diff options
| -rw-r--r-- | acquisition/hardware_inheritance.png | bin | 0 -> 53143 bytes | |||
| -rw-r--r-- | presentation.cls | 1 | ||||
| -rw-r--r-- | presentation.pdf | bin | 813099 -> 1331020 bytes | |||
| -rw-r--r-- | presentation.tex | 106 |
4 files changed, 95 insertions, 12 deletions
diff --git a/acquisition/hardware_inheritance.png b/acquisition/hardware_inheritance.png Binary files differnew file mode 100644 index 0000000..ac1f229 --- /dev/null +++ b/acquisition/hardware_inheritance.png 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 Binary files differindex 7e287ba..b840c9f 100644 --- a/presentation.pdf +++ b/presentation.pdf 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}
|
