diff --git a/lib/jsbml-2472-incl-libs.jar b/lib/jsbml-2482-incl-libs.jar
similarity index 93%
rename from lib/jsbml-2472-incl-libs.jar
rename to lib/jsbml-2482-incl-libs.jar
index 663c09f3..608adcdb 100644
Binary files a/lib/jsbml-2472-incl-libs.jar and b/lib/jsbml-2482-incl-libs.jar differ
diff --git a/lib/sysbio-1388.jar b/lib/sysbio-1390.jar
similarity index 93%
rename from lib/sysbio-1388.jar
rename to lib/sysbio-1390.jar
index 2b5cab01..41eddc08 100644
Binary files a/lib/sysbio-1388.jar and b/lib/sysbio-1390.jar differ
diff --git a/pom.xml b/pom.xml
index fac1c4ea..5b5e5f7f 100644
--- a/pom.xml
+++ b/pom.xml
@@ -51,7 +51,7 @@
     <developer>
       <email>andraeger@eng.ucsd.edu</email>
       <name>Andreas Dräger</name>
-      <url>https://github.com/draeger</url>
+      <url>https://github.com/draeger/</url>
       <id>draeger</id>
     </developer>
   </developers>
@@ -73,14 +73,14 @@
       <!-- mvn install:install-file -Dfile=/path/to/jsbml.jar -DgroupId=org.sbml -DartifactId=JSBML -Dversion=REVISION_NUMBER -Dpackaging=jar -->
       <groupId>org.sbml</groupId>
       <artifactId>JSBML</artifactId>
-      <version>2472</version>
+      <version>2482</version>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <!-- mvn install:install-file -Dfile=/path/to/sysbio.jar -DgroupId=de.zbit -DartifactId=SysBio -Dversion=REVISION_NUMBER -Dpackaging=jar -->
       <groupId>de.zbit</groupId>
       <artifactId>SysBio</artifactId>
-      <version>1388</version> <!-- SVN revision -->
+      <version>1390</version> <!-- SVN revision -->
       <scope>compile</scope>
     </dependency>
     <dependency>
diff --git a/src/edu/ucsd/sbrg/bigg/MIRIAM.java b/src/edu/ucsd/sbrg/bigg/MIRIAM.java
index e92a1227..32b6f7bf 100644
--- a/src/edu/ucsd/sbrg/bigg/MIRIAM.java
+++ b/src/edu/ucsd/sbrg/bigg/MIRIAM.java
@@ -232,7 +232,7 @@ public enum MIRIAM {
        * http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=
        * TODO What is the actual pattern? Using any character!
        */
-      unipathway_reaction(pairOf("http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=", ".*")),
+      unipathway_reaction(pairOf(" http://identifiers.org/unipathway.reaction/", "^UCR\\d{5}$")),
       /**
        * UniPathway is a manually curated resource of enzyme-catalyzed and
        * spontaneous chemical reactions. It provides a hierarchical representation
diff --git a/src/edu/ucsd/sbrg/bigg/ModelPolisher.java b/src/edu/ucsd/sbrg/bigg/ModelPolisher.java
index 691da8e1..48ebddd9 100644
--- a/src/edu/ucsd/sbrg/bigg/ModelPolisher.java
+++ b/src/edu/ucsd/sbrg/bigg/ModelPolisher.java
@@ -57,9 +57,51 @@
 public class ModelPolisher extends Launcher {
 
   /**
-   * Generated serial version identifier.
+   * Helper class to store all parameters for running ModelPolisher in batch mode.
+   * 
+   * @author Andreas Dr&auml;ger
    */
-  private static final long serialVersionUID = 7745344693995142413L;
+  private static final class Parameters {
+    /**
+     * @see ModelPolisherOptions#CHECK_MASS_BALANCE
+     */
+    Boolean checkMassBalance = null;
+    /**
+     * @see ModelPolisherOptions#COMPRESSION_TYPE
+     */
+    Compression compression = Compression.NONE;
+    /**
+     * Can be {@code null}
+     * @see ModelPolisherOptions#DOCUMENT_NOTES_FILE
+     */
+    File documentNotesFile = null;
+    /**
+     * Can be {@code null} (then a default is used).
+     * @see ModelPolisherOptions#DOCUMENT_TITLE_PATTERN
+     */
+    String documentTitlePattern = null;
+    /**
+     * @see ModelPolisherOptions#FLUX_COEFFICIENTS
+     */
+    double[] fluxCoefficients = null;
+    /**
+     * @see ModelPolisherOptions#FLUX_OBJECTIVES
+     */
+    String[] fluxObjectives = null;
+    /**
+     * Can be {@code null}
+     * @see ModelPolisherOptions#MODEL_NOTES_FILE
+     */
+    File modelNotesFile = null;
+    /**
+     * @see ModelPolisherOptions#OMIT_GENERIC_TERMS
+     */
+    Boolean omitGenericTerms = null;
+    /**
+     * @see ModelPolisherOptions#SBML_VALIDATION
+     */
+    Boolean sbmlValidation = null;
+  }
 
   /**
    * Localization support.
@@ -71,6 +113,18 @@ public class ModelPolisher extends Launcher {
    */
   private static final transient Logger logger = Logger.getLogger(ModelPolisher.class.getName());
 
+  /**
+   * Generated serial version identifier.
+   */
+  private static final long serialVersionUID = 7745344693995142413L;
+
+  /**
+   * @param args
+   */
+  public static void main(String[] args) {
+    new ModelPolisher(args);
+  }
+
   /**
    * @param args
    */
@@ -78,6 +132,64 @@ public ModelPolisher(String... args) {
     super(args);
   }
 
+  /* (non-Javadoc)
+   * @see de.zbit.Launcher#addCopyrightToSplashScreen()
+   */
+  @Override
+  protected boolean addCopyrightToSplashScreen() {
+    return false;
+  }
+
+  /* (non-Javadoc)
+   * @see de.zbit.Launcher#addVersionNumberToSplashScreen()
+   */
+  @Override
+  protected boolean addVersionNumberToSplashScreen() {
+    return false;
+  }
+
+  /**
+   * 
+   * @param bigg
+   * @param input
+   * @param output
+   * @param parameters
+   * @throws IOException
+   * @throws XMLStreamException
+   */
+  public void batchProcess(BiGGDB bigg, File input, File output, Parameters parameters) throws IOException,
+  XMLStreamException {
+
+    if (!output.exists() && !output.isFile()
+        && !(input.isFile() && input.getName().equals(output.getName()))) {
+      logger.info(MessageFormat.format("Creating directory {0}.",
+        output.getAbsolutePath()));
+      output.mkdir();
+    }
+    if (input.isFile()) {
+      boolean matFile = SBFileFilter.hasFileType(input, SBFileFilter.FileType.MAT_FILES);
+      if (SBFileFilter.isSBMLFile(input) || matFile) {
+        if (output.isDirectory()) {
+          String fName = input.getName();
+          if (matFile) {
+            fName = FileTools.removeFileExtension(fName) + ".xml";
+          }
+          output = new File(Utils.ensureSlash(output.getAbsolutePath()) + fName);
+        }
+        polish(bigg, input, output, parameters);
+      }
+    } else {
+      if (!output.isDirectory()) {
+        throw new IOException(MessageFormat.format("Cannot write to file {0}.",
+          output.getAbsolutePath()));
+      }
+      for (File file : input.listFiles()) {
+        File target = new File(Utils.ensureSlash(output.getAbsolutePath()) + file.getName());
+        batchProcess(bigg, file, target, parameters);
+      }
+    }
+  }
+
   /* (non-Javadoc)
    * @see de.zbit.Launcher#commandLineMode(de.zbit.AppConf)
    */
@@ -90,6 +202,13 @@ public void commandLineMode(AppConf appConf) {
          * Formatter
          */
         OneLineFormatter formatter = new OneLineFormatter(false, false, false);
+        /* (non-Javadoc)
+         * @see java.util.logging.StreamHandler#flush()
+         */
+        @Override
+        public synchronized void flush() {
+          System.out.flush();
+        }
         /* (non-Javadoc)
          * @see java.util.logging.ConsoleHandler#publish(java.util.logging.LogRecord)
          */
@@ -105,13 +224,6 @@ public void publish(LogRecord record) {
             }
           }
         }
-        /* (non-Javadoc)
-         * @see java.util.logging.StreamHandler#flush()
-         */
-        @Override
-        public synchronized void flush() {
-          System.out.flush();
-        }
       }, getLogPackages());
     }
     try {
@@ -132,208 +244,44 @@ public synchronized void flush() {
         documentTitlePattern = args.getProperty(ModelPolisherOptions.DOCUMENT_TITLE_PATTERN);
       }
 
+      double[] coefficients = null;
+      if (args.containsKey(ModelPolisherOptions.FLUX_COEFFICIENTS)) {
+        String c = args.getProperty(ModelPolisherOptions.FLUX_COEFFICIENTS);
+        String coeff[] = c.substring(1, c.length() - 1).split(",");
+        coefficients = new double[coeff.length];
+        for (int i = 0; i < coeff.length; i++) {
+          coefficients[i] = Double.parseDouble(coeff[i].trim());
+        }
+      }
+      String fObj[] = null;
+      if (args.containsKey(ModelPolisherOptions.FLUX_OBJECTIVES)) {
+        String fObjectives = args.getProperty(ModelPolisherOptions.FLUX_OBJECTIVES);
+        fObj = fObjectives.substring(1, fObjectives.length() - 1).split(":");
+      }
+
+      Parameters parameters = new Parameters();
+      parameters.checkMassBalance = args.getBooleanProperty(ModelPolisherOptions.CHECK_MASS_BALANCE);
+      parameters.compression = ModelPolisherOptions.Compression.valueOf(args.getProperty(ModelPolisherOptions.COMPRESSION_TYPE));
+      parameters.documentNotesFile = documentNotesFile;
+      parameters.documentTitlePattern = documentTitlePattern;
+      parameters.fluxCoefficients = coefficients;
+      parameters.fluxObjectives = fObj;
+      parameters.modelNotesFile = modelNotesFile;
+      parameters.omitGenericTerms = args.getBooleanProperty(ModelPolisherOptions.OMIT_GENERIC_TERMS);
+      parameters.sbmlValidation = args.getBooleanProperty(ModelPolisherOptions.SBML_VALIDATION);
+
       // run polishing operations in background and parallel.
       batchProcess(bigg,
         new File(args.getProperty(IOOptions.INPUT)),
         new File(args.getProperty(IOOptions.OUTPUT)),
-        ModelPolisherOptions.Compression.valueOf(args.getProperty(ModelPolisherOptions.COMPRESSION_TYPE)),
-        args.getBooleanProperty(ModelPolisherOptions.OMIT_GENERIC_TERMS),
-        documentNotesFile, modelNotesFile, documentTitlePattern,
-        args.getBooleanProperty(ModelPolisherOptions.CHECK_MASS_BALANCE),
-        args.getBooleanProperty(ModelPolisherOptions.SBML_VALIDATION));
+        parameters);
+
 
     } catch (SBMLException | XMLStreamException | IOException | SQLException | ClassNotFoundException exc) {
       exc.printStackTrace();
     }
   }
 
-  /**
-   * Scans the given command-line options for a specific file option and returns
-   * the corresponding file if it exists, {@code null} otherwise.
-   * 
-   * @param args
-   *        command-line options.
-   * @param option
-   *        a specific file option to look for.
-   * @return a {@link File} object that corresponds to a desired command-line
-   *         option, or {@code null} if it does not exist.
-   */
-  private File parseFileOption(SBProperties args, Option<File> option) {
-    if (args.containsKey(option)) {
-      File notesFile = new File(args.getProperty(option));
-      if ((notesFile != null) && notesFile.exists() && notesFile.canRead()) {
-        return notesFile;
-      }
-    }
-    return null;
-  }
-
-  /**
-   * 
-   * @param bigg
-   * @param input
-   * @param output
-   * @param compressOutput !
-   * @param omitGenericTerms
-   * @param documentNotesFile can be {@code null}.
-   * @param modelNotesFile can be {@code null}.
-   * @param documentTitlePattern can be {@code null} (then a default is used).
-   * @param checkMassBalance
-   * @param validateOutput
-   * @throws XMLStreamException
-   * @throws IOException
-   */
-  public void polish(BiGGDB bigg, File input, File output,
-    Compression compressOutput, boolean omitGenericTerms,
-    File documentNotesFile, File modelNotesFile, String documentTitlePattern,
-    boolean checkMassBalance, boolean validateOutput)
-        throws XMLStreamException, IOException {
-    long time = System.currentTimeMillis();
-    logger.info(MessageFormat.format("Reading input file {0}.",
-      input.getAbsolutePath()));
-    SBMLDocument doc = null;
-    if (SBFileFilter.hasFileType(input, SBFileFilter.FileType.MAT_FILES)) {
-      doc = COBRAparser.read(input, omitGenericTerms);
-    } else {
-      doc = SBMLReader.read(input, new UpdateListener());
-    }
-    if (!doc.isSetLevelAndVersion()
-        || (doc.getLevelAndVersion().compareTo(ValuePair.of(3, 1)) < 0)) {
-      logger.info("Trying to convert the model to Level 3 Version 2.");
-      org.sbml.jsbml.util.SBMLtools.setLevelAndVersion(doc, 3, 1);
-    }
-    SBMLPolisher polisher = new SBMLPolisher(bigg);
-    polisher.setCheckMassBalance(checkMassBalance);
-    polisher.setOmitGenericTerms(omitGenericTerms);
-    if (documentNotesFile != null) {
-      polisher.setDocumentNotesFile(documentNotesFile);
-    }
-    if (modelNotesFile != null) {
-      polisher.setModelNotesFile(modelNotesFile);
-    }
-    if (documentTitlePattern != null) {
-      polisher.setDocumentTitlePattern(documentTitlePattern);
-    }
-    doc = polisher.polish(doc);
-    // <?xml-stylesheet type="text/xsl"
-    // href="/Users/draeger/Documents/workspace/BioNetView/resources/edu/ucsd/sbrg/bigg/bigg_sbml.xsl"?>
-    logger.info(MessageFormat.format("Writing output file {0}",
-      output.getAbsolutePath()));
-    TidySBMLWriter.write(doc, output, getClass().getSimpleName(),
-      getVersionNumber(), ' ', (short) 2);
-    // SBMLWriter.write(doc, sbmlFile, ' ', (short) 2);
-    if (compressOutput != Compression.NONE) {
-      String fileExtension = compressOutput.getFileExtension();
-      String archive = output.getAbsolutePath() + "." + fileExtension;
-      logger.info(MessageFormat.format("Packing archive file {0}", archive));
-      switch (compressOutput) {
-      case ZIP:
-        ZIPUtils.ZIPcompress(new String[] {output.getAbsolutePath()}, archive,
-          "SBML Archive", true);
-        break;
-      case GZIP:
-        ZIPUtils.GZip(output.getAbsolutePath(), archive);
-        break;
-      default:
-        break;
-      }
-      if (validateOutput) {
-        validate(archive);
-      }
-    }
-    time = System.currentTimeMillis() - time;
-    Calendar calendar = Calendar.getInstance();
-    calendar.setTimeInMillis(time);
-    logger.info(MessageFormat.format("Done ({0,time,ss.sss} s).",
-      calendar.getTime()));
-  }
-
-  /**
-   * 
-   * @param filename
-   */
-  private void validate(String filename) {
-    //org.sbml.jsbml.validator.SBMLValidator.main(new String[] {"-d", "p,u", compressedOutput});
-    String output = "xml";
-    String offcheck = "p,u";
-    HashMap<String, String> parameters = new HashMap<String, String>();
-    parameters.put("output", output);
-    parameters.put("offcheck", offcheck);
-
-    logger.info("Validating  " + filename + "\n");
-
-    SBMLErrorLog sbmlErrorLog = SBMLValidator.checkConsistency(filename, parameters);
-
-    if (sbmlErrorLog != null) {
-      logger.info(MessageFormat.format(
-        "There {0,choice,0#are no errors|1#is one error|1<are {0,number,integer} errors} in file {1}.",
-        sbmlErrorLog.getErrorCount(), filename));
-
-      // printErrors
-      for (int j = 0; j < sbmlErrorLog.getErrorCount(); j++) {
-        SBMLError error = sbmlErrorLog.getError(j);
-        logger.warning(error.toString());
-      }
-    } else {
-      logger.info("No SBML validation possible, process terminated with errors.");
-    }
-  }
-
-  /**
-   * 
-   * @param bigg
-   * @param input
-   * @param output
-   * @param compressOutput
-   * @param omitGenericTerms
-   * @param documentNotesFile can be {@code null}
-   * @param modelNotesFile can be {@code null}
-   * @param documentTitlePattern can be {@code null}
-   * @param validateOutput
-   * @param checkMassBalance
-   * @throws IOException
-   * @throws XMLStreamException
-   */
-  public void batchProcess(BiGGDB bigg, File input, File output,
-    ModelPolisherOptions.Compression compressOutput, boolean omitGenericTerms,
-    File documentNotesFile, File modelNotesFile, String documentTitlePattern,
-    boolean checkMassBalance, boolean validateOutput) throws IOException,
-    XMLStreamException {
-    if (!output.exists() && !output.isFile()
-        && !(input.isFile() && input.getName().equals(output.getName()))) {
-      logger.info(MessageFormat.format("Creating directory {0}.",
-        output.getAbsolutePath()));
-      output.mkdir();
-    }
-    if (input.isFile()) {
-      boolean matFile = SBFileFilter.hasFileType(input, SBFileFilter.FileType.MAT_FILES);
-      if (SBFileFilter.isSBMLFile(input) || matFile) {
-        if (output.isDirectory()) {
-          String fName = input.getName();
-          if (matFile) {
-            fName = FileTools.removeFileExtension(fName) + ".xml";
-          }
-          output = new File(Utils.ensureSlash(output.getAbsolutePath()) + fName);
-        }
-        polish(bigg, input, output, compressOutput, omitGenericTerms,
-          documentNotesFile, modelNotesFile, documentTitlePattern,
-          checkMassBalance, validateOutput);
-      }
-    } else {
-      if (!output.isDirectory()) {
-        throw new IOException(MessageFormat.format("Cannot write to file {0}.",
-          output.getAbsolutePath()));
-      }
-      for (File file : input.listFiles()) {
-        File target = new File(Utils.ensureSlash(output.getAbsolutePath())
-          + file.getName());
-        batchProcess(bigg, file, target, compressOutput, omitGenericTerms,
-          documentNotesFile, modelNotesFile, documentTitlePattern,
-          checkMassBalance, validateOutput);
-      }
-    }
-  }
-
   /* (non-Javadoc)
    * @see de.zbit.Launcher#getCitation(boolean)
    */
@@ -369,6 +317,14 @@ public List<Class<? extends KeyProvider>> getCmdLineOptions() {
     return options;
   }
 
+  /* (non-Javadoc)
+   * @see de.zbit.Launcher#getInstitute()
+   */
+  @Override
+  public String getInstitute() {
+    return baseBundle.getString("INSTITUTE");
+  }
+
   /* (non-Javadoc)
    * @see de.zbit.Launcher#getInteractiveOptions()
    */
@@ -380,14 +336,6 @@ public List<Class<? extends KeyProvider>> getInteractiveOptions() {
     return options;
   }
 
-  /* (non-Javadoc)
-   * @see de.zbit.Launcher#getInstitute()
-   */
-  @Override
-  public String getInstitute() {
-    return baseBundle.getString("INSTITUTE");
-  }
-
   /* (non-Javadoc)
    * @see de.zbit.Launcher#getLogPackages()
    */
@@ -441,22 +389,6 @@ public String getVersionNumber() {
     return version == null ? "?" : version;
   }
 
-  /* (non-Javadoc)
-   * @see de.zbit.Launcher#addCopyrightToSplashScreen()
-   */
-  @Override
-  protected boolean addCopyrightToSplashScreen() {
-    return false;
-  }
-
-  /* (non-Javadoc)
-   * @see de.zbit.Launcher#addVersionNumberToSplashScreen()
-   */
-  @Override
-  protected boolean addVersionNumberToSplashScreen() {
-    return false;
-  }
-
   /* (non-Javadoc)
    * @see de.zbit.Launcher#getYearOfProgramRelease()
    */
@@ -490,10 +422,126 @@ public Window initGUI(AppConf appConf) {
   }
 
   /**
+   * Scans the given command-line options for a specific file option and returns
+   * the corresponding file if it exists, {@code null} otherwise.
+   * 
    * @param args
+   *        command-line options.
+   * @param option
+   *        a specific file option to look for.
+   * @return a {@link File} object that corresponds to a desired command-line
+   *         option, or {@code null} if it does not exist.
    */
-  public static void main(String[] args) {
-    new ModelPolisher(args);
+  private File parseFileOption(SBProperties args, Option<File> option) {
+    if (args.containsKey(option)) {
+      File notesFile = new File(args.getProperty(option));
+      if ((notesFile != null) && notesFile.exists() && notesFile.canRead()) {
+        return notesFile;
+      }
+    }
+    return null;
+  }
+
+  /**
+   * 
+   * @param bigg
+   * @param input
+   * @param output
+   * @param parameters
+   * @throws XMLStreamException
+   * @throws IOException
+   */
+  public void polish(BiGGDB bigg, File input, File output, Parameters parameters)
+      throws XMLStreamException, IOException {
+    long time = System.currentTimeMillis();
+    logger.info(MessageFormat.format("Reading input file {0}.",
+      input.getAbsolutePath()));
+    SBMLDocument doc = null;
+    if (SBFileFilter.hasFileType(input, SBFileFilter.FileType.MAT_FILES)) {
+      doc = COBRAparser.read(input, parameters.omitGenericTerms);
+    } else {
+      doc = SBMLReader.read(input, new UpdateListener());
+    }
+    if (!doc.isSetLevelAndVersion()
+        || (doc.getLevelAndVersion().compareTo(ValuePair.of(3, 1)) < 0)) {
+      logger.info("Trying to convert the model to Level 3 Version 2.");
+      org.sbml.jsbml.util.SBMLtools.setLevelAndVersion(doc, 3, 1);
+    }
+    SBMLPolisher polisher = new SBMLPolisher(bigg);
+    polisher.setCheckMassBalance(parameters.checkMassBalance);
+    polisher.setOmitGenericTerms(parameters.omitGenericTerms);
+    if (parameters.documentNotesFile != null) {
+      polisher.setDocumentNotesFile(parameters.documentNotesFile);
+    }
+    if (parameters.modelNotesFile != null) {
+      polisher.setModelNotesFile(parameters.modelNotesFile);
+    }
+    if (parameters.documentTitlePattern != null) {
+      polisher.setDocumentTitlePattern(parameters.documentTitlePattern);
+    }
+    polisher.setFluxCoefficients(parameters.fluxCoefficients);
+    polisher.setFluxObjectives(parameters.fluxObjectives);
+    doc = polisher.polish(doc);
+    // <?xml-stylesheet type="text/xsl"
+    // href="/Users/draeger/Documents/workspace/BioNetView/resources/edu/ucsd/sbrg/bigg/bigg_sbml.xsl"?>
+    logger.info(MessageFormat.format("Writing output file {0}",
+      output.getAbsolutePath()));
+    TidySBMLWriter.write(doc, output, getClass().getSimpleName(), getVersionNumber(), ' ', (short) 2);
+    // SBMLWriter.write(doc, sbmlFile, ' ', (short) 2);
+    if (parameters.compression != Compression.NONE) {
+      String fileExtension = parameters.compression.getFileExtension();
+      String archive = output.getAbsolutePath() + "." + fileExtension;
+      logger.info(MessageFormat.format("Packing archive file {0}", archive));
+      switch (parameters.compression) {
+      case ZIP:
+        ZIPUtils.ZIPcompress(new String[] {output.getAbsolutePath()}, archive,
+          "SBML Archive", true);
+        break;
+      case GZIP:
+        ZIPUtils.GZip(output.getAbsolutePath(), archive);
+        break;
+      default:
+        break;
+      }
+      if ((parameters.sbmlValidation != null) && parameters.sbmlValidation) {
+        validate(archive);
+      }
+    }
+    time = System.currentTimeMillis() - time;
+    Calendar calendar = Calendar.getInstance();
+    calendar.setTimeInMillis(time);
+    logger.info(MessageFormat.format("Done ({0,time,ss.sss} s).", calendar.getTime()));
+  }
+
+  /**
+   * 
+   * @param filename
+   */
+  private void validate(String filename) {
+    //org.sbml.jsbml.validator.SBMLValidator.main(new String[] {"-d", "p,u", compressedOutput});
+    String output = "xml";
+    String offcheck = "p,u";
+    HashMap<String, String> parameters = new HashMap<String, String>();
+    parameters.put("output", output);
+    parameters.put("offcheck", offcheck);
+
+    logger.info("Validating  " + filename + "\n");
+
+    SBMLErrorLog sbmlErrorLog = SBMLValidator.checkConsistency(filename, parameters);
+
+    if (sbmlErrorLog != null) {
+      logger.info(MessageFormat.format(
+        "There {0,choice,0#are no errors|1#is one error|1<are {0,number,integer} errors} in file {1}.",
+        sbmlErrorLog.getErrorCount(), filename));
+
+      // printErrors
+      for (int j = 0; j < sbmlErrorLog.getErrorCount(); j++) {
+        SBMLError error = sbmlErrorLog.getError(j);
+        logger.warning(error.toString());
+      }
+    } else {
+      logger.info("No SBML validation possible, process terminated with errors.");
+    }
   }
 
 }
diff --git a/src/edu/ucsd/sbrg/bigg/ModelPolisherOptions.java b/src/edu/ucsd/sbrg/bigg/ModelPolisherOptions.java
index ca82e6af..a91b97f6 100644
--- a/src/edu/ucsd/sbrg/bigg/ModelPolisherOptions.java
+++ b/src/edu/ucsd/sbrg/bigg/ModelPolisherOptions.java
@@ -78,6 +78,26 @@ public String getFileExtension() {
       "When set to true, the mass balance of each reaction will be checked where possible. Reactions that are recognized as peudoreactions are excluded from this check, also are reactions that lack information about elementary composition of their participants.",
       Boolean.TRUE);
 
+  /**
+   * 
+   */
+  @SuppressWarnings("unchecked")
+  public static final Option<Double[]> FLUX_COEFFICIENTS = new Option<Double[]>(
+      "FLUX_COEFFICIENTS",
+      (Class<Double[]>) (new Double[0]).getClass(),
+      "The flux coefficients, a comma-separated list",
+      new Double[0]);
+
+  /**
+   * 
+   */
+  @SuppressWarnings("unchecked")
+  public static final Option<String[]> FLUX_OBJECTIVES = new Option<String[]>(
+      "FLUX_OBJECTIVES",
+      (Class<String[]>) (new String[0]).getClass(),
+      "The flux objectives, a colon-separated list",
+      new String[0]);
+
   /**
    * Decides whether or not the output file should directly be compressed and if
    * so, which archive type should be used.
diff --git a/src/edu/ucsd/sbrg/bigg/SBMLPolisher.java b/src/edu/ucsd/sbrg/bigg/SBMLPolisher.java
index 1c57eb3b..8468e995 100644
--- a/src/edu/ucsd/sbrg/bigg/SBMLPolisher.java
+++ b/src/edu/ucsd/sbrg/bigg/SBMLPolisher.java
@@ -156,6 +156,14 @@ public class SBMLPolisher {
    * 
    */
   private String documentNotesFile = "SBMLDocumentNotes.html";
+  /**
+   * 
+   */
+  private double[] fluxCoefficients;
+  /**
+   * 
+   */
+  private String[] fluxObjectives;
 
   /**
    * @param bigg
@@ -349,6 +357,10 @@ public void polish(Compartment c) {
     }
     if (!c.isSetUnits()) {
       // TODO: set compartment units.
+      /*
+       * This is a temporary solution until we agree on something better.
+       */
+      c.setUnits(Unit.Kind.DIMENSIONLESS);
     }
   }
   /**
@@ -1017,7 +1029,7 @@ public boolean polishListOfObjectives(boolean strict, FBCModelPlugin modelPlug)
         progress.DisplayBar(); //"Processing objective " + objective.getId());
         if (!objective.isSetListOfFluxObjectives()) {
           Model model = modelPlug.getParent();
-          strict &= SBMLFix.fixObjective(model.getId(), model.getListOfReactions(), modelPlug);
+          strict &= SBMLFix.fixObjective(model.getId(), model.getListOfReactions(), modelPlug, fluxCoefficients, fluxObjectives);
         }
         if (objective.isSetListOfFluxObjectives()) {
           strict &= polishListOfFluxObjectives(strict, objective);
@@ -1221,4 +1233,20 @@ public void setDocumentNotesFile(File documentNotesFile) {
     this.documentNotesFile = documentNotesFile.getAbsolutePath();
   }
 
+  /**
+   * 
+   * @param fluxCoefficients
+   */
+  public void setFluxCoefficients(double[] fluxCoefficients) {
+    this.fluxCoefficients = fluxCoefficients;
+  }
+
+  /**
+   * 
+   * @param fluxObjectives
+   */
+  public void setFluxObjectives(String[] fluxObjectives) {
+    this.fluxObjectives = fluxObjectives;
+  }
+
 }
diff --git a/src/edu/ucsd/sbrg/cobra/ModelFields.java b/src/edu/ucsd/sbrg/cobra/ModelFields.java
index 48efba9c..97c2d36c 100644
--- a/src/edu/ucsd/sbrg/cobra/ModelFields.java
+++ b/src/edu/ucsd/sbrg/cobra/ModelFields.java
@@ -31,6 +31,8 @@ public enum ModelFields {
    * If this cannot be expressed in SBML, then an error message would be
    * appropriate. The SBML file would probably not result in a functional joined
    * model though.
+   * <p>
+   * Data type: double array. Length must be identical to the number of reactions.
    */
   b,
   /**
@@ -41,7 +43,13 @@ public enum ModelFields {
    */
   B,
   /**
-   * The objective function vector for max(<i>c' &sdot; v</i>)
+   * The objective function vector for max(<i>c' &sdot; v</i>). The dimension
+   * of this element must be identical to the number of reactions. Dimensions
+   * that have a zero value in this field, do not contribute to the objective
+   * function.
+   * <p>
+   * Data type: double array.
+   * Corresponds to {@link FluxObjective#getCoefficient()}.
    */
   c,
   /**
@@ -80,7 +88,8 @@ public enum ModelFields {
    */
   disabled,
   /**
-   * The Enzyme Commission codes for the reactions.
+   * The Enzyme Commission codes for the reactions. Length must be identical to
+   * the number of reactions.
    */
   ecNumbers,
   /**
@@ -92,7 +101,8 @@ public enum ModelFields {
    */
   geneindex,
   /**
-   * The gene products.
+   * The list of gene in the model, where each contained gene corresponds to a
+   * {@link GeneProduct#getId()}. Data type: cell array of string.
    */
   genes,
   /**
@@ -100,7 +110,9 @@ public enum ModelFields {
    */
   genesource,
   /**
-   * 
+   * Boolean GPR rules (AND/OR). Data type: cell array of strings.
+   * Example: {@code (8639.1) or (26.1) or (314.2) or (314.1)}. Dimensions must
+   * be identical to the number of reactions. Corresponds to {@link GeneProductAssociation}
    */
   grRules,
   /**
@@ -108,39 +120,50 @@ public enum ModelFields {
    */
   lb,
   /**
-   * Must have same dimension as {@link #mets}.
+   * Must have same dimension as {@link #mets}. Data type: double array.
+   * For SBML Level < 3, it corresponds to {@link Species#getCharge()}. Since
+   * Level 3, it corresponds to {@link FBCSpeciesPlugin#getCharge()}.
    */
   metCharge,
   /**
    * Optional: if present, it must have same dimension as {@link #mets}.
+   * Data type: cell array of strings. Corresponds to the annotation of
+   * {@link Species}
    */
   metCHEBIID,
   /**
    * Chemical formulas for metabolites, must have same dimension as {@link #mets}.
+   * Datatype: cell array of strings. Corresponds to {@link FBCSpeciesPlugin#getChemicalFormula()}.
    */
   metFormulas,
   /**
    * Optional: if present, it must have same dimension as {@link #mets}.
+   * Data type: cell array of strings.
    */
   metHMDB,
   /**
    * Optional: if present, it must have same dimension as {@link #mets}.
+   * Data type: cell array of strings.
    */
   metInchiString,
   /**
    * Optional: if present, it must have same dimension as {@link #mets}.
+   * Data type: cell array of strings.
    */
   metKeggID,
   /**
-   * Descriptive metabolite names, must have same dimension as {@link #mets}
+   * Descriptive metabolite names, must have same dimension as {@link #mets}.
+   * Datatype: cell array of strings. Corresponds to {@link Species#getName()}
    */
   metNames,
   /**
    * Optional: if present, it must have same dimension as {@link #mets}.
+   * Data type: cell array of strings.
    */
   metPubChemID,
   /**
-   * Metabolite BiGG ids (incl. compartment code)
+   * Metabolite BiGG ids (incl. compartment code). Data type: cell array of
+   * strings. Corresponds to {@link Species#getId()}.
    */
   mets,
   /**
@@ -168,6 +191,8 @@ public enum ModelFields {
   /**
    * A vector consisting of zeros and ones that translate to binary and determine
    * if the corresponding reaction of that index is reversible (1) or not (0).
+   * Dimensions must be equal to the number of reactions. Corresponds to the
+   * value {@linkReaction#isReversible()}
    */
   rev,
   /**
@@ -175,21 +200,58 @@ public enum ModelFields {
    */
   rules,
   /**
-   * 
+   * Cell array of strings, can any value in a range of 0 to 4. Length must be
+   * equal to the number of reactions.
+   */
+  rxnConfidenceEcoIDA,
+  /**
+   * @see #confidenceScores.
+   */
+  rxnConfidenceScores,
+  /**
+   * The Systems Biology Ontology Term to describe the role of a reaction.
+   * Length must be identical to the number of reactions. Value corresponds to
+   * the attribute {@link Reaction#getSBOTerm()}
+   */
+  rxnsboTerm,
+  /**
+   * A matrix with rows corresponding to reaction list and columns corresponding
+   * to gene list. Data type: sparse double. Size of this matrix must be number
+   * of reactions times number of genes. No counterpart in FBC v2.
    */
   rxnGeneMat,
   /**
    * Reaction identifiers in KEGG, but sometimes also contains {@link #ecNumbers}.
+   * Length must be identical to the number of reactions. Entries belong to the
+   * annotation of {@link Reaction}.
    */
   rxnKeggID,
   /**
-   * Descriptive reaction names
+   * Descriptive reaction names, length must be identical to the number of
+   * reactions. Data type: cell array of string. Corresponds to the name of a
+   * {@link Reaction}.
    */
   rxnNames,
   /**
-   * Reaction BiGG ids
+   * @see #ecNumbers
+   */
+  rxnECNumbers,
+  /**
+   * Example:
+   * <pre>
+   * 'Na coupled transport of pyruvate, lactate, and short chain fatty acids, i.e., acetate, propionate, and butyrate mediated by SMCT1
+   * </pre>
+   */
+  rxnReferences,
+  /**
+   * Reaction BiGG ids. Corresponds to the id of {@link Reaction}.
    */
   rxns,
+  /**
+   * Cell array of strings. Text notes (description) about reactions. Length
+   * must be identical to the number of reactions.
+   */
+  rxnNotes,
   /**
    * Stoichiometric matrix
    */
@@ -198,6 +260,9 @@ public enum ModelFields {
    * This defines groups of reactions that belong to a common reaction subsystem.
    * Their number must hence be identical to the reaction count. Subsystems are
    * listed repeatedly in the source file.
+   * If present, the size of this field must be identical to the number of
+   * reactions.
+   * Data type: cell array of strings.
    */
   subSystems,
   /**
diff --git a/src/edu/ucsd/sbrg/util/SBMLFix.java b/src/edu/ucsd/sbrg/util/SBMLFix.java
index 40aad6e2..612009ee 100644
--- a/src/edu/ucsd/sbrg/util/SBMLFix.java
+++ b/src/edu/ucsd/sbrg/util/SBMLFix.java
@@ -56,7 +56,7 @@ public class SBMLFix {
   /**
    * A {@link Logger} for this class.
    */
-  private static final transient Logger logger = Logger.getLogger(SBMLFix.class.getSimpleName());
+  private static final transient Logger logger = Logger.getLogger(SBMLFix.class.getName());
 
   /**
    * 
@@ -143,6 +143,21 @@ public static void fixObjective(String modelDescriptor, Model model) {
    */
   public static boolean fixObjective(String modelDescriptor, ListOf<Reaction> listOfReactions,
     FBCModelPlugin fbcPlug) {
+    return fixObjective(modelDescriptor, listOfReactions, fbcPlug, null, null);
+  }
+
+  /**
+   * 
+   * @param modelDescriptor
+   * @param listOfReactions
+   * @param fbcPlug
+   * @param fluxCoefficients
+   * @param fluxObjectives
+   * @return
+   */
+  public static boolean fixObjective(String modelDescriptor,
+    ListOf<Reaction> listOfReactions, FBCModelPlugin fbcPlug, double[] fluxCoefficients,
+    String[] fluxObjectives) {
     Objective activeObjective = null;
     if (!fbcPlug.isSetActiveObjective()) {
       logger.severe(MessageFormat.format(
@@ -165,20 +180,42 @@ public static boolean fixObjective(String modelDescriptor, ListOf<Reaction> list
           "Trying to identify missing flux objective from model in model {0}.",
           modelDescriptor));
         if (listOfReactions != null) {
-          final Pattern pattern = SBMLPolisher.PATTERN_BIOMASS_CASE_INSENSITIVE;
-          Reaction rBiomass = listOfReactions.firstHit((obj) -> {
-            return (obj instanceof Reaction) && pattern.matcher(((Reaction) obj).getId()).matches();
-          });
-          if (rBiomass != null) {
-            logger.info(MessageFormat.format(
-              "Added biomass function {0} with coefficient {1,number} to model {2}.",
-              rBiomass.getId(), DEFAULT_COEFFICIENT, modelDescriptor));
-            o.createFluxObjective(null, null, DEFAULT_COEFFICIENT, rBiomass);
-
-            return true;
+          if (fluxObjectives != null) {
+            /*
+             * An array of target reactions is provided. We want to use this as flux objectives.
+             */
+            boolean strict = false;
+            for (int i = 0; i < fluxObjectives.length; i++) {
+              final String id = fluxObjectives[i];
+              Reaction r = listOfReactions.firstHit((obj) -> {
+                return (obj instanceof Reaction) && id.equals(((Reaction) obj).getId());
+              });
+              if (r != null) {
+                createFluxObjective(modelDescriptor, r, fluxCoefficients, o, i);
+                // if at least one flux objective exists, the model qualifies as strict model.
+                strict = true;
+              } else {
+                logger.severe(MessageFormat.format(
+                  "Operation failed! Could not identify reaction ''{0}'' in model {1}.",
+                  id, modelDescriptor));
+              }
+            }
+            return strict;
 
           } else {
-            logger.severe("Operation failed! Could not identify biomass reaction.");
+            /*
+             * Search for biomass reaction in the model and use this as objective.
+             */
+            final Pattern pattern = SBMLPolisher.PATTERN_BIOMASS_CASE_INSENSITIVE;
+            Reaction rBiomass = listOfReactions.firstHit((obj) -> {
+              return (obj instanceof Reaction) && pattern.matcher(((Reaction) obj).getId()).matches();
+            });
+            if (rBiomass != null) {
+              createFluxObjective(modelDescriptor, rBiomass, fluxCoefficients, o, 0);
+              return true;
+            } else {
+              logger.severe("Operation failed! Could not identify biomass reaction.");
+            }
           }
         } else {
           logger.severe(MessageFormat.format(
@@ -191,6 +228,26 @@ public static boolean fixObjective(String modelDescriptor, ListOf<Reaction> list
     return false;
   }
 
+  /**
+   * 
+   * @param modelDescriptor
+   * @param r
+   * @param fluxCoefficients
+   * @param o
+   * @param i
+   */
+  private static void createFluxObjective(String modelDescriptor,
+    Reaction r, double[] fluxCoefficients, Objective o, int i) {
+    double coeff = DEFAULT_COEFFICIENT;
+    if ((fluxCoefficients != null) && (fluxCoefficients.length > i)) {
+      coeff = fluxCoefficients[i];
+    }
+    logger.info(MessageFormat.format(
+      "Added flux objective for reaction ''{0}'' with coefficient {1,number} to model {2}.",
+      r.getId(), coeff, modelDescriptor));
+    o.createFluxObjective(null, null, coeff, r);
+  }
+
   /**
    * 
    * @param in