2018-04-20 13:01

4 files changed, 95 insertions, 12 deletions

diff --git a/acquisition/hardware_inheritance.png b/acquisition/hardware_inheritance.png
new 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
index 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}