From a3f37bece8e4c79ca4bc9afdfc7467a7ef12afd1 Mon Sep 17 00:00:00 2001 From: Blaise Thompson Date: Fri, 20 Apr 2018 13:01:25 -0500 Subject: 2018-04-20 13:01 --- acquisition/hardware_inheritance.png | Bin 0 -> 53143 bytes presentation.cls | 1 + presentation.pdf | Bin 813099 -> 1331020 bytes presentation.tex | 106 +++++++++++++++++++++++++++++++---- 4 files changed, 95 insertions(+), 12 deletions(-) create mode 100644 acquisition/hardware_inheritance.png diff --git a/acquisition/hardware_inheritance.png b/acquisition/hardware_inheritance.png new file mode 100644 index 0000000..ac1f229 Binary files /dev/null and b/acquisition/hardware_inheritance.png differ diff --git a/presentation.cls b/presentation.cls index cbf9b48..873b605 100644 --- a/presentation.cls +++ b/presentation.cls @@ -20,6 +20,7 @@ \RequirePackage{enumerate} \RequirePackage{soul} \sethlcolor{yellow} +\RequirePackage{verbatim} %\renewcommand{\familydefault}{\sfdefault} \RequirePackage[cm]{sfmath} diff --git a/presentation.pdf b/presentation.pdf index 7e287ba..b840c9f 100644 Binary files a/presentation.pdf and b/presentation.pdf differ diff --git a/presentation.tex b/presentation.tex index 97bd9de..9f4a3f1 100644 --- a/presentation.tex +++ b/presentation.tex @@ -5,7 +5,6 @@ \institute{University of Wisconsin--Madison} \date{2018-04-23} -%\subject{} \begin{document} \maketitle @@ -34,28 +33,62 @@ What am I doing in a field so rich with fundamental studies? \vspace{\baselineskip} \\ I hope to convince you that CMDS can be used for analytical work. % TODO: better + \begin{itemize} + \item detection (selectivity) + \item unknown identification + \item quantification + \end{itemize} \end{frame} % TODO: in fact, 2DIR is already used regularly... -\begin{frame}{Analytical} +\begin{frame}{Pakoulev et al. (2009)} \fbox{\adjincludegraphics[width=\textwidth]{literature/PakoulevAndreiV2009a}} \end{frame} -% TODO: pakoulev quotes +\begin{frame}{Pakoulev et al. (2009)} + \begin{shadequote} + Spectroscopy forms the heart of the analytical methodology used for routine chemical + measurement. % + Of all the analytical spectroscopic methods, NMR spectroscopy is unique in its ability to + \hl{correlate} spin resonances and \hl{resolve} spectral features from spectra containing + \hl{thousands of peaks}. % + For example, heteronuclear multiple quantum coherence (HMQC) spectroscopy achieves this + capability by exciting $^1$H, $^{15}$N, $^{13}$ C=O, and $^{13}$C$\alpha$ spins to form a + multiple quantum coherence \hl{characteristic of a specific position} in a protein’s backbone. + Three excitations define a specific residue, and a fourth defines the coupling to an adjacent + residue. + Not only does it decongest the spectra, it defines the couplings and connectivity between the + different nuclear spin states. + Coherent multidimensional spectroscopy (CMDS) has emerged as the \hl{optical analogue} of + nuclear magnetic resonance (NMR), and there is great interest in using it as a \hl{general + analytical methodology}. + \end{shadequote} +\end{frame} -\begin{frame}{Proteomics} - \fbox{\adjincludegraphics[width=\textwidth]{literature/FournierFrederic2009a}} +\begin{frame}{Donaldson et al. (2010)} + \fbox{\adjincludegraphics[width=\textwidth]{literature/DonaldsonPaulMurray2010a}} \end{frame} -% TODO: fournier quotes +\begin{frame}{Fournier et al. (2009)} + \fbox{\adjincludegraphics[width=\textwidth]{literature/FournierFrederic2009a}} +\end{frame} -\begin{frame}{Proteomics} - \fbox{\adjincludegraphics[width=\textwidth]{literature/DonaldsonPaulMurray2010a}} +\begin{frame}{Fournier et al. (2009)} + \begin{shadequote} + Our protein identification strategy is based on using EVV 2DIR to quantify the amino acid + content of a protein. % + EVV 2DIR is shown to be able to perform \hl{absolute quantification}, something of major + importance in the field of proteomics but rather difficult and time-consuming to achieve with + mass spectrometry. % + Our technique can be qualified as a top-down \hl{label-free} method; it does not require + intensive sample preparation, the proteins are intact when analyzed, and it does not have any + mass restriction on the proteins to be analyzed. % + Moreover, EVV 2DIR is a \hl{nondestructive} technique; the samples can be kept for reanalysis + in the light of further information. % + \end{shadequote} \end{frame} -% TODO: donaldson quotes - \section{Frequency domain} % ===================================================================== \begin{frame}{Domains of CMDS} @@ -67,7 +100,8 @@ \end{frame} \begin{frame}{Time domain} - Multiple broadband pulses are scanned in \emph{time} to collect a multidimensional interferogram. + Multiple broadband pulses are scanned in \emph{time} to collect a multidimensional interferogram + (analogous to FTIR, NMR). \vspace{\baselineskip} \\ A local oscillator must be used to measure the \emph{phase} of the output. \vspace{\baselineskip} \\ @@ -139,21 +173,64 @@ \end{frame} \begin{frame}{Universal format} + WrightTools defines a \emph{universal file format} for CMDS. + \begin{itemize} + \item store multiple multidimensional arrays + \item metadata + \end{itemize} + Import data from a variety of sources. + \begin{itemize} + \item previous Wright Group acquisition software + \item commercial instruments (JASCO, Shimadzu, Ocean Optics) + \end{itemize} \end{frame} \begin{frame}{Flexible data model} + Flexibility to transform into any desired ``projection'' on component variables. + \adjincludegraphics[width=\textwidth]{processing/fringes_transform} + % mention: including expressions \end{frame} \section{Acquisition} % ========================================================================== \begin{frame}{Acquisition} - PyCMDS. + PyCMDS---unified software for controlling hardware and collecting data. + \adjincludegraphics[width=\textwidth]{acquisition/screenshots/000} \end{frame} +\begin{frame}{Abstraction} + Hardware---something that has a \hl{position} that can be \hl{set}. + \vspace{\baselineskip} \\ + Sensor---something that has a \hl{signal} that can be \hl{read}. +\end{frame} + \begin{frame}{Modular hardware model} + \adjincludegraphics[scale=0.25]{acquisition/hardware_inheritance} +\end{frame} + +\begin{frame}{Modular sensor model} + Can have as many sensors as needed. + \vspace{\baselineskip} \\ + Each sensor contributes one or more channels. + \vspace{\baselineskip} \\ + Sensors with size contribute new variables (dimensions). \end{frame} +\begin{frame}{Central loop} + Set, wait, read, wait, repeat. + \vspace{\baselineskip} \\ + Everything is multi-threaded (simultaneous motion, simultaneous read). +\end{frame} + \begin{frame}{Acquisitions} + Acquisition---a particular set of actions. + \vspace{\baselineskip} \\ + Acquisition modules---a GUI that accepts a user instruction. +\end{frame} + +\begin{frame}{Queue} + Queue. + \adjincludegraphics[width=\textwidth]{acquisition/screenshots/004} \end{frame} \begin{frame}{Queue} @@ -169,6 +246,11 @@ \begin{frame}{Tuning} \end{frame} +\section{Conclusion} % =========================================================================== + +\begin{frame}{Conclusion} +\end{frame} + \section{Supplement} % =========================================================================== \begin{frame}{MR-CMDS theory} -- cgit v1.2.3