From 062ac5a2b29228825c17fe9c51c5d80f2adab097 Mon Sep 17 00:00:00 2001
From: "Robert P. Goldman" <rpgoldman@goldman-tribe.org>
Date: Tue, 2 Mar 2021 14:29:25 -0600
Subject: [PATCH 1/2] Ignore Latex output files.

---
 .gitignore | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/.gitignore b/.gitignore
index af897b6..0ba687f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,15 @@
 opil.cb
 opil.cb2
 opil.pdf
+
+*.aux
+
+*.bbl
+
+*.blg
+
+*.log
+
+*.out
+
+*.toc

From f73b91efd23d24354dd20401daa32d66153cf26d Mon Sep 17 00:00:00 2001
From: "Robert P. Goldman" <rpgoldman@goldman-tribe.org>
Date: Wed, 3 Mar 2021 11:09:39 -0600
Subject: [PATCH 2/2] Clarify overview paragraph.

Replace "parallel construction" with a fuller, more verbose description of what is meant.
---
 opil.tex     |  3 +++
 overview.tex | 16 +++++++++++++---
 2 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/opil.tex b/opil.tex
index b46f00a..275f1d6 100644
--- a/opil.tex
+++ b/opil.tex
@@ -1,4 +1,5 @@
 
+
 \errorcontextlines=200
 
 \documentclass[finalspec]{sbmlpkgspec}
@@ -96,6 +97,8 @@
 % Rarely used. Use refObj you want to put the field in angle brackets.
 \newcommand{\refObj}[1]{$\langle$#1$\rangle$}
 
+\newcommand{\SampleSetSpec}{\opil{SampleSet}\xspace}
+
 % -----------------------------------------------------------------------------
 % Start of document
 % -----------------------------------------------------------------------------
diff --git a/overview.tex b/overview.tex
index 5439451..a2057e9 100644
--- a/overview.tex
+++ b/overview.tex
@@ -4,7 +4,12 @@ \section{Overview of OPIL}
 
 In OPIL, a protocol is an activity that is configured with certain parameters and applied to a set of biological samples in order to produce a set of measurements by particular instruments at particular times, as illustrated in \ref{f:overview}.
 An \opil{ExperimentalRequest} specifies a particular set of \opil{ParameterValue}s, \opil{SampleSet}s, and \opil{Measurement}s to be carried out. 
-A \opil{ProtocolInterface} specifies which \opil{ExperimentalRequest}s are allowed for a given protocol with a parallel construction of \opil{Parameter}s, \opil{SampleSet}s, and \opil{MeasurementType}s
+These must match the corresponding constructs in the \opil{ProtocolInterface}:
+the \opil{ParameterValue}s must match the \opil{Parameter}s; the actual \opil{SampleSet}s the \SampleSetSpec{}s, and \opil{Measurement}s the allowable \opil{MeasurementType}s.
+%  specifies which \opil{ExperimentalRequest}s
+% are allowed for a given protocol, by providing children that parallel
+% those of \opil{ExperimentalRequest}s: \opil{Parameter}s For
+% \opil{ParameterValue}s, \opil{SampleSet}s for , and \opil{MeasurementType}s
 
 \begin{figure}[ht]
 \begin{center}
@@ -15,7 +20,7 @@ \section{Overview of OPIL}
 \end{center}
 \end{figure}
 
-For example, consider a lab that is offering a multi-day bacterial protocol that might be described in prose as follows:
+For example, consider a lab that is offering a multi-day bacterial protocol described in prose as follows:
 \begin{quote}
 ``Run either B. subtilis or E. coli samples in any media with up to 2 inducers for 1 to 4 days, sampling with a flow cytometer no more than once every 12 hours, and have the option of taking one RNAseq measurement. Culturing temperature is normally 37 C but can be set anywhere between 20 and 40 C.''
 \end{quote}
@@ -30,7 +35,7 @@ \section{Overview of OPIL}
 \begin{quote}
 ``Please run all combinations of strains X and Y in media A, B, and C with 0, 0.1, 0.2, 0.5, and 1.0 uM arabinose. Run for 3 days with flow cytometry at hours 12, 30, 48, and 70. Culture at 27 C.''
 \end{quote}
-These specifies could be encoded into an \opil{ExperimentalRequest} by dividing them up as follows:
+These specifies would be encoded into an \opil{ExperimentalRequest} by dividing them up as follows:
 \begin{itemize}
 \item Using \opil{SampleSet} objects: all combinations of strains X and Y in media A, B, and C with 0, 0.1, 0.2, 0.5, and 1.0 uM arabinose.
 \item Using \opil{ParameterValue} objects: run for 3 days, culture at 27 C.
@@ -38,3 +43,8 @@ \section{Overview of OPIL}
 \end{itemize}
 
 The next sections provide complete definitions and details for all of these classes, along with more examples of their use.
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: "opil"
+%%% End: