode sensitivity" ]]
 
 
 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][contact] if you have access to such a machine and
-want to try installing Sawsim).
+I've tested it on Gentoo and Debian, and I've got an ebuild in my
+[[Gentoo overlay]].  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|contact]] if you have access to such a machine
+and want to try installing Sawsim).
 
-See the [[README]] and [[manual|sawsim.pdf]] for more details.
-
-[contact]: http://www.physics.drexel.edu/~wking/contact.shtml
+See the [[README]], [[manual|sawsim.pdf]], and [PyPI page][pypi] for
+more details.
 
+[AFM]: http://en.wikipedia.org/wiki/Atomic_force_microscopy
+[published]: http://dx.doi.org/10.1016/j.ijbiomac.2009.12.001
+[pypi]: http://pypi.python.org/pypi/pysawsim/
 
 [[!tag tags/C]]
 [[!tag tags/papers]]
 [[!tag tags/programming]]
+[[!tag tags/pypi]]
 [[!tag tags/python]]
 [[!tag tags/sawsim]]
 [[!tag tags/theory]]