From 6bca2f4271a9d0e7c987ccd3ec4bd716926c4a6d Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Tue, 24 Sep 2013 12:53:53 -0700 Subject: [PATCH] cv.bib: Add my thesis to the bilbliography --- cv.bib | 93 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 91 insertions(+), 2 deletions(-) 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.", +} -- 2.26.2