Several bug fixes and improvements:

* New version of JSBML with bug fix in compartment.
* New version of sysbio for improved logging.
* New identifiers.org resource in MIRIAM
* New command-line arguments for specifying flux coefficients and target
reaction identifiers
* Refactored parameters for the batch mode (internal class to handle all
the settings)
* Bug fix in logging in the SBMLFix class (former ModelFix).

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>

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