sbol2.tex

\documentclass[finalspec]{sbmlpkgspec}
%% \documentclass[draftspec]{sbmlpkgspec}
\usepackage{microtype}
\usepackage{color}
\usepackage{todonotes}
\usepackage{changebar}
\usepackage{xcolor}
\usepackage{soul}

%% ============================================================================
%% Description:  Documentation for sbmlpkgspec.cls
%% First author: Michael Hucka <mhucka@caltech.edu>
%% Organization: California Institute of Technology
%% Date created: September 2011
%% https://sbml.svn.sourceforge.net/svnroot/sbml/trunk/project/tex/sbmlpkgspec
%%
%% Copyright (C) 2011-2012 California Institute of Technology, Pasadena, CA.
%%
%% SBMLPkgSpec is free software; you can redistribute it and/or modify it
%% under the terms of the GNU Lesser General Public License as published by
%% the Free Software Foundation.  A copy of the license agreement is provided
%% in the file named "LICENSE.txt" included with this software distribution.
%% ============================================================================

% Macros just for this document:

\newcommand{\rfcnum}{112}

\newcommand{\sbmlpkg}{\texorpdfstring{%
    \textls[-25]{\textsc{SBMLPkgSpec}}}{%
    \textsc{SBMLPkgSpec}}\xspace}
\newcommand{\sbmlpkghead}{\texorpdfstring{%
    \textls[-50]{\textsc{SBMLPkgSpec}}}{%
    \textsc{SBMLPkgSpec}}\xspace}
\newcommand{\sbmlpkgfile}{\literalFont{sbmlpkgspec.cls}\xspace}
\newcommand{\latex}{\LaTeX{}\xspace}
\newcommand{\tex}{\TeX{}\xspace}
\newcommand{\distURL}{http://sourceforge.net/projects/sbml/files/specifications/tex}
\newcommand{\srcURL}{https://sbml.svn.sourceforge.net/svnroot/sbml/trunk/project/tex/sbmlpkgspec}
\newcommand{\webURL}{http://sbml.org/Documents/Specifications/The_SBMLPkgSpec_LaTeX_class}
\newcommand{\cmd}[1]{\literalFont{\textbackslash #1}}

% Custom latex listing style, for use with the listings package.  The default
% highlights far too many things, IMHO.  This keeps it simple and only adjusts
% the appearance of comments within listings.

\lstdefinelanguage{mylatex}{%
  morekeywords={},%
  sensitive,%
  alsoother={0123456789$_},%$
  morecomment=[l]\%%
}[keywords,tex,comments]

\lstdefinestyle{latex}{language=mylatex}


%Listing style for SBOL RDF/XML serialization examples
\usepackage{listings}
\usepackage{color}
\usepackage{xcolor}
\definecolor{dkgreen}{rgb}{0,0.6,0}
\definecolor{gray}{rgb}{0.5,0.5,0.5}
\definecolor{light-gray}{gray}{0.97}
\lstdefinelanguage{sbol}
    {morekeywords={xmlns:sbol,rdf:about,sbol:displayId,sbol:persistentIdentity,sbol:version,sbol:timeStamp,sbol:name,sbol:description,sbol:member,sbol:Collection,sbol:type,
        sbol:role, sbol:roleIntegration, sbol:ComponentDefinition, sbol:MapsTo, sbol:sequence,sbol:wasDerivedFrom,sbol:Component,sbol:subComponent,sbol:SequenceAnnotation,sbol:component,sbol:location, sbol:sequenceAnnotation, sbol:Range, sbol:start, sbol:end, sbol:orientation,sbol:SequenceConstraint, sbol:restriction, sbol:subject, sbol:object,sbol:Sequence, sbol:elements, sbol:encoding,sbol:Model, sbol:source, sbol:language, sbol:framework,sbol:FunctionalComponent, sbol:Module, sbol:Interaction, sbol:interaction, sbol:module, sbol:model,sbol:Model,sbol:definition, sbol:access, sbol:direction, sbol:mapsTo, sbol:refinement, sbol:local, sbol:remote, sbol:participation, sbol:Participation, sbol:participant,sbol:sequenceConstraint,sbol:at,sbol:Cut,sbol:functionalComponent,sbol:ModuleDefinition,prov:wasDerivedFrom,dcterms:title,dcterms:description},
     basicstyle=\fontsize{7}{9}\selectfont\ttfamily,
     backgroundcolor=\color{light-gray},
     keywordstyle=\color{blue},
     commentstyle=\color{gray},
     stringstyle=\color{dkgreen},
     tabsize=2,
     showspaces=false,
     showstringspaces=false,
     breaklines=true,                           % wrap text
     sensitive=true,                            % keywords are case sensitive
     %morecomment=[l][commentstyle]{\#},         % comment format
     morestring=[b]",                           % string format
     escapeinside={[}{]},
     alsoletter=:
     %breakatwhitespace=true,
     %literate={\-}{}{0\discretionary{a}{\\}{}}
}



%Command to format the listings containing SBOL RDF/XML serialization examples
\newcommand{\lstsetsbol}{
 \lstset{language=sbol,
        tabsize=2
 }
}

%Commands to format SBOL terms in the document

% Use sbolheading when you are referencing an SBOL data model class/field in a
% section heading.
\newcommand{\sbolheading}[1]{\texttt{#1}}

% Use sbol when you are referencing an SBOL data model class/field in text.
\newcommand{\sbol}[1]{\texttt{\hyperref[sec:#1]{#1}}}

% Use sbolmult for SBOL fields that appear in multiple classes, for example
% \sbolmult{types:CD}{types}. This ensures the reference links to the correct
% section.
\newcommand{\sbolmult}[2]{\texttt{\hyperref[sec:#1]{#2}}}

% Rarely used. Use refObj you want to put the field in angle brackets.
\newcommand{\refObj}[1]{$\langle$#1$\rangle$}

%Command to format external terms in the document
\newcommand{\external}[1]{\texttt{#1}}

%Commands to highlight SBOL versions
\newcommand{\twozeroone}[1]{%
\cbcolor{red}
\cbstart%
{\color{red}%
\version{2.0.1}%
#1
}
\cbend
}

%Commands to highlight SBOL versions
\newcommand{\twoonezero}[1]{%
\cbcolor{red}
\cbstart%
{\color{red}%
\version{2.1.0}%
#1
}
\cbend
}

% -----------------------------------------------------------------------------
% Start of document
% -----------------------------------------------------------------------------

\begin{document}

\packageTitle{\latex Class for SBML Package Specifications}
\packageVersion{Version 2.1.0}
\packageVersionDate{October 28, 2016}

\title{BBF RFC \rfcnum{}: Synthetic Biology Open Language \texorpdfstring{\\[3pt]}{}\mbox{(SBOL) Version~2.1.0}}


\author{{\bf Editors:}\hfil\\
\begin{tabular}{l>{\hspace*{15pt}}r}
Jacob Beal		& \emph{Raytheon BBN Technologies, USA}\\
Robert Sidney Cox	& \emph{Kobe University, Japan}\\
Raik Grunberg		& \emph{University of Montreal, Canada}\\
James McLaughlin	& \emph{Newcastle University, UK}\\
Tramy Nguyen 		& \emph{University of Utah, USA}\\
\end{tabular}\\
{\bf Chair:}\hfil\\
\begin{tabular}{l>{\hspace*{15pt}}r}
Anil Wipat & \emph{Newcastle University, UK}\\[8pt]
\end{tabular}\\
\href{mailto:editors@sbolstandard.org}{\sffamily editors@sbolstandard.org}\\
\\
{\bf Additional authors, by institution:}\\
\begin{tabular}{l>{\hspace*{15pt}}r}
Chris Macklin, Michael Bissell & \emph{Amyris, Inc., USA}\\
Curtis Madsen, Nicholas Roehner	& \emph{Boston University, USA}\\
Ernst Oberortner & \emph{DOE Joint Genome Institute, USA}\\
Goksel Misirli, Matthew Pocock & \emph{Newcastle University, UK}\\
Kevin Clancy		& \emph{ThermoFisher Scientific, USA}\\
Zhen Zhang, Chris Myers & \emph{University of Utah, USA}\\
Bryan Bartley, John H. Gennari, Herbert Sauro & \emph{University of Washington, USA}\\
\end{tabular}\\
}

\maketitlepage
\maketableofcontents

\todo[inline]{Update authorship, making sure to add new editors}

\input{purpose}

\input{relation}

\input{copyright}

\input{history}

\input{vocabulary}

\input{overview}

\input{model}

\input{examples_model}

\input{serialization}

\input{compliance}

\input{practices}

\newpage
\bibliography{sbol}

\appendix

\input{apdx-validation}

\input{examples_serialization}

\end{document}


% -----------------------------------------------------------------------------
% Random non-printing junk at the end: this section contains examples of potentially useful code for formatting tables, bullets, etc.

\begin{table}[hb]
  \begin{edtable}{tabular}{ll}
    \toprule
    \textbf{Item} & \textbf{Location} \\
    \midrule
    Distribution archive & \url{\distURL}\\
    Web page		 & \url{\webURL}\\
    Source tree (SVN)    & \url{\srcURL}\\
    \bottomrule
  \end{edtable}
  \caption{Where to find \sbmlpkg on the Internet.}
  \label{where}
\end{table}

\begin{table}[htb]
  \rowcolors{2}{sbmlrowgray}{}
  \renewcommand{\arraystretch}{1.05}
  \begin{edtable}{tabular}{ll}
    \toprule
    \textbf{Command}                      & \textbf{Object} \\
    \midrule
    \cmd{AlgebraicRule}                   & \AlgebraicRule \\
    \cmd{Annotation}                      & \Annotation \\
    \cmd{AssignmentRule}                  & \AssignmentRule \\
    \cmd{Compartment}                     & \Compartment \\
    \cmd{Constraint}                      & \Constraint \\
    \cmd{Delay}                           & \Delay \\
    \cmd{EventAssignment}                 & \EventAssignment \\
    \cmd{Event}                           & \Event \\
    \cmd{FunctionDefinition}              & \FunctionDefinition \\
    \cmd{InitialAssignment}               & \InitialAssignment \\
    \cmd{KineticLaw}                      & \KineticLaw \\
    \cmd{ListOfCompartments}              & \ListOfCompartments \\
    \cmd{ListOfConstraints}               & \ListOfConstraints \\
    \cmd{ListOfEventAssignments}          & \ListOfEventAssignments \\
    \cmd{ListOfEvents}                    & \ListOfEvents \\
    \cmd{ListOfFunctionDefinitions}       & \ListOfFunctionDefinitions \\
    \cmd{ListOfInitialAssignments}        & \ListOfInitialAssignments \\
    \cmd{ListOfLocalParameters}           & \ListOfLocalParameters \\
    \cmd{ListOfModifierSpeciesReferences} & \ListOfModifierSpeciesReferences \\
    \cmd{ListOfPackages}                  & \ListOfPackages \\
    \cmd{ListOfParameters}                & \ListOfParameters \\
    \cmd{ListOfReactions}                 & \ListOfReactions \\
    \cmd{ListOfRules}                     & \ListOfRules \\
    \cmd{ListOfSpeciesReferences}         & \ListOfSpeciesReferences \\
    \cmd{ListOfSpecies}                   & \ListOfSpecies \\
    \cmd{ListOfUnitDefinitions}           & \ListOfUnitDefinitions \\
    \cmd{ListOfUnits}                     & \ListOfUnits \\
    \cmd{LocalParameter}                  & \LocalParameter \\
    \cmd{Message}                         & \Message \\
    \cmd{Model}                           & \Model \\
    \cmd{ModifierSpeciesReference}        & \ModifierSpeciesReference \\
    \cmd{Notes}                           & \Notes \\
    \cmd{Package}                         & \Package \\
    \cmd{Parameter}                       & \Parameter \\
    \cmd{Priority}                        & \Priority \\
    \cmd{RateRule}                        & \RateRule \\
    \cmd{Reaction}                        & \Reaction \\
    \cmd{Rule}                            & \Rule \\
    \cmd{SBML}                            & \SBML \\
    \cmd{SBase}                           & \SBase \\
    \cmd{SimpleSpeciesReference}          & \SimpleSpeciesReference \\
    \cmd{SpeciesReference}                & \SpeciesReference \\
    \cmd{Species}                         & \Species \\
    \cmd{StoichiometryMath}               & \StoichiometryMath \\
    \cmd{Trigger}                         & \Trigger \\
    \cmd{UnitDefinition}                  & \UnitDefinition \\
    \cmd{Unit}                            & \Unit \\
    \bottomrule
  \end{edtable}
  \caption{Commands for the names of object classes defined in the SBML Level~3
    Core specification.}
  \label{sbmlcore}
\end{table}

\begin{example}[style=latex]
\documentclass{sbmlpkgspec}
\begin{document}

\packageTitle{Example}
\packageVersion{Version 1 (Draft)}
\packageVersionDate{14 August 2011}
\packageGeneralURL{http://sbml.org/Documents/Specifications/Example}
\packageThisVersionURL{http://sbml.org/Documents/Specifications/Example_14_August_2011}

\author{Michael Hucka\\[0.25em]
  \mailto{mhucka@caltech.edu}\\[0.25em]
  Computing and Mathematical Sciences\\
  California Institute of Technology\\
  Pasadena, CA, USA
}

\maketitlepage
\maketableofcontents

\section{...}
...
\end{document}
\end{example}


\begin{description}[font=\normalfont\ttfamily\color{black},style=nextline]

\item[draftspec] This option causes the front page of the document to contain
  the word ``DRAFT'' in large gray letters, and the footer of every page of
  the document to contain the word ``(DRAFT)''.  Authors can use this
  option until such time as the specification document is considered a
  release candidate or a final release.

\end{description}

\begin{description}

\item[\hspace*{6.5pt}\vSymbol\vsp] A \vSymbolName indicates a
  \emph{requirement} for conformance. If a model fails to follow this rule,
  it does not conform to the specification.  (Mnemonic intention behind the
  choice of symbol: ``This MUST be checked.'')

\item[\hspace*{6.5pt}\cSymbol\csp] A \cSymbolName indicates a
  \emph{recommendation} for model consistency.  If a model does not follow
  this rule, it is not considered strictly invalid as far as the
  specification is concerned; however, it indicates that the model contains
  a physical or conceptual inconsistency.  (Mnemonic intention behind the
  choice of symbol: ``This is a cause for warning.'')

\item[\hspace*{6.5pt}\mSymbol\msp] A \mSymbolName indicates a strong
  recommendation for good modeling practice.  This rule is not
  strictly a matter of SBML encoding, but the recommendation comes
  from logical reasoning.  As in the previous case, if a model does
  not follow this rule, it is not strictly considered an invalid SBML
  encoding.  (Mnemonic intention behind the choice of symbol: ``You're
  a star if you heed this.'')

\end{description}

\begin{itemize}

\item \texttt{amssymb}: This package defines many symbols and special
  characters.  In \sbmlpkg, it is used to get the symbols defined by the
  validation rule commands \cmd{validRule}, \cmd{consistencyRule} and
  \cmd{modelingRule} described in \sec{validation-rules}.

\end{itemize}
% * <myers@ece.utah.edu> 2015-06-03T17:34:31.200Z:
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