From: W. Trevor King Date: Thu, 16 May 2013 01:06:24 +0000 (-0400) Subject: pyafm/overview.tex: Pull introductory text from pyafm/main.tex X-Git-Tag: v1.0~192 X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=c8a3c86ff657007c36753a9d61515fbe7d3db78d;p=thesis.git pyafm/overview.tex: Pull introductory text from pyafm/main.tex Make the main.tex switchyard cleaner by pulling out text that probably won't see much more editing. --- diff --git a/src/pyafm/main.tex b/src/pyafm/main.tex index c47f2b0..d3f97ff 100644 --- a/src/pyafm/main.tex +++ b/src/pyafm/main.tex @@ -8,45 +8,7 @@ horses, and must only be made at decisive moments.}{Alfred North Whitehead\citep{whitehead11}} -Velocity clamp experiments have been carried out since the initial -work by \citet{rief97a}, so I was somewhat surprised that there -weren't already community-driven packages for carrying out and -analyzing these -experiments\citep{claerbout92,buckheit95,schwab00,vandewalle09}. When -I joined Prof.~Yang's lab, we were using experiment control software -written in \citetalias{labview} and analysis software written in -\citetalias{wavemetrics-igor}, both developed in-house. The existing -software was not designed to control sample temperature or for easy -extension, so I proceeded to write my own control and analysis stack -to add this capabilities. - -For those of you thinking, ``Why is he calling this thing a stack?'', -software is rarely developed as a single monolithic program. Instead, -developers write a software as a series of modular components, with -each layer in the stack using lower level features from the layers -below it to supply higher level features to the layers above it -(\cref{fig:pyafm:stack}). New high-level programs will contain logic -for the new idea (perform velocity-clamp unfolding experiments) and -leverage pre-existing packages for all the old ideas that you need to -get the job done (open a file, Fourier transform an array, \ldots). A -well structured suite of software breaks the task at hand up into many -sub-components, with a distinct package handling each component. - -\citet{whitehead11} introduces his claim about civilization and -subconscious operations to motivate the utility of symbolism in -subconcious reasoning. By encapsulating already established ideas in -a compact form, we can focus on the crux of an issue -(\cref{fig:unfold-protein:unfolder}) without being distracted by the -peripheral boilerplate (\cref{fig:labview}). - -In this chapter, I will discuss the earlier frameworks and abortive -attempts that lead me towards my current architecture -(\cref{sec:aio-frameworks,sec:pyafm:stack}). I will also discuss some -auxiliary packages I developed to support the main stack -(\cref{sec:pyafm:auxiliary}). I'll wrap up by comparing my stack with -Prof.~Yang's earlier framework and summarizing lessons I've learned -along the way (\cref{sec:pyafm:discussion,sec:pyafm:conclusions}). - +\input{pyafm/overview} \input{pyafm/frameworks} \input{pyafm/stack} \input{pyafm/auxiliary} diff --git a/src/pyafm/overview.tex b/src/pyafm/overview.tex new file mode 100644 index 0000000..9a49d5a --- /dev/null +++ b/src/pyafm/overview.tex @@ -0,0 +1,38 @@ +Velocity clamp experiments have been carried out since the initial +work by \citet{rief97a}, so I was somewhat surprised that there +weren't already community-driven packages for carrying out and +analyzing these +experiments\citep{claerbout92,buckheit95,schwab00,vandewalle09}. When +I joined Prof.~Yang's lab, we were using experiment control software +written in \citetalias{labview} and analysis software written in +\citetalias{wavemetrics-igor}, both developed in-house. The existing +software was not designed to control sample temperature or for easy +extension, so I proceeded to write my own control and analysis stack +to add this capabilities. + +For those of you thinking, ``Why is he calling this thing a stack?'', +software is rarely developed as a single monolithic program. Instead, +developers write a software as a series of modular components, with +each layer in the stack using lower level features from the layers +below it to supply higher level features to the layers above it +(\cref{fig:pyafm:stack}). New high-level programs will contain logic +for the new idea (perform velocity-clamp unfolding experiments) and +leverage pre-existing packages for all the old ideas that you need to +get the job done (open a file, Fourier transform an array, \ldots). A +well structured suite of software breaks the task at hand up into many +sub-components, with a distinct package handling each component. + +\citet{whitehead11} introduces his claim about civilization and +subconscious operations to motivate the utility of symbolism in +subconcious reasoning. By encapsulating already established ideas in +a compact form, we can focus on the crux of an issue +(\cref{fig:unfold-protein:unfolder}) without being distracted by the +peripheral boilerplate (\cref{fig:labview}). + +In this chapter, I will discuss the earlier frameworks and abortive +attempts that lead me towards my current architecture +(\cref{sec:aio-frameworks,sec:pyafm:stack}). I will also discuss some +auxiliary packages I developed to support the main stack +(\cref{sec:pyafm:auxiliary}). I'll wrap up by comparing my stack with +Prof.~Yang's earlier framework and summarizing lessons I've learned +along the way (\cref{sec:pyafm:discussion,sec:pyafm:conclusions}).