This week, I have been working on the actual conversion from SBML Layout to CellDesigner Annotation. I have started the conversions for species and compartment using the informations from their glyphs. The chart below shows how much I have covered so far for conversion. Blue means it's completed, red means it's not yet completed, green means it's unconvertable.

Another thing I have been doing is that I have been creating a command line interface.

git clone https://github.com/funasoul/celldesigner-parser

mvn install

java -jar celldesigner-parser-0.0.1-SNAPSHOT-jar-with-dependencies.jar input.xml [output.xml] [CD2Layout / Layout2CD]

First create the runnable jar file with maven. Then run the jar with arguments input file, path to output (optional), and which direction CellDesigner to Layout or Layout to CellDesigner (optional).

Also, I tried to provide a visual aid on the progress I have made, however CellDesigner can't read my converted model yet. Currently something is wrong with the Species Alias and throws an exception. For next week, my first goal is to get some graphical output on the converted model.

Here are the result I get for my current implementation.

Layout model

CellDesigner Annotation Model

One last thing. I have noticed an error when unmarshaling the SBML file. In the kinetic law, the math equation is converted in the wrong form.

Original Model is written like on the below.

<mathml:math>

<mathml:apply>

<mathml:times/>

<mathml:ci> k1 </mathml:ci>

<mathml:ci> s1 </mathml:ci>

</mathml:apply>

</mathml:math>

When unmarshaled, the duplicating ci attribute is removed.

<mathml:math>

<mathml:apply>

<mathml:ci> k1 </mathml:ci>

<mathml:times/>

</mathml:apply>

</mathml:math>

So whenever I convert the model to SBML Layout to CellDesigner Annotation, it changes the equation. I presume something might be wrong with the MathML schema (sbml-mathml.xsd).

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