Propagate existing model to new draft model

[hites77]

Is there any way to propagate existing model for a genome to new draft model using gapseq ?

[jotech]

I'm not sure if I got your question right. You have already a model and want to use it in gapseq? What namespace (reaction ids) does the model have? In gapseq, there is a submodule adapt which can update a model based on prior information, for example if you know that a certain pathway is present:

gapseq adapt add 14DICHLORBENZDEG-PWY toy/myb71.RDS

Will add reactions involved in dichlorobenzene degradation.

[hites77]

If I generate a model with gapseq and want to compare and curate it with nearest existing model, than is there any way ? Or I just have to find what reactions are missing and have add manually with gapseq adapt.

[jotech]

depends on the namespace of the model (kegg, bigg, vmh). When the namespace differs comparing and merging is a bit tricky although possible. Do you mind to provide some details on the existing model which you want to use for comparison?

[hites77]

I was testing the model described in the paper (Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction; DOI: 10.1002/jcp.25428). I prepared the model of Thermosynechococcus elongatus BP-1 using gapseq but when I try to do gapfilling it was unable to grow in autotrophic media (without glucose). Whereas in their paper it was able to grow as they have merged it with iJN678 model of Synechocystis sp. PCC 6803.
Also when I do gapfilling using Minimal media with glucose and then uploaded the full model in Memote for validation it reported error in biomass consistency.
So I am unsure how to resolve this.

[jotech]

Hi @hites77, I see now I'm getting a bit better what you are trying to do :)

Actually the autotrophic growth should work in gapseq! Have you tried using a autotrophic medium (I just uploaded one example medium) in the gapfilling step?
./gapseq fill -m toy/ecoli-draft.RDS -n dat/media/autotrophic.csv -c toy/ecoli-rxnWeights.RDS -g toy/ecoli-rxnXgenes.RDS
If you already tried this, then it would be great to have the genome file and your medium file in order to tackle the problem. Did you use refseq GCF_000011345.1 as input?

Concerning memote, we had some changes due to this issue #40, does it help in your case?

[hites77]

Hi, jotech, thanks for providing that media file, seems that composition of my media was wrong, now the growth rate is 0.056.

However now the xml file generated is showing valid by sbml validator but it shows following warning:

Warning: As a principle of best modeling practice, the should set an initial value (amount or concentration) rather than be left undefined. Doing so improves the portability of models between different simulation and analysis systems, and helps make it easier to detect potential errors in models. The with the id 'M_cpd00001_c0' does not have an 'initialConcentration' or 'initialAmount' attribute, nor is its initial value set by an or .

Also when I try to run in memote it shows following error which was not being shown previously

critical: The model could not be loaded due to the following SBML errors.
error: Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the cobra.io.sbml.validate_sbml_model function or via the online validator at http://sbml.org/validator .
error: (model, errors) = validate_sbml_model(filename)
error: If the model is valid and cannot be read please open an issue at https://github.com/opencobra/cobrapy/issues .
error: Line 2, Column 0 - #1013: Invalid or undefined XML namespace prefix.
error: - Category: XML content, Severity: 2

the error occur even when I do a fresh install of memote in new virtual environment.

I also check with cobra validation command cobra.io.sbml.validate_sbml_model('TelongatusBP-1.xml')
and it give following error

(None, {'SBML_FATAL': [], 'SBML_ERROR': ['E0 (Error): XML content (core, L2); Bad XML prefix; Invalid or undefined XML namespace prefix.\n'], 'SBML_SCHEMA_ERROR': [], 'SBML_WARNING': [], 'COBRA_FATAL': [], 'COBRA_ERROR': ['No SBML model detected in file.'], 'COBRA_WARNING': [], 'COBRA_CHECK': []})

[jotech]

thanks for trying again! We will have a look at this memote issue. Do you mind if we create a new issue for this because it's a different question now?

[hites77]

Yes we can create a new issue as question has now changed

[jotech]

please reopen the issue if it is still relevant