Created version 2.1 and updated the User Guide and screenshots.

dist/gadget_config.xml

@@ -29,7 +29,7 @@
   <Name>[GADGET_NAME]</Name>
   <LaunchCommand>cmd /c start javaw.exe -jar "gadgets/[GADGET_UUID]/[JAR_NAME]"</LaunchCommand>
   <LaunchCommandWin>cmd /c start javaw.exe -jar "gadgets/[GADGET_UUID]/[JAR_NAME]"</LaunchCommandWin>
-  <LaunchCommandMac>open "gadgets/[GADGET_UUID]/[JAR_NAME]"</LaunchCommandMac>
+  <LaunchCommandMac>java -jar "gadgets/[GADGET_UUID]/[JAR_NAME]"</LaunchCommandMac>
   <LaunchCommandLinux>java -jar "gadgets/[GADGET_UUID]/[JAR_NAME]"</LaunchCommandLinux>
   <IconPaths>
     <Icon32Path>icons/SBMLsqueezerIcon_64.png</Icon32Path>

doc/tutorials/user_guide/UserGuide.tex

@@ -56,8 +56,8 @@
   breaklinks={true},
   colorlinks={false},
   pdfpagemode={UseOutlines},
-  pdftitle={SBMLsqueezer 2: a context-based generator of kinetic equations for models in systems biology},
-  pdfauthor={{Andreas Dr\"ager} {Roland Keller} {Matthias Fall} {Johannes Eichner} {Bernhard \O.} {Andreas Zell}},
+  pdftitle={SBMLsqueezer 2.1: a context-based generator of kinetic equations for models in systems biology},
+  pdfauthor={{Andreas Dr\"ager} {Daniel C. Zielinski} {Roland Keller} {Matthias Fall} {Johannes Eichner} {Bernhard O.} {Andreas Zell}},
   pdfsubject={User's Guide},
 %  pdftex,
   pdffitwindow={true},
@@ -87,15 +87,16 @@
 \titlehead{\centering\includegraphics[width=0.75\textwidth]{UT_WBMW_mathnat_4C}\\
 \noindent\makebox[\linewidth]{\color{gold}\rule{\textwidth}{1pt}}}
 \subject{Users' Guide}
-\title{SBMLsqueezer~2}
+\title{SBMLsqueezer~2.1}
 \subtitle{A context-based generator of kinetic equations}
 
 \author{Andreas Dr\"ager$^{1,2,}$\thanks{Corresponding author: \href{mailto:[email protected]}{\url{[email protected]}}}
 \and
-Roland Keller$^{2}$\and
-Matthias Rall$^{2}$\and
-Johannes Eichner$^{2}$\and
-Bernhard \O. Palsson$^{1}$\and
+Daniel C. Zielinski$^{1}$\and%
+Roland Keller$^{2}$\and%
+Matthias Rall$^{2}$\and%
+Johannes Eichner$^{2}$\and%
+Bernhard O. Palsson$^{1}$\and%
 Andreas Zell$^{2}$}
 \date{\today}
 \publishers{\includegraphics[width=48px]{img/LOGO}\\[2cm]%

doc/tutorials/user_guide/tex/Release_Notes.tex

@@ -557,11 +557,30 @@ \section{Version 2.0.1}
 
 Release date: October 24\textsuperscript{th} 2014.
 
-This release has become necessary due to major changes in the \Garuda backend and also includes an updated version of \JSBML.
+This release has become necessary due to major changes in the \Garuda backend
+and also includes an updated version of \JSBML.
 
-\section{Version 2.0.2}
+\section{Version 2.1}
 
-Release date: December 8\textsuperscript{th} 2014.
+Release date: October 10\textsuperscript{th} 2015.
 
-This bug-fix release solves issues related to the new \Garuda backend, includes an updated version of \JSBML, and has a slightly improved \API documentation.
+\subsection{New Features}
 
+\begin{dinglist}{52}
+\itemcolor{blue}
+\item SBMLsqueezer fully supports all Levels and Versions of \SBML up to the most
+recent specifications Level~2 Version~5 and Level~3 Version~1.
+\item The \CellDesigner plug-in version has been adapted to work with version 4.4.
+\item The \Garuda backend has been updated.
+\item The report generator \SBMLLaTeX has been updated and the new version is now
+      part of this release of SBMLsqueezer.
+\item SBMLsqueezer comes with the most recent version of \JSBML (revision 2354),
+      which can read all current extension packages.
+\item Slightly improved \href{http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsqueezer/doc/api/SBMLsqueezer2.1/}{\API documentation} and updated \href{http://vg08.met.vgwort.de/na/d4b8e9ae1bed423884cea07e52756b43?l=http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsqueezer/doc/SBMLsqueezer2.1UsersGuide.pdf}{Users' Guide}.
+\item Correctly indented \SBML output files.
+\end{dinglist}  
+
+\subsection{Bug Fixes}
+
+Under \Windows, it was sometimes not possible to correctly display user messages.
+This has been fixed. Several minor issues have been solved.

doc/tutorials/user_guide/tex/literature.bib

@@ -1,6 +1,88 @@
 % This file was created with JabRef 2.10.
 % Encoding: UTF8
 
+@article{Draeger2014a,
+  author = {Dr\"ager, Andreas and Palsson, Bernhard {\O}.},
+  title = {Improving collaboration by standardization efforts in systems biology},
+  journal = {Frontiers in Bioengineering},
+  year = {2014},
+  volume = {2},
+  number = {61},
+  month = dec,
+  abstract = {Collaborative genome-scale reconstruction endeavors of metabolic networks
+	would not be possible without a common, standardized formal representation
+	of these systems. The ability to precisely define biological building
+	blocks together with their dynamic behavior has even been considered
+	a prerequisite for upcoming synthetic biology approaches.
+	
+	Driven by the requirements of such ambitious research goals, standardization
+	itself has become an active field of research on nearly all levels
+	of granularity in biology. In addition to the originally envisaged
+	exchange of computational models and tool interoperability, new standards
+	have been suggested for an unambiguous graphical display of biological
+	phenomena, to annotate, archive, as well as to rank models, and to
+	describe execution and the outcomes of simulation experiments. The
+	spectrum now even covers the interaction of entire neurons in the
+	brain, three-dimensional motions, and the description of pharmacometric
+	studies.
+	
+	Thereby, the mathematical description of systems and approaches for
+	their (repeated) simulation are clearly separated from each other
+	and also from their graphical representation. Minimum information
+	definitions constitute guidelines and common operation protocols
+	in order to ensure reproducibility of findings and a unified knowledge
+	representation. Central database infrastructures have been established
+	that provide the scientific community with persistent links from
+	model annotations to on-line resources. A rich variety of open-source
+	software tools thrives for all data formats, often supporting a multitude
+	of programming languages. Regular meetings and workshops of developers
+	and users lead to continuous improvement and ongoing development
+	of these standardization efforts.
+	
+	This article gives a brief overview about the current state of the
+	growing number of operation protocols, markup languages, graphical
+	descriptions, and fundamental software support with relevance to
+	systems biology.},
+  doi = {10.3389/fbioe.2014.00061},
+  issn = {2296-4185},
+  keywords = {model formats, modeling guidelines, ontologies, model databases, network
+	visualization, software support},
+  pdf = {http://journal.frontiersin.org/Journal/10.3389/fbioe.2014.00061/pdf},
+  url = {http://journal.frontiersin.org/Journal/10.3389/fbioe.2014.00061/}
+}
+
+
+@article{Rodriguez2015,
+  author = {Rodriguez, Nicolas and Thomas, Alex and Watanabe, Leandro and
+    Vazirabad, Ibrahim Y. and Kofia, Victor and G\'omez, Harold F. and Mittag,
+    Florian and Matthes, Jakob and Rudolph, Jan and Wrzodek, Finja and Netz,
+    Eugen and Diamantikos, Alexander and Eichner, Johannes and Keller, Roland
+    and Wrzodek, Clemens and Fr\"ohlich, Sebastian and Lewis, Nathan E. and
+    Myers, Chris J. and {Le Nov\`{e}re}, Nicolas and Palsson, Bernhard {\O}. and
+    Hucka, Michael and Dr\"ager, Andreas},
+  title = {{JSBML 1.0: providing a smorgasbord of options to encode systems biology models}},
+  journal = {Bioinformatics},
+  year = {2015},
+  month = jun,
+  doi = {10.1093/bioinformatics/btv341},
+  abstract = {Summary: JSBML, the official pure Java programming library for the
+    SBML format, has evolved with the advent of different modeling formalisms in
+    systems biology and their ability to be exchanged and represented via
+    extensions of SBML. JSBML has matured into a major, active open-source
+    who not only maintain compatibility with SBML, but also drive steady
+    improvements to the Java interface and promote ease-of-use with end users.
+    
+    Availability: Source code, binaries and documentation for JSBML can be 
+    freely obtained under the terms of the LGPL 2.1 from the website
+    \url{http://sbml.org/Software/JSBML}.
+    
+    Supplementary Information: More information about JSBML can be found in the
+    user guide at \url{http://sbml.org/Software/JSBML/docs/}.
+    
+    Contact: \url{mailto:[email protected]}},
+  url = {http://bioinformatics.oxfordjournals.org/content/early/2015/06/15/bioinformatics.btv341},
+  eprint = {http://bioinformatics.oxfordjournals.org/content/early/2015/06/15/bioinformatics.btv341.full.pdf+html},
+}
 
 @Article{Arnold2011,
   Title                    = {A quantitative comparison of Calvin-Benson cycle models},
@@ -390,6 +472,14 @@ @TechReport{Finney2006
   Month                    = sep
 }
 
+@TechReport{Hucka2015,
+  Title = {{Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions}},
+  Author = {Hucka, Michael and Bergmann, Frank T. and Dr\"ager, Andreas and Hoops, Stefan and Keating, Sarah M. and Le Nov\`{e}re, Nicolas and Myers, Chris J. and Olivier, Brett G. and Sahle, Sven and Schaff, James C. and Smith, Lucian P. and Waltemath, Dagmar and Wilkinson, Darren J.},
+  Year = {2015},
+  Month = aug,
+  url = {http://sbml.org/Documents/Specifications#SBML_Level_2_Version_5}
+}
+
 @InProceedings{Funahashi2006,
   Title                    = {{CellDesigner: a modeling tool for biochemical networks}},
   Author                   = {Funahashi, Akira and Matsuoka, Yukiko and Jouraku, Akiya and Kitano, Hiroaki and Kikuchi, Norihiro},

examples/src/org/sbml/squeezer/test/MiniSBML.java

@@ -30,8 +30,8 @@
 import org.sbml.jsbml.Reaction;
 import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.SBMLException;
-import org.sbml.jsbml.SBMLWriter;
 import org.sbml.jsbml.Species;
+import org.sbml.jsbml.TidySBMLWriter;
 
 /**
  * 
@@ -55,7 +55,7 @@ public static void main(String[] args) throws SBMLException, XMLStreamException
     Reaction r = model.createReaction("r1");
     r.createReactant("s1ref", s1);
     r.createProduct("s2Ref", s2);
-    SBMLWriter.write(doc, System.out, ' ', (short) 2);
+    TidySBMLWriter.write(doc, System.out, ' ', (short) 2);
   }
 
 }

examples/src/org/sbml/squeezer/test/SABIORKApplication.java

@@ -39,7 +39,7 @@
 import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.SBMLException;
 import org.sbml.jsbml.SBMLReader;
-import org.sbml.jsbml.SBMLWriter;
+import org.sbml.jsbml.TidySBMLWriter;
 import org.sbml.squeezer.sabiork.wizard.SABIORKWizard;
 
 /**
@@ -81,7 +81,7 @@ public void actionPerformed(ActionEvent e) {
         }
         try {
           if (result != null) {
-            SBMLWriter.write(result, output, ' ', (short) 2);
+            TidySBMLWriter.write(result, output, ' ', (short) 2);
           }
         } catch (SBMLException e1) {
           e1.printStackTrace();
@@ -137,7 +137,7 @@ public static void main(String[] args) throws Throwable{
       isEntriesInsertedSince, dateSubmitted);
 
     // Save the changed document
-    SBMLWriter.write(doc, new File(args[1]), ' ', (short) 2);
+    TidySBMLWriter.write(doc, new File(args[1]), ' ', (short) 2);
   }
 
 }

examples/src/org/sbml/squeezer/test/SqueezeReaction.java

@@ -29,7 +29,7 @@
 import org.sbml.jsbml.Reaction;
 import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.SBMLReader;
-import org.sbml.jsbml.SBMLWriter;
+import org.sbml.jsbml.TidySBMLWriter;
 import org.sbml.squeezer.KineticLawGenerator;
 import org.sbml.squeezer.UnitConsistencyType;
 import org.sbml.squeezer.kinetics.ConvenienceKinetics;
@@ -70,7 +70,7 @@ public static void main(String args[]) throws Throwable {
     klg.storeKineticLaws();
 
     // Save the result in another file
-    SBMLWriter.write(doc, new File(args[1]), ' ', (short) 2);
+    TidySBMLWriter.write(doc, new File(args[1]), ' ', (short) 2);
   }
 
 }

resources/org/sbml/squeezer/resources/html/ReleaseNotes.html

@@ -39,15 +39,17 @@ <h2>Download of SBMLsquezeezer</h2>
 <h2>New Features</h2>
 
 <ul>
-    <li>SBMLsqueezer fully supports all Levels and Versions of <a href="http://sbml.org" target="blank">SBML</a> up to the
+    <li>SBMLsqueezer fully supports all Levels and Versions of <a href="http://sbml.org" target="_blank">SBML</a> up to the
         most recent specifications Level 2 Version 5 and Level 3 Version 1.</li>
-    <li>The <a href="http://www.celldesigner.org" target="blank">CellDesigner</a> plug-in version has been adapted to work with
+    <li>The <a href="http://www.celldesigner.org" target="_blank">CellDesigner</a> plug-in version has been adapted to work with
         version 4.4.</li>
-    <li>The <a href="http://www.garuda-alliance.org/" target="blank">Garuda</a> backend has been updated.</li>
-    <li>The report generator <a href="http://www.cogsys.cs.uni-tuebingen.de/software/SBML2LaTeX/" target="blank">SBML2LaTeX</a> has been updated and the new version
+    <li>The <a href="http://www.garuda-alliance.org/" target="_blank">Garuda</a> backend has been updated.</li>
+    <li>The report generator <a href="http://www.cogsys.cs.uni-tuebingen.de/software/SBML2LaTeX/" target="_blank">SBML2LaTeX</a> has been updated and the new version
         is now part of this release of SBMLsqueezer.</li>
-    <li>SBMLsqueezer comes with the most recent version of <a href="http://sbml.org/Software/JSBML" target="blank">JSBML</a> (<a href="http://sourceforge.net/p/jsbml/code/2354/" target="blank">revision 2354</a>),
+    <li>SBMLsqueezer comes with the most recent version of <a href="http://sbml.org/Software/JSBML" target="_blank">JSBML</a> (<a href="http://sourceforge.net/p/jsbml/code/2354/" target="_blank">revision 2354</a>),
         which can read all current extension packages.</li>
+    <li>Slightly improved <a href="http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsqueezer/doc/api/SBMLsqueezer2.1/" target="_blank">API documentation</a> and updated <a href="http://vg08.met.vgwort.de/na/d4b8e9ae1bed423884cea07e52756b43?l=http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsqueezer/doc/SBMLsqueezer2.1UsersGuide.pdf" target="_blank">Users' Guide</a>.</li>
+    <li>Correctly indented SBML output files.</li>
 </ul>
 
 <h2>Bug Fixes</h2>

src/org/sbml/squeezer/gui/SBMLsqueezerUI.java

@@ -208,7 +208,6 @@ public static void initImages() {
         "SBMLsqueezerIcon_64.png",
         "SBMLsqueezerIcon_32.png",
         "SBMLsqueezerIcon_16.png",
-        "SBMLsqueezerLogo_16.png",
         "SBMLsqueezerWatermark.png"
     };
     String prefix = "resources/img/";

src/org/sbml/squeezer/io/SqSBMLWriter.java

@@ -34,7 +34,7 @@
 import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.SBMLException;
 import org.sbml.jsbml.SBMLOutputConverter;
-import org.sbml.jsbml.SBMLWriter;
+import org.sbml.jsbml.TidySBMLWriter;
 import org.sbml.squeezer.util.Bundles;
 
 import de.zbit.util.ResourceManager;
@@ -92,7 +92,7 @@ public boolean writeSBML(Model object, String filename,
     // write SBML to file
     boolean success = true;
     try {
-      SBMLWriter.write(sbmlDocument, filename, programName, versionNumber);
+      TidySBMLWriter.write(sbmlDocument, filename, programName, versionNumber);
     } catch (XMLStreamException e) {
       success = false;
     }

src/org/sbml/squeezer/sabiork/AutomaticSearch.java

@@ -45,7 +45,7 @@
 import org.sbml.jsbml.Reaction;
 import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.SBMLReader;
-import org.sbml.jsbml.SBMLWriter;
+import org.sbml.jsbml.TidySBMLWriter;
 import org.sbml.jsbml.util.filters.CVTermFilter;
 import org.sbml.jsbml.xml.parsers.SBMLCoreParser;
 import org.sbml.squeezer.sabiork.util.WebServiceConnectException;
@@ -279,10 +279,11 @@ public static void automaticSearch(String rootFolder, String taxonomyFile, Strin
            */
           String outputFile = file.getAbsolutePath().replace("\\", "/")
               .replace(parentFolder, sabioRootFolder);
-          SBMLWriter.write(sbmlDocument, new File(outputFile), ' ', (short) 4);
+          // TODO: use SBMLio!
+          TidySBMLWriter.write(sbmlDocument, new File(outputFile), ' ', (short) 2);
         }
       }
-      writer.write(organism+"\t" + matched_Organism + "\t" + noKineticLawFound_Organism + "\t" + + matchingNotPossible_Organism + "\t" + noReactionID_Organism);
+      writer.write(organism + "\t" + matched_Organism + "\t" + noKineticLawFound_Organism + "\t" + + matchingNotPossible_Organism + "\t" + noReactionID_Organism);
       writer.newLine();
       writer.newLine();
 

test/org/sbml/squeezer/test/cases/GeneralizedMassActionTest.java

@@ -35,8 +35,8 @@
 import org.sbml.jsbml.Reaction;
 import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.SBMLException;
-import org.sbml.jsbml.SBMLWriter;
 import org.sbml.jsbml.Species;
+import org.sbml.jsbml.TidySBMLWriter;
 import org.sbml.jsbml.UnitDefinition;
 import org.sbml.squeezer.OptionsGeneral;
 import org.sbml.squeezer.ReactionType;
@@ -182,7 +182,7 @@ public Model initModel() {
 
     if (!printed) {
       try {
-        SBMLWriter.write(doc, System.out, ' ', (short) 2);
+        TidySBMLWriter.write(doc, System.out, ' ', (short) 2);
         System.out.println();
       } catch (SBMLException exc) {
         exc.printStackTrace();

test/org/sbml/squeezer/test/cases/ReversibleKinetics.java

@@ -29,8 +29,8 @@
 import org.sbml.jsbml.Model;
 import org.sbml.jsbml.Reaction;
 import org.sbml.jsbml.SBMLDocument;
-import org.sbml.jsbml.SBMLWriter;
 import org.sbml.jsbml.Species;
+import org.sbml.jsbml.TidySBMLWriter;
 import org.sbml.squeezer.UnitConsistencyType;
 import org.sbml.squeezer.kinetics.AdditiveModelLinear;
 import org.sbml.squeezer.kinetics.TypeStandardVersion;
@@ -91,7 +91,7 @@ public Model initModel() {
    */
   @Test
   public void testAdditiveLinear() throws Throwable{
-    SBMLWriter.write(model.getSBMLDocument(), System.out, ' ', (short) 2);
+    TidySBMLWriter.write(model.getSBMLDocument(), System.out, ' ', (short) 2);
     KineticLaw kl = klg.createKineticLaw(r1, AdditiveModelLinear.class, false, TypeStandardVersion.cat, UnitConsistencyType.concentration, 1d);
     test(r1, kl, "m_r1*(w_r1_p1*p1+w_r1_p2*p2+(b_r1+(v_r1_a1*a1+v_r1_k1*k1+v_r1_i1*i1)))");
   }