From: W. Trevor King <wking@tremily.us>
Date: Thu, 16 May 2013 01:05:09 +0000 (-0400)
Subject: pyafm/main.tex: Explain 'stack' and why modularization is useful
X-Git-Tag: v1.0~193
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=c4ce88fc704a7fe994e677c237afb0c29ff06211;p=thesis.git

pyafm/main.tex: Explain 'stack' and why modularization is useful
---

diff --git a/src/pyafm/main.tex b/src/pyafm/main.tex
index 964e0e7..c47f2b0 100644
--- a/src/pyafm/main.tex
+++ b/src/pyafm/main.tex
@@ -18,10 +18,31 @@ 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.  In this chapter, I will discuss the earlier
-frameworks and some 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
+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}).