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Benchmarking-Initiative / Benchmark-Models-PEtab

A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling
BSD 3-Clause "New" or "Revised" License
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Make Bertozzi consistent #218

Closed stephanmg closed 2 months ago

stephanmg commented 2 months ago

Make Bertozzi's Susceptible_to_Infected consistent.

dilpath commented 2 months ago

What is inconsistent? The Susceptible -> Infected reaction is not reversible, right?

stephanmg commented 2 months ago 
Susceptible_to_Infected
Rate Law for Susceptible_to_Infected_1
The kinetic function is marked as irreversible but at least one of its variables is labeled as product.
dilpath commented 2 months ago

Is this forbidden in SBML? The interaction between susceptible + infected causes susceptible -> infected, not infected -> susceptible, right?

stephanmg commented 2 months ago

Is this forbidden in SBML? The interaction between susceptible + infected causes susceptible -> infected, not infected -> susceptible, right?

Ah, the interaction should be non-reversible true. So what about this message from COPASI/SBML validator? False-positive warning?

dilpath commented 2 months ago

False-positive warning?

I'm not sure, but this is my guess -- maybe it's unusual to see direct positive-feedback with the product in the kinetic law.

FFroehlich commented 2 months ago

I think the rate law should be susceptible + infected -> infected + infected rather than susceptible -> infected

dilpath commented 2 months ago

I think the rate law should be susceptible + infected -> infected + infected rather than susceptible -> infected

Ah thanks, makes sense, done in #222 , where the problem is further modified to be a more reasonable parameter estimation problem.

stephanmg commented 2 months ago

Can this issue then be closed in light of additional fixes in #222?