NullPointerException when saving model

[Edward Smith]

When trying to save or export a model I get the error:

NullPointerException-Cannot invoke "cbit.vcell.model.Feature.getName()" because the return value of "cbit.vcell.model.Model$StructureTopology.getInsideFeature(cbit.vcell.model.Membrane)" is null

I can't find the parameter to update to prevent this. Uploading, local saving and export are all affected. 

Thanks for any help you can provide! 

Ed 

[Edward Smith]

I found the issue in the .vcml file. No "InsideFeature" and no "OutsideFeature" is defined for some membranes. 

<Membrane InsideFeature="Phloem_cell" OutsideFeature="sink_apoplast" PositiveFeature="Phloem_cell" NegativeFeature="sink_apoplast" MembraneVoltage="Voltage_sink_phloem_membrane" Name="sink_phloem_membrane" KeyValue="51267860" />

<Membrane PositiveFeature="Phloem_cell_source" NegativeFeature="source_apoplast" MembraneVoltage="Voltage_source_membrane" Name="source_membrane" />

The "sink_phloem_membrane" has no issue but the "source_membrane" membrane does not have the parameters defined. I can update them manually in the .vcml file but they are lost again upon opening the file in vcell. I have defined the positive and negative features but there doesn't seem to be a way to define what is inside and what is outside. 

Thanks for any help! 

Ed

[James Schaff]

Hi Ed,

Sorry for the late reply.

Modern VCell models no longer use the InsideFeature and OutsideFeature attributes for Membranes.  I would suggest that you remove these attributes entirely.

Here is some context: VCell previously had a notion of compartmental encapsulation (e.g. extracellular is outside of plasma_membrane and cytosol is inside of plasma_membrane).  Now, VCell compartments no longer have such a hierarchical organization - to accommodate more general topologies such as gap junctions.

If you still have trouble, please email me at sch...@uchc.edu and attach your model file, I will repair it for you.

Best regards,

Jim Schaff.

--
You received this message because you are subscribed to the Google Groups "VCell Open Discussion Forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to vcell-discus...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/vcell-discuss/eb9b0fe2-e3b8-4525-867c-99d7f4648b9bn%40googlegroups.com.

[Edward Smith]

Ok that makes sense - I had built the model based on one from 2011. By removing the "InsideFeature"  "OutsideFeature" attributes of the membrane in the model file I am now able to save and load the model with no issue. So the problem is now solved thanks to your insight - thanks very much! 

Best wishes, 

Ed 

You received this message because you are subscribed to a topic in the Google Groups "VCell Open Discussion Forum" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/vcell-discuss/RHbxfPbQ5UQ/unsubscribe.
To unsubscribe from this group and all its topics, send an email to vcell-discus...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/vcell-discuss/CAHs-fZLuyUUjGsE6JkOcE8Y3kvQLVgn0GL8XVEf4b47AmtBgjA%40mail.gmail.com.