diff --git a/CHANGELOG b/CHANGELOG
index 3a90d38ee1cb0ccf1dbf70f473d230b2c811f89c..a40bc79c254fbc39973f14dd438963155203759d 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -4,6 +4,16 @@ minerva (15.0.0~beta.3) unstable; urgency=medium
     name was empty (#1147)
   * Bug fix: flybase and pato annotations from CellDesigner were not picked
     (#1113)
+  * Bug fix: invalid data overlays in uploaded zip file created "valid" project
+    that could not be opened (#1086)
+  * Bug fix: export to GPML preserves font color of compartments (#1111)
+  * Bug fix: export to GPML preserves information about hypotetical complexes
+    (#1111)
+  * Bug fix: export to GPML preserves complex name (#1111)
+  * Bug fix: export to GPML preserves reaction color (#1111)
+  * Bug fix: modification residues are exported to gpml (#1111)
+  * Bug fix: information about reaction reversibility is exported to gpml
+    (#1111)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 1 Apr 2020 14:00:00 +0200
 
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/DataNodeParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/DataNodeParser.java
index 82812c02c67cc4045e5dc080c987a051a4801716..6e9c6263d26813655a9ab3774d5d402a32fa6c2b 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/DataNodeParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/DataNodeParser.java
@@ -111,12 +111,12 @@ public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
   }
 
   @Override
-  public String toXml(DataNode node) throws ConverterException {
+  public String toXml(DataNode node, LogMarker logMarker) throws ConverterException {
     throw new NotImplementedException();
   }
 
   @Override
-  public String toXml(Collection<DataNode> list) throws ConverterException {
+  public String toXml(Collection<DataNode> list, LogMarker logMarker) throws ConverterException {
     throw new NotImplementedException();
   }
 
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParser.java
index a3553184d0fcb1998a8585156578a2aab225755e..a667ea8a9c63aae4c5f3e502912470a5e5c61780 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeLineParser.java
@@ -10,6 +10,7 @@ import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.LogMarker;
 import lcsb.mapviewer.wikipathway.model.Edge;
 
 /**
@@ -86,12 +87,12 @@ public class EdgeLineParser extends ElementGpmlParser<Edge> {
   }
 
   @Override
-  public String toXml(Edge node) throws ConverterException {
+  public String toXml(Edge node, LogMarker logMarker) throws ConverterException {
     throw new NotImplementedException();
   }
 
   @Override
-  public String toXml(Collection<Edge> list) throws ConverterException {
+  public String toXml(Collection<Edge> list, LogMarker logMarker) throws ConverterException {
     throw new NotImplementedException();
   }
 }
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java
index 08edc2dc63c815b9f6f7b96dfd571f2b77f3db3e..5f7c411c7f8abcf7e0b7bb7c851d5d20175e3fde 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/EdgeParser.java
@@ -139,12 +139,12 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
   }
 
   @Override
-  public String toXml(Edge node) throws ConverterException {
+  public String toXml(Edge node, LogMarker logMarker) throws ConverterException {
     throw new NotImplementedException();
   }
 
   @Override
-  public String toXml(Collection<Edge> list) throws ConverterException {
+  public String toXml(Collection<Edge> list, LogMarker logMarker) throws ConverterException {
     throw new NotImplementedException();
   }
 
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParser.java
index 3e354316d2715b44a6d9f238cfd3bb791098f728..783de3cbb46481670e477aff3f4fa80231937794 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ElementGpmlParser.java
@@ -10,6 +10,7 @@ import org.w3c.dom.*;
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.LogMarker;
 
 /**
  * Generic parser for GPML xml structures.
@@ -57,7 +58,7 @@ public abstract class ElementGpmlParser<T> {
    * @throws ConverterException
    *           thrown when there is a problem with converting into xml
    */
-  public abstract String toXml(T object) throws ConverterException;
+  public abstract String toXml(T object, LogMarker logMarker) throws ConverterException;
 
   /**
    * Converts list of objects into xml string (in GPML format) representing this
@@ -69,7 +70,7 @@ public abstract class ElementGpmlParser<T> {
    * @throws ConverterException
    *           thrown when there is a problem with converting into xml
    */
-  public abstract String toXml(Collection<T> list) throws ConverterException;
+  public abstract String toXml(Collection<T> list, LogMarker logMarker) throws ConverterException;
 
   /**
    * Creates list of object from list of xml nodes.
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
index 5076795b41d5d51850acc581116bfe815151858b..67221ef6315bd0ade84a710c9be94ad5db76dc65 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
@@ -133,7 +133,7 @@ public class GpmlParser {
    * @throws UnknownAttributeValueException
    *           thrown when there is a problem with xml attributes
    */
-  protected void addGroups(List<Node> groups, Graph graph) throws UnknownAttributeValueException {
+  protected void addGroups(List<Node> groups, Graph graph) throws ConverterException {
     // Adding Groups to graph
     for (Node nNode : groups) {
       if (nNode.getNodeType() == Node.ELEMENT_NODE) {
@@ -143,24 +143,46 @@ public class GpmlParser {
         if (graphId.equals("") || graphId == null) {
           graphId = groupId;
         }
-        String style = eElement.getAttribute("Style");
-        if ("".equals(style)) {
-          style = null;
-        }
-        if (style != null &&
-            !"Complex".equalsIgnoreCase(style) &&
-            !"Pathway".equalsIgnoreCase(style) &&
-            !"Group".equalsIgnoreCase(style)) {
-          throw new UnknownAttributeValueException(
-              "Unknown value of \"style\" attribute for group node: " + style
-                  + ". Only null, Complex, Group are supported.");
-        }
+
         Group group = new Group(graphId, groupId, graph.getMapName());
-        group.setStyle(style);
 
-        String zIndex = eElement.getAttribute("ZOrder");
-        if (zIndex != null && !zIndex.isEmpty()) {
-          group.setzOrder(Integer.valueOf(zIndex));
+        NamedNodeMap attributes = eElement.getAttributes();
+        for (int i = 0; i < attributes.getLength(); i++) {
+          String value = attributes.item(i).getTextContent();
+          switch (attributes.item(i).getNodeName()) {
+          case ("GraphId"):
+          case ("GroupId"):
+            break;
+          case ("GroupRef"):
+            group.setGroupRef(value);
+            break;
+          case ("BiopaxRef"):
+            group.addBiopaxReference(value);
+            break;
+          case ("TextLabel"):
+            group.setTextLabel(value);
+            break;
+          case ("ZOrder"):
+            if (!value.isEmpty()) {
+              group.setzOrder(Integer.valueOf(value));
+            }
+          case ("Style"):
+            if (!"".equals(value)) {
+              if (!"Complex".equalsIgnoreCase(value) &&
+                  !"Pathway".equalsIgnoreCase(value) &&
+                  !"Group".equalsIgnoreCase(value)) {
+                throw new UnknownAttributeValueException(
+                    "Unknown value of \"style\" attribute for group node: " + value
+                        + ". Only null, Complex, Group are supported.");
+              }
+              group.setStyle(value);
+            }
+            break;
+          default:
+            logger.warn(group.getLogMarker(),
+                "Unknown sub-node of " + eElement.getNodeName() + " node: " + eElement.getNodeName());
+            break;
+          }
         }
         graph.addGroup(group);
       }
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java
index 72f63ca3a92104577623a3d0a3255209cd97244a..a003e34d460ef55c3fa7265adf5127b84a1d2e1e 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/LabelParser.java
@@ -102,12 +102,12 @@ public class LabelParser extends GraphicalPathwayElementParser<Label> {
   }
 
   @Override
-  public String toXml(Label node) throws ConverterException {
+  public String toXml(Label node, LogMarker logMarker) throws ConverterException {
     throw new NotImplementedException();
   }
 
   @Override
-  public String toXml(Collection<Label> list) throws ConverterException {
+  public String toXml(Collection<Label> list, LogMarker logMarker) throws ConverterException {
     throw new NotImplementedException();
   }
 
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
index 0257396293be80a15d372697ac92ebb2e8939fbd..48f47a774d49d4ee069c76e2354fc357ff7e2371 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
@@ -13,7 +13,6 @@ import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
 import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
 import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionLineData;
 import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
@@ -100,39 +99,39 @@ public class ModelContructor {
    * @return {@link Species} created from input {@link DataNode}
    */
   protected Species createSpecies(DataNode dataNode) {
-    Species res = null;
+    Species species = null;
     String type = dataNode.getType();
     if (type == null || type.equals("")) {
       type = null;
     }
 
     if (type != null && type.equalsIgnoreCase("Metabolite")) {
-      res = new SimpleMolecule(dataNode.getGraphId());
+      species = new SimpleMolecule(dataNode.getGraphId());
     } else if (type != null && type.equalsIgnoreCase("GeneProduct")) {
-      res = new Gene(dataNode.getGraphId());
+      species = new Gene(dataNode.getGraphId());
     } else if (type != null && type.equalsIgnoreCase("Pathway")) {
-      res = new Phenotype(dataNode.getGraphId());
+      species = new Phenotype(dataNode.getGraphId());
     } else if (type != null && type.equalsIgnoreCase("Rna")) {
-      res = new Rna(dataNode.getGraphId());
+      species = new Rna(dataNode.getGraphId());
     } else if (type != null && type.equalsIgnoreCase("Protein")) {
-      res = new GenericProtein(dataNode.getGraphId());
+      species = new GenericProtein(dataNode.getGraphId());
     } else if (type != null && type.equalsIgnoreCase("Complex")) {
-      res = new Complex(dataNode.getGraphId());
+      species = new Complex(dataNode.getGraphId());
     } else if (type != null && type.equalsIgnoreCase("None")) {
-      res = new Unknown(dataNode.getGraphId());
+      species = new Unknown(dataNode.getGraphId());
     } else {
       logger.warn(dataNode.getLogMarker(), "Unknown species type: " + type + ". Using Unknown");
-      res = new Unknown(dataNode.getGraphId());
+      species = new Unknown(dataNode.getGraphId());
     }
 
-    res.addMiriamData(dataNode.getReferences());
-    res.setName(dataNode.getName());
+    species.addMiriamData(dataNode.getReferences());
+    species.setName(dataNode.getName());
     StringBuilder notes = new StringBuilder();
     for (String comment : dataNode.getComments()) {
       notes.append(comment + "\n\n");
     }
-    res.setNotes(notes.toString());
-    return res;
+    species.setNotes(notes.toString());
+    return species;
   }
 
   /**
@@ -158,7 +157,7 @@ public class ModelContructor {
         ((Complex) element).setHypothetical(true);
       }
 
-      element.setName(group.getGraphId());
+      element.setName(group.getName());
 
       Rectangle2D rec = group.getRectangle();
       if (rec == null) {
@@ -539,15 +538,15 @@ public class ModelContructor {
   private Species createSpecies(Label label) {
     logger.warn(label.getLogMarker(), " Label cannot be part of reaction. Tranforming to Unknown");
 
-    Species res = new Unknown(label.getGraphId());
-    res.addMiriamData(label.getReferences());
-    res.setName(label.getName());
+    Unknown unknown = new Unknown(label.getGraphId());
+    unknown.addMiriamData(label.getReferences());
+    unknown.setName(label.getName());
     StringBuilder notes = new StringBuilder();
     for (String comment : label.getComments()) {
       notes.append(comment + "\n\n");
     }
-    res.setNotes(notes.toString());
-    return res;
+    unknown.setNotes(notes.toString());
+    return unknown;
   }
 
   /**
@@ -560,14 +559,14 @@ public class ModelContructor {
   private Species createSpecies(Shape shape) {
     logger.warn(shape.getLogMarker(), " Shape can not be part of reaction. Tranforming to Unknown");
 
-    Species res = new Unknown(shape.getGraphId());
+    Unknown unknown = new Unknown(shape.getGraphId());
     StringBuilder notes = new StringBuilder();
     for (String comment : shape.getComments()) {
       notes.append(comment + "\n\n");
     }
-    res.setNotes(notes.toString());
-    res.setName(shape.getName());
-    return res;
+    unknown.setNotes(notes.toString());
+    unknown.setName(shape.getName());
+    return unknown;
   }
 
   /**
@@ -608,7 +607,7 @@ public class ModelContructor {
         } else if (graph.getLabelByGraphId(pe.getGraphId()) != null) {
           Label label = graph.getLabelByGraphId(pe.getGraphId());
           // if complex has generic name then change it into label
-          if (parent.getName().equals(group.getGraphId())) {
+          if (parent.getName().equals(group.getGraphId()) || parent.getName().trim().isEmpty()) {
             parent.setName(label.getTextLabel());
             parent.setNamePoint(label.getRectangle().getCenterX(), label.getRectangle().getCenterY());
             parent.setNameHorizontalAlign(HorizontalAlign.CENTER);
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
index 92044659777a9c81392c5d0ed05a3ab2c50c8054..64175434840ea4c2b1b415deaccf4abcff050a62 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
@@ -12,6 +12,8 @@ import org.apache.logging.log4j.Logger;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.geometry.ColorParser;
 import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
@@ -20,6 +22,7 @@ import lcsb.mapviewer.model.map.compartment.OvalCompartment;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.reaction.*;
 import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.map.species.field.*;
 import lcsb.mapviewer.wikipathway.utils.Geo;
 
 /**
@@ -285,36 +288,41 @@ public class ModelToGPML {
    * @return String that encodes all compartments in GPML format
    */
   private String getComparments(Model model) {
-    StringBuilder comparments = new StringBuilder("");
-    for (Compartment ca : model.getCompartments()) {
-
-      double x = ca.getCenterX(), y = ca.getCenterY(), h = ca.getHeight(), w = ca.getWidth();
-      String shape;
-      if (ca instanceof OvalCompartment) {
-        shape = "Oval";
-      } else {
-        shape = "Rectangle";
-      }
+    StringBuilder result = new StringBuilder("");
+    for (Compartment compartment : model.getCompartments()) {
+      result.append(compartmentToXml(compartment));
+    }
+    return result.toString();
+  }
 
-      comparments.append("  <Shape TextLabel=\"" + ca.getName() + "\" GraphId=\"" + ca.getElementId() + "\">\n");
-      comparments.append("    <Comment>" + getAllNames(ca) + "</Comment>\n");
-      comparments.append("    <Attribute Key=\"org.pathvisio.CellularComponentProperty\" Value=\"Cell\" />\n");
-      comparments.append("    <Attribute Key=\"org.pathvisio.DoubleLineProperty\" Value=\"Double\" />\n");
-      comparments.append(
-          "    <Graphics CenterX=\"" + x + "\" "
-              + "CenterY=\"" + y + "\" "
-              + "Width=\"" + w + "\" "
-              + "Height=\"" + h + "\" "
-              + "ZOrder=\"" + ca.getZ() + "\" "
-              + "FontSize=\"" + ca.getFontSize().intValue() + "\" "
-              + "Valign=\"Bottom\" "
-              + "ShapeType=\"" + shape + "\" "
-              + "LineThickness=\"3.0\" "
-              + "Color=\"" + colorToString(ca.getBorderColor()) + "\" "
-              + "FillColor=\"" + colorToString(ca.getFillColor()) + "\" "
-              + "Rotation=\"0.0\" />\n");
-      comparments.append("  </Shape>\n");
+  String compartmentToXml(Compartment ca) {
+    StringBuilder comparments = new StringBuilder("");
+    double x = ca.getCenterX(), y = ca.getCenterY(), h = ca.getHeight(), w = ca.getWidth();
+    String shape;
+    if (ca instanceof OvalCompartment) {
+      shape = "Oval";
+    } else {
+      shape = "Rectangle";
     }
+
+    comparments.append("  <Shape TextLabel=\"" + ca.getName() + "\" GraphId=\"" + ca.getElementId() + "\">\n");
+    comparments.append("    <Comment>" + getAllNames(ca) + "</Comment>\n");
+    comparments.append("    <Attribute Key=\"org.pathvisio.CellularComponentProperty\" Value=\"Cell\" />\n");
+    comparments.append("    <Attribute Key=\"org.pathvisio.DoubleLineProperty\" Value=\"Double\" />\n");
+    comparments.append(
+        "    <Graphics CenterX=\"" + x + "\" "
+            + "CenterY=\"" + y + "\" "
+            + "Width=\"" + w + "\" "
+            + "Height=\"" + h + "\" "
+            + "ZOrder=\"" + ca.getZ() + "\" "
+            + "FontSize=\"" + ca.getFontSize().intValue() + "\" "
+            + "Valign=\"Bottom\" "
+            + "ShapeType=\"" + shape + "\" "
+            + "LineThickness=\"3.0\" "
+            + "Color=\"" + colorToString(ca.getFontColor()) + "\" "
+            + "FillColor=\"" + colorToString(ca.getFillColor()) + "\" "
+            + "Rotation=\"0.0\" />\n");
+    comparments.append("  </Shape>\n");
     return comparments.toString();
   }
 
@@ -356,8 +364,15 @@ public class ModelToGPML {
     if (rn instanceof Reactant) {
       for (Point2D p2d : line.getPoints()) {
         if (p2d.equals(ps)) {
-          interaction.append("      <Point X=\"" + ps.getX() + "\" Y=\"" + ps.getY() + "\" GraphRef=\""
-              + rn.getElement().getElementId() + "\"/>\n");
+          interaction.append("      <Point "
+              + "X=\"" + ps.getX() + "\" "
+              + "Y=\"" + ps.getY() + "\" ");
+
+          if (rn.getReaction().isReversible()) {
+            interaction.append("ArrowHead=\"mim-conversion\" ");
+          }
+
+          interaction.append("GraphRef=\"" + rn.getElement().getElementId() + "\"/>\n");
         } else if (p2d.equals(pe)) {
           interaction
               .append("      <Point X=\"" + pe.getX() + "\" Y=\"" + pe.getY() + "\" GraphRef=\"" + anchId + "\"/>\n");
@@ -403,15 +418,15 @@ public class ModelToGPML {
     }
     anchors.append("      <Anchor Position=\"" + anchorPosition + "\" Shape=\"None\" GraphId=\"" + anchId + "\"/>\n");
     interaction.append("    </Graphics>\n");
-    interaction.append(referenceParser.toXml((MiriamData) null));
+    interaction.append(referenceParser.toXml((MiriamData) null, null));
     interaction.append("  </Interaction>\n");
 
     return interaction.toString();
   }
 
   /**
-   * This function encode SpeciesAliases into DataNodes from GPML format. Empty
-   * complexes are also transformed into DataNodes.
+   * This function encode Species into DataNodes from GPML format. Empty complexes
+   * are also transformed into DataNodes.
    * 
    * @param model
    *          model where aliases are placed
@@ -454,7 +469,8 @@ public class ModelToGPML {
                 "FillColor=\"" + colorToString(ca.getFillColor()) + "\" " +
                 "LineStyle=\"Broken\"/>\n");
 
-        dataNodes.append(referenceParser.toXml(ca.getMiriamData()));
+        dataNodes
+            .append(referenceParser.toXml(ca.getMiriamData(), new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, ca)));
         dataNodes.append("  </DataNode>\n");
       }
     }
@@ -495,7 +511,8 @@ public class ModelToGPML {
             "Color=\"" + colorToString(species.getFontColor()) + "\" " +
             "FillColor=\"" + colorToString(species.getFillColor()) + "\"/>\n");
 
-    result.append(referenceParser.toXml(species.getMiriamData()));
+    result.append(
+        referenceParser.toXml(species.getMiriamData(), new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, species)));
     result.append("  </Label>\n");
     return result.toString();
   }
@@ -503,8 +520,9 @@ public class ModelToGPML {
   private String speciesToDataNode(Species species) throws ConverterException {
     StringBuilder result = new StringBuilder();
     result.append(
-        "  <DataNode TextLabel=\"" + species.getName() + "\" GraphId=\"" + species.getElementId() + "\" Type=\""
-            + getType(species) + "\"");
+        "  <DataNode TextLabel=\"" + species.getName() + "\" "
+            + "GraphId=\"" + species.getElementId() + "\""
+            + " Type=\"" + getType(species) + "\"");
     if (species.getComplex() != null) {
       result.append(" GroupRef=\"" + species.getComplex().getElementId() + "\"");
     }
@@ -526,8 +544,44 @@ public class ModelToGPML {
             "Color=\"" + colorToString(species.getFontColor()) + "\" " +
             "FillColor=\"" + colorToString(species.getFillColor()) + "\"/>\n");
 
-    result.append(referenceParser.toXml(species.getMiriamData()));
+    result.append(
+        referenceParser.toXml(species.getMiriamData(), new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, species)));
     result.append("  </DataNode>\n");
+
+    if (species instanceof SpeciesWithModificationResidue) {
+      for (ModificationResidue mr : ((SpeciesWithModificationResidue) species).getModificationResidues()) {
+        result.append(modifictionResidueToState(mr));
+      }
+    }
+
+    return result.toString();
+  }
+
+  private String modifictionResidueToState(ModificationResidue mr) {
+    StringBuilder result = new StringBuilder();
+    result.append("<State " +
+        "GraphRef=\"" + mr.getSpecies().getElementId() + "\" " +
+        "GraphId=\"" + mr.getSpecies().getElementId() + "-" + mr.getIdModificationResidue() + "\" ");
+    if (mr instanceof AbstractSiteModification) {
+      ModificationState state = ((AbstractSiteModification) mr).getState();
+      String stateString = "";
+      if (state != null) {
+        stateString = state.getAbbreviation();
+      }
+      result.append("TextLabel=\"" + stateString + "\" ");
+
+    }
+    result.append(">");
+    double relX = ((mr.getPosition().getX() - mr.getSpecies().getX()) / mr.getSpecies().getWidth() - 0.5) * 2;
+    double relY = ((mr.getPosition().getY() - mr.getSpecies().getY()) / mr.getSpecies().getHeight() - 0.5) * 2;
+    result.append("<Graphics " +
+        "RelX=\"" + relX + "\" " +
+        "RelY=\"" + relY + "\" " +
+        "Width=\"15.0\" " +
+        "Height=\"15.0\" " +
+        "ShapeType=\"Oval\" " +
+        "/>");
+    result.append("</State>");
     return result.toString();
   }
 
@@ -541,11 +595,17 @@ public class ModelToGPML {
   protected String getGroups(Model model) {
     StringBuilder groups = new StringBuilder("");
 
-    for (Complex ca : model.getComplexList()) {
-      if (ca.getElements().size() > 0) {
-        groups.append("  <Group GroupId=\"" + ca.getElementId() + "\" GraphId=\"" + ca.getElementId() + "\"");
-        if (ca.getComplex() != null) {
-          groups.append(" GroupRef=\"" + ca.getComplex().getElementId() + "\"");
+    for (Complex complex : model.getComplexList()) {
+      if (complex.getElements().size() > 0) {
+        groups.append("  <Group"
+            + " GroupId=\"" + complex.getElementId() + "\""
+            + " GraphId=\"" + complex.getElementId() + "\""
+            + " TextLabel=\"" + complex.getName() + "\"");
+        if (complex.getComplex() != null) {
+          groups.append(" GroupRef=\"" + complex.getComplex().getElementId() + "\"");
+        }
+        if (!complex.isHypothetical()) {
+          groups.append(" Style=\"Complex\"");
         }
         groups.append("/>\n");
       }
@@ -574,6 +634,7 @@ public class ModelToGPML {
       interactions.append("    <Graphics "
           + "ConnectorType=\"Segmented\" "
           + "ZOrder=\"" + reaction.getZ() + "\" "
+          + "Color=\"" + colorToString(reaction.getLine().getColor()) + "\" "
           + "LineThickness=\"" + reaction.getLine().getWidth() + "\">\n");
 
       /** Start and End **/
@@ -588,8 +649,15 @@ public class ModelToGPML {
 
       for (Point2D p2d : line.getPoints()) {
         if (p2d.equals(ps)) {
-          interactions
-              .append("      <Point X=\"" + ps.getX() + "\" Y=\"" + ps.getY() + "\" GraphRef=\"" + sid + "\"/>\n");
+          interactions.append("      <Point "
+              + "X=\"" + ps.getX() + "\" "
+              + "Y=\"" + ps.getY() + "\" ");
+
+          if (reaction.isReversible()) {
+            interactions.append("ArrowHead=\"mim-conversion\" ");
+          }
+
+          interactions.append("GraphRef=\"" + sid + "\"/>\n");
         } else if (p2d.equals(pe)) {
           interactions.append("      <Point X=\"" + pe.getX() + "\" Y=\"" + pe.getY() + "\" GraphRef=\"" + eid
               + "\" ArrowHead=\"mim-conversion\"/>\n");
@@ -622,7 +690,8 @@ public class ModelToGPML {
 
       interactions.append(anchors.toString());
       interactions.append("    </Graphics>\n");
-      interactions.append(referenceParser.toXml(reaction.getMiriamData()));
+      interactions.append(
+          referenceParser.toXml(reaction.getMiriamData(), new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, reaction)));
       interactions.append("  </Interaction>\n");
       interactions.append(tmp.toString());
     }
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/PointDataParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/PointDataParser.java
index 8c436e2b64eba345a7ea5caa341f33f86f2c5220..4b26c6cb23e62fe18705ff6f6600e6ef2cfb210f 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/PointDataParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/PointDataParser.java
@@ -9,6 +9,7 @@ import org.w3c.dom.Element;
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.LogMarker;
 import lcsb.mapviewer.wikipathway.model.*;
 
 /**
@@ -64,12 +65,12 @@ public class PointDataParser extends ElementGpmlParser<PointData> {
   }
 
   @Override
-  public String toXml(PointData node) throws ConverterException {
+  public String toXml(PointData node, LogMarker logMarker) throws ConverterException {
     throw new NotImplementedException();
   }
 
   @Override
-  public String toXml(Collection<PointData> list) throws ConverterException {
+  public String toXml(Collection<PointData> list, LogMarker logMarker) throws ConverterException {
     throw new NotImplementedException();
   }
 }
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java
index 5f230ef31ffad584e4aecedd0554416c41f58ed5..cf01da603470a58643cc09349deb8e4fef1e5e0e 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ReferenceParser.java
@@ -157,7 +157,7 @@ public class ReferenceParser extends ElementGpmlParser<MiriamData> {
   }
 
   @Override
-  public String toXml(MiriamData md) throws ConverterException {
+  public String toXml(MiriamData md, LogMarker logMarker) throws ConverterException {
     if (md == null) {
       return "<Xref ID=\"\" Database=\"\"/>\n";
     } else if (MiriamType.PUBMED.equals(md.getDataType())) {
@@ -177,7 +177,7 @@ public class ReferenceParser extends ElementGpmlParser<MiriamData> {
   }
 
   @Override
-  public String toXml(Collection<MiriamData> miriamData) throws ConverterException {
+  public String toXml(Collection<MiriamData> miriamData, LogMarker logMarker) throws ConverterException {
     StringBuilder result = new StringBuilder("");
     int counter = 0;
     for (MiriamData md : miriamData) {
@@ -186,7 +186,7 @@ public class ReferenceParser extends ElementGpmlParser<MiriamData> {
         if (counter == 1) {
           MinervaLoggerAppender appender = MinervaLoggerAppender.createAppender();
           try {
-            result.append(toXml(md));
+            result.append(toXml(md, logMarker));
             if (appender.getWarnings().size() > 0) {
               counter--;
             }
@@ -194,13 +194,13 @@ public class ReferenceParser extends ElementGpmlParser<MiriamData> {
             MinervaLoggerAppender.unregisterLogEventStorage(appender);
           }
         } else {
-          logger.warn("Annotation ommited - gpml support only one annotation per element: " + md.getDataType() + ": "
+          logger.warn(logMarker, "Annotation ommited - gpml support only one annotation per element: " + md.getDataType() + ": "
               + md.getResource());
         }
       }
     }
     if (counter == 0) {
-      return toXml((MiriamData) null);
+      return toXml((MiriamData) null, null);
     }
     return result.toString();
   }
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java
index 6bade4543815e4943f1ae431d5a73a56623bd95d..2065134461bfff4c39a91ba15990d02fc4694453 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ShapeParser.java
@@ -12,6 +12,7 @@ import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.LogMarker;
 import lcsb.mapviewer.model.graphics.LineType;
 import lcsb.mapviewer.wikipathway.model.Shape;
 import lcsb.mapviewer.wikipathway.model.UnknownTypeException;
@@ -84,12 +85,12 @@ public class ShapeParser extends GraphicalPathwayElementParser<Shape> {
   }
 
   @Override
-  public String toXml(Shape node) throws ConverterException {
+  public String toXml(Shape node, LogMarker logMarker) throws ConverterException {
     throw new NotImplementedException();
   }
 
   @Override
-  public String toXml(Collection<Shape> list) throws ConverterException {
+  public String toXml(Collection<Shape> list, LogMarker logMarker) throws ConverterException {
     throw new NotImplementedException();
   }
 
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/StateParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/StateParser.java
index d6fde52c3d47288f9bc24e0df46da36226affc41..a1af4bce4e17ee6f4d699df780269b566c8d6ab8 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/StateParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/StateParser.java
@@ -10,6 +10,7 @@ import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.LogMarker;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.species.field.ModificationState;
 import lcsb.mapviewer.wikipathway.model.*;
@@ -26,7 +27,7 @@ public class StateParser extends ElementGpmlParser<State> {
   /**
    * Default class logger.
    */
-  private final Logger logger = LogManager.getLogger(StateParser.class);
+  private final Logger logger = LogManager.getLogger();
 
   /**
    * Parser used for extracting {@link lcsb.mapviewer.model.map.MiriamData
@@ -109,12 +110,12 @@ public class StateParser extends ElementGpmlParser<State> {
   }
 
   @Override
-  public String toXml(State node) throws ConverterException {
+  public String toXml(State node, LogMarker logMarker) throws ConverterException {
     throw new NotImplementedException();
   }
 
   @Override
-  public String toXml(Collection<State> list) throws ConverterException {
+  public String toXml(Collection<State> list, LogMarker logMarker) throws ConverterException {
     throw new NotImplementedException();
   }
 
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownAttributeValueException.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownAttributeValueException.java
index b4d755fd5b2a395cca588f3726891692c129d5a7..2b34701857436298c76d12442e4be6af9aa855f6 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownAttributeValueException.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/UnknownAttributeValueException.java
@@ -3,7 +3,7 @@ package lcsb.mapviewer.wikipathway.XML;
 import lcsb.mapviewer.converter.ConverterException;
 
 /**
- * Exception that shold be thrown when the value of the attribute in xml is
+ * Exception that should be thrown when the value of the attribute in xml is
  * invalid.
  * 
  * @author Piotr Gawron
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java
index b0443a560c5b329b48ea777d1eeca9d50b37a998..e1149687ac6955dfe81452ece9116ed053d5ff21 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java
@@ -39,11 +39,6 @@ public class DataNode extends GraphicalPathwayElement {
    */
   private String textLabel;
 
-  /**
-   * Where this node belongs to.
-   */
-  private String groupRef;
-
   /**
    * Font weight (like italic, bold) that should be used.
    */
@@ -74,7 +69,7 @@ public class DataNode extends GraphicalPathwayElement {
 
   @Override
   public String toString() {
-    return textLabel + " " + getGraphId() + " " + groupRef + " " + type;
+    return textLabel + " " + getGraphId() + " " + getGroupRef() + " " + type;
   }
 
   @Override
@@ -116,23 +111,6 @@ public class DataNode extends GraphicalPathwayElement {
     this.textLabel = textLabel;
   }
 
-  /**
-   * @return the groupRef
-   * @see #groupRef
-   */
-  public String getGroupRef() {
-    return groupRef;
-  }
-
-  /**
-   * @param groupRef
-   *          the groupRef to set
-   * @see #groupRef
-   */
-  public void setGroupRef(String groupRef) {
-    this.groupRef = groupRef;
-  }
-
   /**
    * @return the references
    * @see #references
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Group.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Group.java
index 27188db64a136a4a7f6d01529928a898e7f22475..9aba05aa3f710eccd2fdaf458f71148e4f0c7041 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Group.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Group.java
@@ -8,7 +8,7 @@ import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
 /**
- * Class used to store data from Group from .gpml.
+ * Class used to store data from Group from GPML.
  * 
  * @author Jan Badura
  * 
@@ -38,6 +38,11 @@ public class Group extends PathwayElement {
    */
   private String style;
 
+  /**
+   * Style of the group.
+   */
+  private String textLabel;
+
   /**
    * Elements in the group.
    */
@@ -67,11 +72,10 @@ public class Group extends PathwayElement {
 
   @Override
   public String getName() {
-    StringBuilder sb = new StringBuilder("");
-    for (PathwayElement n : nodes) {
-      sb.append(n.getName() + ":");
+    if (getTextLabel() == null) {
+      return getGraphId();
     }
-    return sb.toString();
+    return getTextLabel();
   }
 
   @Override
@@ -151,4 +155,12 @@ public class Group extends PathwayElement {
     this.additionalBounds.add(bounds);
   }
 
+  public String getTextLabel() {
+    return textLabel;
+  }
+
+  public void setTextLabel(String textLabel) {
+    this.textLabel = textLabel;
+  }
+
 }
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java
index ecd0c164a3304b1836255a59b344b3b7e3a0cc1f..ed1444c030932c9cd1e3f92ee699f37dc81fd383 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java
@@ -43,11 +43,6 @@ public class Label extends GraphicalPathwayElement {
    */
   private String vAlign;
 
-  /**
-   * Where this node belongs to.
-   */
-  private String groupRef;
-
   private Set<MiriamData> references = new HashSet<>();
 
   /**
@@ -96,23 +91,6 @@ public class Label extends GraphicalPathwayElement {
     this.textLabel = textLabel;
   }
 
-  /**
-   * @return the groupRef
-   * @see #groupRef
-   */
-  public String getGroupRef() {
-    return groupRef;
-  }
-
-  /**
-   * @param groupRef
-   *          the groupRef to set
-   * @see #groupRef
-   */
-  public void setGroupRef(String groupRef) {
-    this.groupRef = groupRef;
-  }
-
   /**
    * @return the treatAsNode
    * @see #treatAsNode
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java
index d4edc1e56ab01664887423c7b7351ebafc69d63d..12cb06883296560e7609a4654d022b419e6d1893 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java
@@ -12,8 +12,8 @@ import lcsb.mapviewer.model.ProjectLogEntryType;
  * Abstract class for pathway elements. It defines common functionalities for
  * all elements in the model. There are two known subclasses:
  * <ul>
- * <li>{@link GraphicalPathwayElement}, representing elements with some graphical
- * representation</li>
+ * <li>{@link GraphicalPathwayElement}, representing elements with some
+ * graphical representation</li>
  * <li>{@link Group}, representing just groups of elements</li>
  * </ul>
  * 
@@ -42,6 +42,11 @@ public abstract class PathwayElement implements Serializable {
    */
   private String graphId;
 
+  /**
+   * Where this node belongs to.
+   */
+  private String groupRef;
+
   /**
    * 
    * Reference to BioPax node with references about this element.
@@ -91,7 +96,8 @@ public abstract class PathwayElement implements Serializable {
   abstract Rectangle2D getRectangle();
 
   public LogMarker getLogMarker() {
-    return new LogMarker(ProjectLogEntryType.PARSING_ISSUE, this.getClass().getSimpleName(), getGraphId(), getMapName());
+    return new LogMarker(ProjectLogEntryType.PARSING_ISSUE, this.getClass().getSimpleName(), getGraphId(),
+        getMapName());
   }
 
   /**
@@ -162,4 +168,13 @@ public abstract class PathwayElement implements Serializable {
   public void setMapName(String mapName) {
     this.mapName = mapName;
   }
+
+  public String getGroupRef() {
+    return groupRef;
+  }
+
+  public void setGroupRef(String groupRef) {
+    this.groupRef = groupRef;
+  }
+
 }
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java
index aba876c1253aa9f757628af95bfdf29d5e9af001..6879be832e8b5ac4bb3b79855d33d067d22b5b14 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PointData.java
@@ -25,7 +25,7 @@ public class PointData implements Serializable {
   /**
    * Default class logger.
    */
-  private final transient Logger logger = LogManager.getLogger(PointData.class);
+  private final transient Logger logger = LogManager.getLogger();
 
   /**
    * X coordinate.
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java
index 092552c71d23032fc581f2b3e51ec80ce8d78506..aae322eb91ad11ec47198801f717ef49971d1bd9 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java
@@ -34,11 +34,6 @@ public class Shape extends GraphicalPathwayElement {
    */
   private String textLabel;
 
-  /**
-   * Where this node belongs to.
-   */
-  private String groupRef;
-
   /**
    * Is shape a compartment.
    */
@@ -159,23 +154,6 @@ public class Shape extends GraphicalPathwayElement {
     this.compartment = compartment;
   }
 
-  /**
-   * @return the groupRef
-   * @see #groupRef
-   */
-  public String getGroupRef() {
-    return groupRef;
-  }
-
-  /**
-   * @param groupRef
-   *          the groupRef to set
-   * @see #groupRef
-   */
-  public void setGroupRef(String groupRef) {
-    this.groupRef = groupRef;
-  }
-
   /**
    * @return the vAlign
    * @see #vAlign
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
index d00f02f1f4cbbba9be981749e81d2c1c9ab15cc9..d43153a919938d8bcb5401569c9d5da8aef8d30a 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
@@ -2,6 +2,8 @@ package lcsb.mapviewer.wikipathway.XML;
 
 import static org.junit.Assert.*;
 
+import java.awt.Color;
+import java.awt.geom.Point2D;
 import java.awt.geom.Rectangle2D;
 import java.io.ByteArrayInputStream;
 import java.nio.charset.StandardCharsets;
@@ -10,19 +12,28 @@ import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.junit.*;
 
+import lcsb.mapviewer.common.geometry.PointTransformation;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.graphics.ArrowType;
+import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.*;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
 import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.Residue;
 import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
 
 public class ModelToGPMLTest extends WikipathwaysTestFunctions {
   Logger logger = LogManager.getLogger();
 
+  int speciesCounter = 0;
+
   @Before
   public void setUp() throws Exception {
   }
@@ -52,12 +63,12 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
     model.setWidth(1000);
     model.setHeight(1000);
 
-    GenericProtein alias = createProtein();
-    alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
-    alias.addMiriamData(new MiriamData(MiriamType.PUBMED, "123"));
-    alias.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
+    GenericProtein protein = createProtein();
+    protein.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+    protein.addMiriamData(new MiriamData(MiriamType.PUBMED, "123"));
+    protein.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
 
-    model.addElement(alias);
+    model.addElement(protein);
 
     ModelToGPML parser = new ModelToGPML(model.getName());
     String xml = parser.getGPML(model);
@@ -66,19 +77,190 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
 
     Model model2 = new GPMLToModel().getModel(new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8)));
 
-    Element p = model2.getElementByElementId("sa");
+    Element p = model2.getElementByElementId(protein.getElementId());
 
-    assertEquals(alias.getMiriamData().size(), p.getMiriamData().size());
+    assertEquals(protein.getMiriamData().size(), p.getMiriamData().size());
     for (MiriamData md : p.getMiriamData()) {
-      assertTrue(alias.getMiriamData().contains(md));
+      assertTrue(protein.getMiriamData().contains(md));
     }
   }
 
+  @Test
+  public void testHypoteticalComplex() throws Exception {
+
+    Model model = new ModelFullIndexed(null);
+    model.setWidth(1000);
+    model.setHeight(1000);
+
+    Complex complex = createComplex();
+    complex.addSpecies(createProtein());
+    complex.setHypothetical(false);
+
+    Complex complex2 = createComplex();
+    complex2.addSpecies(createProtein());
+    complex2.setHypothetical(true);
+
+    model.addElement(complex);
+    model.addElement(complex2);
+    model.addElements(complex.getElements());
+    model.addElements(complex2.getElements());
+
+    ModelToGPML parser = new ModelToGPML(model.getName());
+    String xml = parser.getGPML(model);
+    assertNotNull(xml);
+    assertEquals(0, getWarnings().size());
+
+    Model model2 = new GPMLToModel().getModel(new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8)));
+
+    Complex newComplex = model2.getElementByElementId(complex.getElementId());
+    Complex newComplex2 = model2.getElementByElementId(complex2.getElementId());
+
+    assertEquals(complex.isHypothetical(), newComplex.isHypothetical());
+    assertEquals(complex2.isHypothetical(), newComplex2.isHypothetical());
+  }
+
+  @Test
+  public void testComplexName() throws Exception {
+
+    Model model = new ModelFullIndexed(null);
+    model.setWidth(1000);
+    model.setHeight(1000);
+
+    Complex complex = createComplex();
+    complex.addSpecies(createProtein());
+    complex.setName("blabla");
+
+    model.addElement(complex);
+    model.addElements(complex.getElements());
+
+    ModelToGPML parser = new ModelToGPML(model.getName());
+    String xml = parser.getGPML(model);
+    assertNotNull(xml);
+    assertEquals(0, getWarnings().size());
+
+    Model model2 = new GPMLToModel().getModel(new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8)));
+
+    Complex newComplex = model2.getElementByElementId(complex.getElementId());
+
+    assertEquals(complex.getName(), newComplex.getName());
+  }
+
+  @Test
+  public void testReactionColor() throws Exception {
+
+    Model model = new ModelFullIndexed(null);
+    model.setWidth(1000);
+    model.setHeight(1000);
+
+    Protein p1 = createProtein();
+    Protein p2 = createProtein();
+
+    model.addElement(p1);
+    model.addElement(p2);
+
+    Reaction reaction = createReaction(p1, p2);
+
+    model.addReaction(reaction);
+
+    ModelToGPML parser = new ModelToGPML(model.getName());
+    String xml = parser.getGPML(model);
+
+    Model model2 = new GPMLToModel().getModel(new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8)));
+
+    Reaction newReaction = model2.getReactionByReactionId(reaction.getElementId());
+
+    assertEquals(reaction.getLine().getColor(), newReaction.getLine().getColor());
+  }
+
+  @Test
+  public void testReversibleReaction() throws Exception {
+
+    Model model = new ModelFullIndexed(null);
+    model.setWidth(1000);
+    model.setHeight(1000);
+
+    Protein p1 = createProtein();
+    Protein p2 = createProtein();
+
+    model.addElement(p1);
+    model.addElement(p2);
+
+    Reaction reaction = createReaction(p1, p2);
+    reaction.setReversible(true);
+    reaction.getReactants().get(0).getLine().getBeginAtd().setArrowType(ArrowType.FULL);
+
+    model.addReaction(reaction);
+
+    ModelToGPML parser = new ModelToGPML(model.getName());
+    String xml = parser.getGPML(model);
+
+    Model model2 = new GPMLToModel().getModel(new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8)));
+
+    Reaction newReaction = model2.getReactionByReactionId(reaction.getElementId());
+
+    assertEquals(reaction.isReversible(), newReaction.isReversible());
+  }
+
+  private Reaction createReaction(Protein p1, Protein p2) {
+    Reaction reaction = new TransportReaction("re" + (speciesCounter++));
+    Reactant reactant = new Reactant(p1);
+    Product product = new Product(p2);
+    reaction.addReactant(reactant);
+    reaction.addProduct(product);
+
+    Point2D start = p1.getCenter();
+    Point2D end = p2.getCenter();
+
+    PointTransformation pt = new PointTransformation();
+    reactant.setLine(new PolylineData(start, pt.getPointOnLine(start, end, 0.3)));
+    reaction.setLine(new PolylineData(pt.getPointOnLine(start, end, 0.3), pt.getPointOnLine(start, end, 0.6)));
+    product.setLine(new PolylineData(pt.getPointOnLine(start, end, 0.6), end));
+
+    reaction.getLine().setColor(Color.BLUE);
+    reactant.getLine().setColor(Color.BLUE);
+    product.getLine().setColor(Color.BLUE);
+    product.getLine().getEndAtd().setArrowType(ArrowType.FULL);
+
+    reaction.setZ(20);
+    return reaction;
+  }
+
+  @Test
+  public void testProteinModification() throws Exception {
+
+    Model model = new ModelFullIndexed(null);
+    model.setWidth(1000);
+    model.setHeight(1000);
+
+    Protein p1 = createProtein();
+    p1.addResidue(createResidue(p1));
+
+    model.addElement(p1);
+
+    ModelToGPML parser = new ModelToGPML(model.getName());
+    String xml = parser.getGPML(model);
+
+    Model model2 = new GPMLToModel().getModel(new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8)));
+
+    Protein newProtein = model2.getElementByElementId(p1.getElementId());
+
+    assertEquals(p1.getModificationResidues().size(), newProtein.getModificationResidues().size());
+    assertEquals(p1.getModificationResidues().get(0).getPosition(),
+        newProtein.getModificationResidues().get(0).getPosition());
+  }
+
+  private Residue createResidue(Protein p1) {
+    Residue residue = new Residue("mr" + speciesCounter++);
+    residue.setState(ModificationState.PHOSPHORYLATED);
+    residue.setPosition(new Point2D.Double(p1.getCenterX(), p1.getY()));
+    return residue;
+  }
+
   @Test
   public void testGetRectangle() throws Exception {
     ModelToGPML parser = new ModelToGPML("xyz");
     Compartment compartment = createCompartment();
-    Rectangle2D r= parser.getRectangle(compartment);
+    Rectangle2D r = parser.getRectangle(compartment);
     assertNotNull(r);
   }
 
@@ -90,7 +272,7 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
   }
 
   private Unknown createUnknown() {
-    Unknown result = new Unknown("id");
+    Unknown result = new Unknown("id" + (speciesCounter++));
     result.setName("s2");
     result.setWidth(10);
     result.setHeight(10);
@@ -101,18 +283,29 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
   }
 
   private GenericProtein createProtein() {
-    GenericProtein protein = new GenericProtein("sa");
+    GenericProtein protein = new GenericProtein("sa" + (speciesCounter++));
     protein.setName("s2");
     protein.setWidth(10);
     protein.setHeight(10);
-    protein.setX(1);
-    protein.setY(1);
+    protein.setX(100 * speciesCounter);
+    protein.setY(10 + 100 * speciesCounter * Math.random());
     protein.setZ(15);
     return protein;
   }
 
+  private Complex createComplex() {
+    Complex complex = new Complex("sa" + (speciesCounter++));
+    complex.setName("s2");
+    complex.setWidth(10);
+    complex.setHeight(10);
+    complex.setX(1);
+    complex.setY(1);
+    complex.setZ(15);
+    return complex;
+  }
+
   private Compartment createCompartment() {
-    Compartment compartment= new Compartment("ca");
+    Compartment compartment = new Compartment("ca" + (speciesCounter++));
     compartment.setName("s2");
     compartment.setWidth(10);
     compartment.setHeight(10);
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReferenceParserTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReferenceParserTest.java
index d1eb97045562f644521c8fb08a6e1425ec7e69be..997a49d4d7b40fe7f0a71baae39706fe0475455f 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReferenceParserTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ReferenceParserTest.java
@@ -44,7 +44,7 @@ public class ReferenceParserTest extends WikipathwaysTestFunctions {
   @Test
   public void testToXml() throws Exception {
     MiriamData md = new MiriamData(MiriamType.CHEBI, "CHEBI:123");
-    String xml = mc.toXml(md);
+    String xml = mc.toXml(md, null);
 
     Node node = super.getNodeFromXmlString(xml);
     MiriamData md2 = mc.parse((Element) node);
@@ -57,7 +57,7 @@ public class ReferenceParserTest extends WikipathwaysTestFunctions {
   public void testToXmlUnknownType() throws Exception {
     @SuppressWarnings("deprecation")
     MiriamData md = new MiriamData(MiriamType.UNKNOWN, "xyz");
-    String xml = mc.toXml(md);
+    String xml = mc.toXml(md, null);
 
     assertNotNull(xml);
     assertEquals(1, getWarnings().size());
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
index 449260cfebd151d5f0be1642a9a39a9901eafb74..e93c4ad9f39ca06c360f573afffdfbd8aea7b033 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -2,6 +2,7 @@ package lcsb.mapviewer.services.impl;
 
 import java.awt.Color;
 import java.io.IOException;
+import java.io.InputStream;
 import java.util.*;
 import java.util.Comparator;
 
@@ -151,21 +152,9 @@ public class LayoutService implements ILayoutService {
   @Override
   public Layout createLayout(final CreateLayoutParams params) throws IOException, InvalidColorSchemaException {
     ColorSchemaReader reader = new ColorSchemaReader();
-    Map<String, String> parameters = TextFileUtils.getHeaderParametersFromFile(params.getColorInputStream());
-    ColorSchemaType colorSchemaType = params.getColorSchemaType();
-    if (colorSchemaType == null) {
-      String type = parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE);
-      if (type != null) {
-        colorSchemaType = ColorSchemaType.valueOf(type);
-      }
-    }
-    if (colorSchemaType == null) {
-      colorSchemaType = ColorSchemaType.GENERIC;
-    }
-
-    if (parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE) == null && params.getColorSchemaType() != null) {
-      parameters.put(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE, params.getColorSchemaType().name());
-    }
+    Map<String, String> parameters = extractHeaderParameters(params.getColorInputStream(), params.getColorSchemaType());
+    ColorSchemaType colorSchemaType = ColorSchemaType
+        .valueOf(parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE));
     final Collection<ColorSchema> schemas = reader.readColorSchema(params.getColorInputStream(), parameters);
 
     // check if we can color our model using this schema,
@@ -218,6 +207,25 @@ public class LayoutService implements ILayoutService {
     return topLayout;
   }
 
+  protected Map<String, String> extractHeaderParameters(InputStream colorInputStream, ColorSchemaType colorSchemaType)
+      throws IOException {
+    Map<String, String> parameters = TextFileUtils.getHeaderParametersFromFile(colorInputStream);
+    if (colorSchemaType == null) {
+      String type = parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE);
+      if (type != null) {
+        colorSchemaType = ColorSchemaType.valueOf(type);
+      }
+    }
+    if (colorSchemaType == null) {
+      colorSchemaType = ColorSchemaType.GENERIC;
+    }
+
+    if (parameters.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE) == null) {
+      parameters.put(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE, colorSchemaType.name());
+    }
+    return parameters;
+  }
+
   @Override
   public Layout createLayoutWithImages(final CreateLayoutParams params)
       throws IOException, InvalidColorSchemaException, CommandExecutionException {
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 68d6f8a729a4f2b6fe0b2173d9d46d7111155ca8..0c3cc3f23188bed1d931dc4ee9153d003f547b9f 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -50,8 +50,7 @@ import lcsb.mapviewer.services.overlay.AnnotatedObjectTreeRow;
 import lcsb.mapviewer.services.search.chemical.IChemicalService;
 import lcsb.mapviewer.services.search.drug.IDrugService;
 import lcsb.mapviewer.services.search.mirna.IMiRNAService;
-import lcsb.mapviewer.services.utils.CreateProjectParams;
-import lcsb.mapviewer.services.utils.EmailSender;
+import lcsb.mapviewer.services.utils.*;
 import lcsb.mapviewer.services.utils.data.BuildInLayout;
 
 /**
@@ -694,9 +693,11 @@ public class ProjectService implements IProjectService {
    *          project where the model should be placed
    * @throws InvalidInputDataExecption
    *           thrown when there is a problem with input file
+   * @throws InvalidColorSchemaException
+   * @throws IOException
    */
   protected void createModel(final CreateProjectParams params, Project dbProject)
-      throws InvalidInputDataExecption, ConverterException {
+      throws InvalidInputDataExecption, ConverterException, IOException, InvalidColorSchemaException {
     User dbUser = userDao.getById(params.getUser().getId());
     UserAnnotationSchema userAnnotationSchema = dbUser.getAnnotationSchema();
     if (userAnnotationSchema == null) {
@@ -830,7 +831,7 @@ public class ProjectService implements IProjectService {
       l.setOrderIndex(order++);
     }
     projectDao.update(project);
-
+    validateDataOverlays(project);
     if (params.isUpdateAnnotations()) {
       Map<Class<?>, List<ElementAnnotator>> annotators = null;
       if (params.getAnnotatorsMap() != null) {
@@ -853,6 +854,21 @@ public class ProjectService implements IProjectService {
 
   }
 
+  private void validateDataOverlays(final Project project) throws IOException, InvalidColorSchemaException {
+    for (Layout l : project.getLayouts()) {
+      if (l.getInputData() != null) {
+        ColorSchemaReader reader = new ColorSchemaReader();
+        Map<String, String> parameters = new LayoutService(null, null, null, null)
+            .extractHeaderParameters(new ByteArrayInputStream(l.getInputData().getFileContent()), null);
+        try {
+          reader.readColorSchema(new ByteArrayInputStream(l.getInputData().getFileContent()), parameters);
+        } catch (InvalidColorSchemaException e) {
+          throw new InvalidColorSchemaException("Problematic data overlay: " + l.getTitle() + ". " + e.getMessage(), e);
+        }
+      }
+    }
+  }
+
   private void assignZoomLevelDataToModel(Model topModel) throws InvalidInputDataExecption {
     Integer maxZoomLevels = Integer
         .parseInt(configurationService.getValue(ConfigurationElementType.MAX_NUMBER_OF_MAP_LEVELS).getValue());
diff --git a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTestWithoutTransaction.java b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTestWithoutTransaction.java
index 3f3441dd8e6bd98b92115f424d54b8cdf7d21f81..591a1fa0299944be6b01036e91950442f3cf008b 100644
--- a/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTestWithoutTransaction.java
+++ b/web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTestWithoutTransaction.java
@@ -1,5 +1,6 @@
 package lcsb.mapviewer.web;
 
+import static org.junit.Assert.assertEquals;
 import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
 import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
 
@@ -20,8 +21,11 @@ import org.springframework.http.MediaType;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.test.web.servlet.RequestBuilder;
 
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.ProjectStatus;
 import lcsb.mapviewer.model.cache.UploadedFileEntry;
 import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.interfaces.IProjectService;
 import lcsb.mapviewer.services.interfaces.IUserService;
 
 @RunWith(SpringJUnit4ClassRunner.class)
@@ -36,6 +40,9 @@ public class ProjectControllerIntegrationTestWithoutTransaction extends Controll
   @Autowired
   private IUserService userService;
 
+  @Autowired
+  private IProjectService projectService;
+
   @Before
   public void setup() {
   }
@@ -327,4 +334,60 @@ public class ProjectControllerIntegrationTestWithoutTransaction extends Controll
     }
   }
 
+  @Test
+  public void addComplexProjectWithInvalidOverlay() throws Exception {
+    User admin = userService.getUserByLogin(BUILT_IN_ADMIN_LOGIN);
+    UploadedFileEntry fileEntry = createFileInSeparateThread(
+        Files.readAllBytes(Paths.get("./src/test/resources/complex_model_with_invalid_layouts.zip")), admin);
+    try {
+      String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
+          new BasicNameValuePair("file-id", String.valueOf(fileEntry.getId())),
+          new BasicNameValuePair("mapCanvasType", "OPEN_LAYERS"),
+          new BasicNameValuePair("parser", "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser"),
+
+          new BasicNameValuePair("zip-entries[0][_type]", "MAP"),
+          new BasicNameValuePair("zip-entries[0][_filename]", "main.xml"),
+          new BasicNameValuePair("zip-entries[0][_data][root]", "true"),
+          new BasicNameValuePair("zip-entries[0][_data][name]", "s1"),
+          new BasicNameValuePair("zip-entries[0][_data][type][id]", "UNKNOWN"),
+          new BasicNameValuePair("zip-entries[0][_data][type][name]", "Unknown"),
+
+          new BasicNameValuePair("zip-entries[1][_type]", "OVERLAY"),
+          new BasicNameValuePair("zip-entries[1][_filename]", "layouts/badSchema.txt"),
+          new BasicNameValuePair("zip-entries[1][_data][name]", "test-o")
+
+      )));
+
+      RequestBuilder request = post("/projects/" + TEST_PROJECT)
+          .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+          .content(body)
+          .session(createSession(BUILT_IN_ADMIN_LOGIN, BUILT_IN_ADMIN_PASSWORD));
+
+      mockMvc.perform(request).andExpect(status().is2xxSuccessful());
+      callInSeparateThread(() -> {
+        try {
+          waitForProjectToFinishLoading(TEST_PROJECT);
+        } catch (InterruptedException e) {
+          e.printStackTrace();
+        }
+        return null;
+      });
+
+      Project project = projectService.getProjectByProjectId(TEST_PROJECT);
+      assertEquals(ProjectStatus.FAIL, project.getStatus());
+
+    } finally {
+      callInSeparateThread(() -> {
+        try {
+          waitForProjectToFinishLoading(TEST_PROJECT);
+        } catch (InterruptedException e) {
+          e.printStackTrace();
+        }
+        return null;
+      });
+
+      removeProjectInSeparateThread(TEST_PROJECT);
+    }
+  }
+
 }
diff --git a/web/src/test/resources/complex_model_with_invalid_layouts.zip b/web/src/test/resources/complex_model_with_invalid_layouts.zip
new file mode 100644
index 0000000000000000000000000000000000000000..a5984b116b380434cc5c8026d6a152f41076d00b
Binary files /dev/null and b/web/src/test/resources/complex_model_with_invalid_layouts.zip differ