From: W. Trevor King <wking@tremily.us>
Date: Tue, 24 Sep 2013 19:53:53 +0000 (-0700)
Subject: cv.bib: Add my thesis to the bilbliography
X-Git-Url: http://git.tremily.us/?p=cv-latex.git;a=commitdiff_plain;h=6bca2f4271a9d0e7c987ccd3ec4bd716926c4a6d

cv.bib: Add my thesis to the bilbliography
---

diff --git a/cv.bib b/cv.bib
index aefe963..30ed594 100644
--- a/cv.bib
+++ b/cv.bib
@@ -1,9 +1,81 @@
+% Journals
+
 @string{IJBMM = "International Journal of Biological Macromolecules"}
+@string{SCI = "Science"}
+
+% Institutions
+
+@string{Drexel = "Drexel University"}
+
+% Addresses
+
+@string{DrexelPhysics = "Department of Physics, Drexel University, 3141
+                         Chestnut Street, Philadelphia, PA 19104, USA."}
+
+% People
 
 @string{WKing = "King, W.~Trevor"}
+
+@string{JFernandez = "Fernandez, Julio M."}
+@string{HEGaub = "Gaub, Hermann E."}
+@string{MGautel = "Gautel, Mathias"}
+@string{FOesterhelt = "Oesterhelt, Filipp"}
+@string{MRief = "Rief, Matthias"}
 @string{MSu = "Su, Meihong"}
 @string{GYang = "Yang, Guoliang"}
 
+% 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.",
+}
+
 @article { king10,
     author = WKing #" and "# MSu #" and "# GYang,
     title = "{M}onte {C}arlo simulation of mechanical unfolding of proteins
@@ -11,8 +83,7 @@
     year = 2010,
     month = mar,
     day = 1,
-    address =      "Department of Physics, Drexel University, 3141
-                   Chestnut Street, Philadelphia, PA 19104, USA.",
+    address = DrexelPhysics,
     journal = IJBMM,
     volume = 46,
     number = 2,
@@ -163,3 +234,21 @@
     note= {Biophysical Society Annual Meeting},
     address = {Long Beach, California},
 }
+
+% References
+
+@article { rief97a,
+    author = MRief #" and "# MGautel #" and "# FOesterhelt #" and "# JFernandez
+        #" and "# HEGaub,
+    title = "Reversible Unfolding of Individual Titin Immunoglobulin Domains by
+        {AFM}",
+    year = 1997,
+    journal = SCI,
+    volume = 276,
+    number = 5315,
+    pages = "1109--1112",
+    doi = "10.1126/science.276.5315.1109",
+    eprint = "http://www.sciencemag.org/cgi/reprint/276/5315/1109.pdf",
+    url = "http://www.sciencemag.org/cgi/content/abstract/276/5315/1109",
+    note = "Seminal paper for force spectroscopy on Titin.",
+}