model summary empty no metabolites no reactions no nothing

[norm vinson]

**newbie warning** I'm still trying to figure things out.

summary

---------------

I downoaded a model from biomodels  (https://www.ebi.ac.uk/biomodels/MODEL3618435756).

the problem is the model summary doesn't list any metabolites, fluxes, etc.

Objective

1.0 reac5CC520A3 = 0.0

Uptake
MetaboliteReactionFluxC-NumberC-Flux

Secretion

MetaboliteReactionFluxC-NumberC-Flux

why would tthat be?

Details.

=========

reference

---------------

the model is from biomodels:  https://www.ebi.ac.uk/biomodels/MODEL3618435756

A Genome-scale Metabolic Model of Arabidopsis thaliana and Some of its Properties.
Poolman MG, Miguet L, Sweetlove LJ and Fell DA. Plant Physiol. 2009 Sep 15.  PMID: 19755544 , doi: 10.1104/pp.109.141267

model xml header

----------------------------

sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" fbc:required="false" level="3" version="1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:html="http://www.w3.org/1999/xhtml"

model validation:

---------------------------

added a lot of exchange reactions like:

Adding exchange reaction EX_MNXM729302@BOUNDARY with default bounds for boundary metabolite: MNXM729302@BOUNDARY.',
the sboTerm on line 1233 was causing a validation error in cobra py. i removed it. According to the SBML spec, that's fine. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core, Section 5

cobra tests

-----------------

cobra.test.test_all()

passed

model

-----------

there are metabolites and rections in there:

print('Nb of reactions: ',len(arabi_model.reactions))
print('Nb of metabolites: ',len(arabi_model.metabolites))
print('Nb of genes: ',len(arabi_model.genes))

Nb of reactions: 1584 Nb of metabolites: 1916 Nb of genes: 1196

[ch.d...@gmail.com]

The summary is empty because your objective is zero. If there is no flux or growth nothing needs to be consumed or produced. I tried to reproduce what you did but when I download the model it reads fine with the current COBRAPY version but it has no objective set (will warn about that) and there is also no reaction called reac5CC520A for me...

[norm vinson]

i will download again and try from scratch. I will set an objective. Thanks.