Andrew Miller wrote: >> > Have you actually looked at what exactly is happening? Is this an > overflow where quantities are getting so big they go to infinity because > you have a loop which doesn't have any self-regulation? > Hi Andrew,
Yes, I have looked at what's happening. In some cases the integrator only gets up to the second time point, which isn't that useful. For the models that get further than that, I don't see any evidence of numbers getting absurdly small or absurdly big. Although some of the fluxes in the asthagiri_lauffenburger csv file that I've sent you seem to start off extremely small - like 10E^-38 small. I don't know. That's with the BDF integrator. With most of the other integrators (example Implicit Gear M1) they get up to the second time step and then start producing NaN outputs.] > I presume that the model that is being generated from the reactions by > my script would be exactly identical to what you would enter if you > recreated the model by hand (assuming that the entered rate laws are an > accurate representation of the paper). If the rates were specified using > one of the common formulae for enzyme rates, you would get product > inhibition and these overflows wouldn't happen, but I think that perhaps > the entered rate laws are too simple. I would presume that too. > > Obviously, getting rid of the reactions is the overall goal, but I don't > see any reason why you would be better to re-create the models from > scratch, rather than starting from the original model with reactions, I am starting from the original model with reactions, not building it totally from scratch. > running it through my script to generate equations for this, and then > fixing any problems such as rate laws which don't represent what the > authors of the paper actually used and/or result in species getting > exponential increases to such high concentrations they overflow the > floating point representation. > I don't think that this process is possible to automate due to the way the models have been coded up using reaction components. Of course, I may be wrong. It's something that's difficult to explain over email. If you want to see what I mean, come see me and I'll show you an example. Then perhaps you might have a better idea about whether the process can be automated or now. Additionally, rebuilding the model provides a really good opportunity for curation. I've been rebuilding the bertram_arnot_zamponi model and I've actually found a few errors and omissions, which I definitely wouldn't have found without looking at the model in the depth required to rebuild it. >> > My script could generate metadata as well if required. However, as Poul > suggested at the CellML meeting, feedback from Matt on exactly what > metadata we should generate it and where that metadata should be stored > (I think it preferably should be in the model, but Matt might have a > different opinion). Yep. Kind regards, James _______________________________________________ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
