Upload tutorial/Fix #88

tutorial/pom.xml

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+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+
+  <groupId>mySBOLexamples</groupId>
+  <artifactId>crispr</artifactId>
+  <version>0.0.1-SNAPSHOT</version>
+  <packaging>jar</packaging>
+
+  <name>crispr</name>
+  <url>http://maven.apache.org</url>
+
+  <properties>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+  </properties>
+
+  <dependencies>
+    <dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <version>3.8.1</version>
+      <scope>test</scope>
+    </dependency>
+  </dependencies>
+
+  <build>
+    <pluginManagement>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.1</version>
+                <configuration>
+                    <source>1.7</source>
+                    <target>1.7</target>
+                </configuration>
+            </plugin>
+        </plugins>
+    </pluginManagement>
+</build>
+</project>

tutorial/setupMavenPrj.tex

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+\noindent In this tutorial, we describe steps for setting up a Maven
+project that uses {\tt libSBOLj} in Eclipse, and explain how we use SBOL
+2.0 to represent the function of a state-of-the-art design, namely a
+CRISPR-based repression module Kiani~\textit{et
+  al.}~\cite{kiani2014crispr} using the Java library. 
+
+\section*{Set up Maven plugins in Eclipse}
+In this section, we describe steps for installing Maven plugins in Eclipse. The Eclipse version used is Luna Service Release 2 (4.4.2). Here are the steps:
+\begin{enumerate}
+\item In Eclipse, go to Help and select Install New Software, 
+\item Add a new software site: Name = slf4j, URL = \url{http://www.fuin.org/p2-repository/}, 
+\item Select this site to work with, expand Maven osgi-bundles, and select slf4j.api, 
+\item Click Next and follow the installation process, 
+\item Add a new software site: Name = Maven Plugins, URL = \url{http://download.eclipse.org/technology/m2e/releases}, 
+\item Select this site to work with, expand Maven Integration for Eclipse, and select m2e - Maven Integration for Eclipse, and
+\item Click Next and follow the installation process.
+\end{enumerate}
+
+\section*{Creating a new project}
+After the Maven plugin is installed, we are now ready to create a new Maven project in Eclipse. The following text describe the necessary steps. 
+
+In the package explorer window, right click and select {\bf New $\rightarrow$ Other}.
+\begin{center}
+  \includegraphics[width=0.8\textwidth]{figures/createNewMavenProject1}
+\end{center}
+
+Under the {\bf Maven} folder, choose {\bf Maven Project}, and then follow the default options for the project setup.
+\begin{center}
+  \includegraphics[width=0.75\textwidth]{figures/createNewMavenProject2}
+\end{center}
+
+% \begin{center}
+%   \includegraphics[width=0.8\textwidth]{figures/createNewMavenProject3}
+% \end{center}
+
+\begin{center}
+  \includegraphics[width=0.75\textwidth]{figures/createNewMavenProject4}
+\end{center}
+
+In the window for specifying archetype parameters, you may type your group ID and artifact ID. In this tutorial, they are specified as shown below. 
+\begin{center}
+  \includegraphics[width=0.8\textwidth]{figures/createNewMavenProject5}
+\end{center}
+
+Once the project setup is finished, you should be able to see two Java source folders, a {\bf JRE System Library} and a {\bf Maven Dependencies} library, and a {\bf pom.xml} file. 
+\begin{center}
+  \includegraphics[width=0.8\textwidth]{figures/createNewMavenProject6}
+\end{center}
+
+It is possible that the JRE System Library created by Maven is not compatible with the installed JREs. In the screenshot shown below, it is set to {\bf J2SE-1.5}, but the Maven compiler is compatible with {\bf JavaSE-1.7} instead. To change it, right-click on JRE System Library, and select {\bf Build Path $\rightarrow$ Configure Build Path}. 
+\begin{center}
+  \includegraphics[width=0.8\textwidth]{figures/createNewMavenProject7}
+\end{center}
+
+In the popup properties window, select {\bf Edit} under {\bf Libraries}. 
+\begin{center}
+  \includegraphics[width=0.8\textwidth]{figures/createNewMavenProject8}
+\end{center}
+
+We can now change the execution environment to JavaSE-1.7 as shown below. 
+\begin{center}
+  \includegraphics[width=0.8\textwidth]{figures/createNewMavenProject9}
+\end{center}
+
+This solution, however, is temporary. If we right-click on the ``crispr'' project and then select {\bf Maven $\rightarrow$  Update Project}, the JRE will reset itself back to J2SE-1.5. 
+\begin{center}
+  \includegraphics[width=0.8\textwidth]{figures/createNewMavenProject10}
+\end{center}
+
+A permanent fix would be to manually add the plugin management information below to the pom.xml file.
+
+\begin{minipage}{\textwidth} 
+\begin{lstlisting}[language=xml,basicstyle=\footnotesize\ttfamily]
+<build>
+    <pluginManagement>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.1</version>
+                <configuration>
+                    <source>1.7</source>
+                    <target>1.7</target>
+                </configuration>
+            </plugin>
+        </plugins>
+    </pluginManagement>
+</build>
+\end{lstlisting}
+\end{minipage}
+
+The pom.xml should look like the one shown below after this modification. Remember to save the file and then do {\bf Maven $\rightarrow$  Update Project}.
+
+\begin{minipage}{\textwidth} 
+\lstinputlisting[language=xml,basicstyle=\footnotesize\ttfamily]{pom.xml}
+\end{minipage}
+
+\section*{Adding {\tt libSBOLj} as dependency}
+We are now ready to add libSBOLj as a Maven dependency. This can be easily done by right-clicking on the ``crispr'' project and then select {\bf Maven $\rightarrow$ Add Dependency}.
+% \begin{center}
+%   \includegraphics[width=0.55\textwidth]{figures/addMavenDependency1}
+% \end{center}
+In the popup window shown below, fill in the information for the {\tt libSBOLj} library. The group ID is {\bf org.sbolstandard}, and the artifact ID is {\bf libSBOLj} and the version is {\bf 2.1.0}. 
+\begin{center}
+  \includegraphics[width=0.55\textwidth]{figures/addMavenDependency2}
+\end{center}
+
+After this dependency is added, Maven automatically brings in the  {\tt libSBOLj-2.1.0.jar} and its dependencies from the Maven Central Repository, and places them under the {\bf Maven Dependencies} directory.
+\begin{center}
+  \includegraphics[width=0.8\textwidth]{figures/addMavenDependency3}
+\end{center}
+
+

tutorial/top.aux

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+\relax 
+\providecommand\hyper@newdestlabel[2]{}
+\providecommand\HyperFirstAtBeginDocument{\AtBeginDocument}
+\HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined
+\global\let\oldcontentsline\contentsline
+\gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}}
+\global\let\oldnewlabel\newlabel
+\gdef\newlabel#1#2{\newlabelxx{#1}#2}
+\gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}}
+\AtEndDocument{\ifx\hyper@anchor\@undefined
+\let\contentsline\oldcontentsline
+\let\newlabel\oldnewlabel
+\fi}
+\fi}
+\global\let\hyper@last\relax 
+\gdef\HyperFirstAtBeginDocument#1{#1}
+\providecommand\HyField@AuxAddToFields[1]{}
+\providecommand\HyField@AuxAddToCoFields[2]{}
+\citation{kiani2014crispr}
+\citation{kiani2014crispr}
+\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces  Illustration of a hierarchical CRISPR-based repression module represented in SBOL 2.0 (adapted from Figure\nobreakspace  {}1a in \cite  {kiani2014crispr}). The CRISPR-based Repression Template \textbf  {ModuleDefinition} describes a generic CRISPR repression circuit that combines a Cas9 protein with a gRNA to form a complex (represented by the dashed arrows) that represses a target gene (represented by the arrow with the tee arrowhead). These relationships between these \textbf  {FunctionalComponents} (instances of \textbf  {ComponentDefinitions}) are represented in SBOL 2.0 using \textbf  {Interactions}. This \textbf  {Module} is instantiated in the outer CRPb Characterization Circuit \textbf  {ModuleDefinition} in order to specify the precise (including \textbf  {Sequences} when provided) \textbf  {FunctionalComponents} used for each generic \textbf  {FunctionalComponent}. The undirected dashed lines going into the template \textbf  {Module} represent \textbf  {MapsTo} objects that specify how specific \textbf  {FunctionalComponents} replace the generic ones.}}{2}{figure.1}}
+\newlabel{fig:fig-CRPb}{{1}{2}{Illustration of a hierarchical CRISPR-based repression module represented in SBOL 2.0 (adapted from Figure~1a in \cite {kiani2014crispr}). The CRISPR-based Repression Template \sbol {ModuleDefinition} describes a generic CRISPR repression circuit that combines a Cas9 protein with a gRNA to form a complex (represented by the dashed arrows) that represses a target gene (represented by the arrow with the tee arrowhead). These relationships between these \sbol {FunctionalComponents} (instances of \sbol {ComponentDefinitions}) are represented in SBOL 2.0 using \sbol {Interactions}. This \sbol {Module} is instantiated in the outer CRPb Characterization Circuit \sbol {ModuleDefinition} in order to specify the precise (including \sbol {Sequences} when provided) \sbol {FunctionalComponents} used for each generic \sbol {FunctionalComponent}. The undirected dashed lines going into the template \sbol {Module} represent \sbol {MapsTo} objects that specify how specific \sbol {FunctionalComponents} replace the generic ones}{figure.1}{}}
+\citation{Courtot2011}
+\citation{kiani2014crispr}
+\@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces \textbf  {ComponentDefinition} objects}}{8}{table.1}}
+\newlabel{tbl:tbl-ComponentDef}{{1}{8}{\sbol {ComponentDefinition} objects}{table.1}{}}
+\@writefile{lot}{\contentsline {table}{\numberline {2}{\ignorespaces \textbf  {SequenceConstraint} objects}}{8}{table.2}}
+\newlabel{tbl:tbl-SeqConstraint}{{2}{8}{\sbol {SequenceConstraint} objects}{table.2}{}}
+\citation{kiani2014crispr}
+\@writefile{lot}{\contentsline {table}{\numberline {3}{\ignorespaces \textbf  {Interaction} objects}}{9}{table.3}}
+\newlabel{tbl:tbl-Interaction}{{3}{9}{\sbol {Interaction} objects}{table.3}{}}
+\citation{SBML}
+\citation{roehner2015generating}
+\bibstyle{ieeetr}
+\bibdata{top}
+\bibcite{kiani2014crispr}{1}
+\bibcite{Courtot2011}{2}
+\bibcite{SBML}{3}
+\bibcite{roehner2015generating}{4}

tutorial/top.bbl

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+\begin{thebibliography}{1}
+
+\bibitem{kiani2014crispr}
+S.~Kiani, J.~Beal, M.~Ebrahimkhani, J.~Huh, R.~Hall, Z.~Xie, Y.~Li, and
+  R.~Weiss, ``Crispr transcriptional repression devices and layered circuits in
+  mammalian cells,'' {\em Nature Methods}, vol.~11, no.~7, pp.~723--726, 2014.
+
+\bibitem{Courtot2011}
+M.~Courtot, N.~Juty, C.~Kn\"{u}pfer, D.~Waltemath, A.~Zhukova, A.~Dr\"{a}ger,
+  M.~Dumontier, A.~Finney, M.~Golebiewski, J.~Hastings, S.~Hoops, S.~Keating,
+  D.~Kell, S.~Kerrien, J.~Lawson, A.~Lister, J.~Lu, R.~Machne, P.~Mendes,
+  M.~Pocock, N.~Rodriguez, A.~Villeger, D.~Wilkinson, S.~Wimalaratne, C.~Laibe,
+  M.~Hucka, and N.~{Le Nov\`{e}re}, ``{Controlled vocabularies and semantics in
+  systems biology},'' {\em Molecular Systems Biology}, vol.~7, 2011.
+
+\bibitem{SBML}
+M.~Hucka, A.~Finney, H.~Sauro, H.~Bolouri, J.~Doyle, H.~Kitano, A.~Arkin,
+  B.~Bornstein, D.~Bray, A.~Cornish-Bowden, {\em et~al.}, ``The systems biology
+  markup language (sbml): a medium for representation and exchange of
+  biochemical network models,'' {\em Bioinformatics}, vol.~19, no.~4,
+  pp.~524--531, 2003.
+
+\bibitem{roehner2015generating}
+N.~Roehner, Z.~Zhang, T.~Nguyen, and C.~Myers, ``Generating systems biology
+  markup language models from the synthetic biology open language,'' {\em ACS
+  Synthetic Biology}, vol.~4, no.~8, pp.~873--879, 2015.
+
+\end{thebibliography}