+% 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{TGuy = "Guy, Tommy"}
+@string{CKoch = "Koch, Christina"}
+@string{FOesterhelt = "Oesterhelt, Filipp"}
+@string{MRief = "Rief, Matthias"}
+@string{TSibley = "Sibley, Thomas"}
@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 = "https://idea.library.drexel.edu/islandora/object/idea%3A4188/datastream/OBJ/download/Open_source_single_molecule_force_spectroscopy.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
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,
% Talks
+@unpublished{ 2015-04-uw,
+ title= {Databases and and {SQL}},
+ author = TSibley #" and "# WKing,
+ year = 2015,
+ month = apr,
+ note= {Software Carpentry workshop, University of Washington},
+ address = {University of Washington},
+}
+% Message-ID: <54D3F261.7040808 at uw.edu>
+
+@unpublished{ 2014-03-uw,
+ title= {Bash, {P}ython, and {SQL}},
+ author = TGuy #" and "# WKing #" and "# CKoch,
+ year = 2014,
+ month = mar,
+ note= {Software Carpentry workshop, University of Washington},
+ address = {University of Washington},
+}
+% Message-ID: <20140226041514.GE13371 at odin.tremily.us>
+
+@unpublished{ 2013-05-thesis,
+ title= {Open source single molecule force spectroscopy},
+ author = WKing,
+ year = 2013,
+ month = may,
+ day = 28,
+ note= {Thesis defense, Drexel University},
+ address = {Drexel University},
+ url = {http://blog.tremily.us/posts/Thesis/talk/},
+}
+
@unpublished{ 2013-01-columbia,
title= {Collaborative version control with {G}it},
author = WKing,
year = 2013,
month = jan,
- note= {Software Carpentry boot camp, Columbia University},
+ note= {Software Carpentry workshop, Columbia University},
address = {Columbia University},
}
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.",
+}
projects / cv-latex.git / blobdiff