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where there's multiple references to same complex, that complex needs to be cloned (once per reference).
https://github.com/MICommunity/ComplexViewer/issues/199#issuecomment-2205340761
in this c…
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I've been digging some into the stoichiometry differences in CASA and MIMICS and was surprised to see how different the litterfall C:N fluxes are.
These are calculated for MIMICS by summing the fo…
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Up to now, `dingo` supports sampling using the uniform, the
multivariate exponential and the multivariate Gaussian distributions.
A quite interesting addition from the biologist-point-of-view wou…
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Hello again
Presumably it was an intentional decision, but it's inconvenient having to always use, for example, ```AbstractFBCModels.genes()``` when using model accessors, instead of just ```genes(…
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Currently, for metabolic flux analysis, MFAPipe models the independent fluxes of the reaction network as the independent variables of the regression. Hence, the values of the independent fluxes are fi…
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I have a question on case 974: `Xref` is assigned to multiple variables. But what determines the value of `Xref`?
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Hi, I am trying to predict a complex with stoichiometry A6B6 using AFM v2.3.
I get a strange error related to something in tf, but don't really know why. Using the same MSAs, I can predict a smaller …
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I would like to run modnet on a dataset in which I have compositions that have very complex stoichiometries. On example would be `C100H3815Br21I279N2185Pb100`
To reproduce, this could be an example…
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[Fitting_lambda.txt](https://github.com/akulikovsky/Fitting_Procs/files/1084090/Fitting_lambda.txt)
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Lets first focus on the interior spec:
```
{
"name": "cool reaction",
"molecules": ["8e102b34c4441c4b164a7d678591df550c90de74", "dbbacd78247e7b39ee5cb8e78d74423e98639203"],
…