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Minor tweaks to document #5

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062ac5a
Ignore Latex output files.
rpgoldman Mar 2, 2021
f73b91e
Clarify overview paragraph.
rpgoldman Mar 3, 2021
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12 changes: 12 additions & 0 deletions .gitignore
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Expand Up @@ -3,3 +3,15 @@
opil.cb
opil.cb2
opil.pdf

*.aux

*.bbl

*.blg

*.log

*.out

*.toc
3 changes: 3 additions & 0 deletions opil.tex
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@@ -1,4 +1,5 @@


\errorcontextlines=200

\documentclass[finalspec]{sbmlpkgspec}
Expand Down Expand Up @@ -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
% -----------------------------------------------------------------------------
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16 changes: 13 additions & 3 deletions overview.tex
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Expand Up @@ -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}
Expand All @@ -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}
Expand All @@ -30,11 +35,16 @@ \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.
\item Using \opil{Measurement} objects: flow cytometry at hours 12, 30, 48, and 70.
\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: