+% Papers
+
+@phdthesis { king13,
+ author = WKing,
+ title = "Open source single molecule force spectroscopy",
+ school = Drexel,
+ year = 2013,
+ month = jun,
+ address = DrexelPhysics,
+ url = "http://hdl.handle.net/1860/4188",
+ eprint = "http://dspace.library.drexel.edu/bitstream/1860/4188/1/King_WilliamPhD.pdf",
+ keywords = "Physics; Molecular spectroscopy; Biophysics",
+ 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.
+ %
+ \par
+ In this thesis, I introduce an SMFS sofware suite for
+ cantilever calibration
+ (\href{https://pypi.python.org/pypi/calibcant/}{calibcant}),
+ experiment control
+ (\href{https://pypi.python.org/pypi/unfold-protein}{unfold-protein}),
+ analysis (\href{https://pypi.python.org/pypi/Hooke}{Hooke}),
+ and postprocessing
+ (\href{http://blog.tremily.us/posts/sawsim/}{sawsim}) in the
+ context of velocity clamp unfolding of I27 octomers in buffers
+ with varying concentrations of \CaCl\textsubscript{2}. All of
+ the 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
+ unfold-protein and calibcant is still nominally OS agnostic,
+ but those packages depend on
+ \href{https://pypi.python.org/pypi/pyafm}{more fundamental
+ packages} that control the physical hardware in use. At the
+ bottom of the physical-interface stack are the
+ \href{http://www.comedi.org/}{Comedi} drivers from the Linux
+ kernel. Users running other operating systems should be able
+ to swap in analogous low level physical-interface packages if
+ Linux is not an option.",
+}
+