SBML to mrgsolve

[mhismail]

Hi @kylebaron , I was wondering if there are any open-source SBML to mrgsolve translators available, or generally any tips for programmatically going from SBML to mrgsolve. Appreciate any insights.

Thanks.

[kylebaron]

Hi @mhismail -

Nothing open source, but I've done it several times. Most of the code is the same but IMO little tweaks are needed pretty regularly since the structure / assumptions can vary depending on where the SBML is coming from.

I have the code to handle this SBML:
https://www.nature.com/articles/s41540-017-0016-1

I can put that somewhere as an example if that'd be helpful.

Kyle

[mhismail]

Hi @kylebaron, that would be really helpful if you could share that as an example. Thank you!

[KGmax]

Can you share it, or describe how to make this conversion? It would help me tremendously. SMBL is too complicated and converting it to mrgsolve would takes a lot of time for a beginner like me.

[KGmax]

In the article (doi:10.1002/psp4.12467) you write, "The translation code was written in R and utilized an R interface to libSBML as linked from https://sbml.org.". But how was this done? I've been trying all day but haven't made any progress.

[kylebaron]

@mhismail You might look at this too:

https://github.com/sn248/r2sbml

Written by @sn248; it is not on cran but might be less monkey business than what I've written to interface with libSBML (it probably is less monkey business).

[mhismail]

Thanks @kylebaron, I was able to get things running with the other script you shared. I'll definitely give this package a try next time.

[Mutaz94]

Hi @kylebaron, this is interesting since I was looking around. Did you share libSBML code? I was looking around but without luck!

[kylebaron]

Hi @Mutaz94 - I never got something to the point where I wanted to share publicly. Kyle