SBML Support in Morpheus

[lean...@gmail.com]

Hi,

I noticed that you have added support for SBML import and export. I would like to know how much support do you have. Do you support all of the SBML core elements? Any packages?

I am also fairly new to Morpheus so I haven't been able to use the SBML import/export feature. I would appreciate if someone could instruct me on how to use it.

Thanks,
Leandro

[Walter de Back]

Dear Leandro,

Welcome to the Morpheus user forum.

I noticed that you have added support for SBML import and export.

​  

I would like to know how much support do you have. Do you support all of the SBML core elements? Any packages?

​Morpheus has (rudimentary) support for importing SBML models, up to level 2 I believe, by converting SBML reactions into an system of coupled ODEs in MorpheusML. Exporting MorpheusML to SBML is not support. 

There is a description in the user manual (page 10):

https://imc.zih.tu-dresden.de//morpheus/Morpheus_User_Manual_v1.1_rev881.pdf

Note ​

​that not all SBML models can be simulated in Morpheus.​ Notably, ODE systems that are stiff (

http://www.scholarpedia.org/article/Stiff_systems)

​ require implicit​

 

​solvers whereas Morpheus only provides explicit/forward solvers. 

I am also fairly new to Morpheus so I haven't been able to use the SBML import/export feature. I would appreciate if someone could instruct me on how to use it.

​In principle:

- you create a SBML model or download one from a repository such as https://www.ebi.ac.uk/biomodels-main. 

- in Morpheus, File -> Import SBML. (Not: if you do not see this option, your Morpheus version was not compiled with SBML support.)

This will create a Morpheus model where the SBML reactions have been converted to a set of ODEs and defined in a CellType / System / DiffEqn. You should be able to execute the model immediately. 

​You can have a look at the example model available in Morpheus: Example -> ODE -> MAPK_SBML.xml. This model was automatically converted from the SBML model by Kholodenko et al. downloaded from Biomodels: http://www.ebi.ac.uk/biomodels-main/BIOMD0000000010.

​I must admit that

the SBML support has not been actively maintained for a while and may have a few issues. If you encounter them, please report them here or at the GitLab issue tracker: 

https://gitlab.com/morpheus.lab/morpheus/issues

​.

​

​

B

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est​

​,

Walter​

[Leandro Watanabe]

Thank you Walter. I was using the stable release so that's why I didn't see the import option. 

I compiled Morpheus on my machine but whenever I try to import an SBML file, the program crashes. I reported the problems in the issue tracker on GitLab.

Let me know if you can figure out what the problem is. 

BTW, I don't know how hard it would be to add this feature, but it would be nice if you could move the sbml converter to core and let people run the conversion from command-line. 

Thanks,

Leandro