From: W. Trevor King <wking@tremily.us>
Date: Sun, 24 Jun 2012 06:52:26 +0000 (-0400)
Subject: Add abstract text.
X-Git-Tag: v1.0~334
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=6153eb89c9f803f21c631aa8af26c3e28697f16b;p=thesis.git

Add abstract text.
---

diff --git a/src/blurb/abstract.tex b/src/blurb/abstract.tex
index 97af138..f926fd9 100644
--- a/src/blurb/abstract.tex
+++ b/src/blurb/abstract.tex
@@ -1,2 +1,29 @@
 \begin{abstract}
+Single molecule force spectroscopy (SMFS) experiments provide an
+experimental benchmark for testing simulated and theoretical
+predictions of protein unfolding behavior.  Despite it use since
+1997\citep{rief97a}, the labs currently engaged in SMFS use in-house
+software and procedures for critical tasks such as cantilever
+calibration and Monte Carlo unfolding simulation.  Besides wasting
+developer time producing and maintaining redundant implementations,
+the lack of transparency makes it more difficult to share data and
+techniques between labs, which slows progress.  In some cases it can
+also lead to ambiguity as to which of several similar approaches,
+correction factors, etc.\ were used in a particular paper.
+\nomenclature{SMFS}{Single molecule force spectroscopy}
+
+In this thesis, I introduce an SMFS sofware suite for cantilever
+calibration (\calibcant), experiment control (\pyafm), analysis
+(\Hooke), and postprocessing
+(\sawsim)\citep{calibcant,pyafm,sandal09,king10}.  All of these tools
+are licensed under open source licenses, which allows SMFS researchers
+to centralize future development.  Where possible, care has been taken
+to keep these packages operating system (OS) agnostic.  The experiment
+logic in \pyafm\ and \calibcant\ is still nominally OS agnostic, but
+those packages depend on more fundamental packages that control the
+physical hardware in use\citep{pyafm}.  At the bottom of the
+physical-interface stack are the \Comedi\ drivers from the Linux
+kernel\citep{comedi}.  Users running other OSes should be able to swap
+in analogous low level physical-interface packages if Linux is not an
+option.  \nomenclature{OS}{Operating system}
 \end{abstract}