From 6153eb89c9f803f21c631aa8af26c3e28697f16b Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Sun, 24 Jun 2012 02:52:26 -0400 Subject: [PATCH] Add abstract text. --- src/blurb/abstract.tex | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) 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} -- 2.26.2