geckopy
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ginkgobioworks
Enzyme-constrained genome-scale models in python
### Description [MultiTFA](https://github.com/biosustain/multitfa/) is a multivariate thermodynamics-based metabolic flux analysis package. It constrains the thermodynamic calculations more tightly by making use of the covariance matrix of formation energies instead of...
Geckopy should support 3.10. There is a problem with the requests dependency on CI for python 3.10 that needs to be investigated, that's why it is not there for now.
Hi @carrascomj, minor issue and question on setting experimental protein concentrations in the yeast model. - Small issue: experimental.limit_proteins() fails to find the correct reaction in the ecyeast8 model. It...
It is nice to avoid all those REV reactions but the complexity of managing this under the hood in the solver is too hard to debug and does not produce...
### Description `geckopy` currently supports adding a global protein pool or a protein pool to a handful of specified reactions but does not easily allow for adding multiple protein pools...
This is pending on https://github.com/pypa/pypi-support/issues/1124 For users that stumble upon this issue, please install it from source, as any normal python package: ```bash git clone https://github.com/ginkgobioworks/geckopy cd geckopy pip install...
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Enzyme-constrained genome-scale models in python