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Here is a record of the discussion of low LAI we have been having on an email thread.
@kovenock
Abby and I are looking for ways to simulate higher LAI ecosystems in our Fates simulations at bci.…
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The L2 specs never mention that having a model be undetermined or unsimulatable is permitted. This should be mentioned somewhere. The spec currently only talks about how overdetermined models are di…
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The way I see it, `knockout` right now is an in-place modification. However:
```
using COBREXA,Tulip
m=load_model("test/downloaded/e_coli_core.mat")
om=make_optimization_model(m,Tulip.Optimizer)…
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In the documentation it says
```
# List all available tools in whitebox-tools
print(wbt_list_tools())
```
Instead an Error is printed
```
> print(wbt_list_tools())
All 0 Tools containing key…
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I made a metabolic model and now I have to simulate the growth by using defined media from literature.
I am using following command from COBRA
medium = model.medium
medium["EX_o2_e"] = 0.0
model.…
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All functions should have an examples section in their docstrings showcasing at least some of the functionality, e.g. using optional arguments etc. For example, `flux_variability_analysis` is super po…
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---
id: cobrapy
version: 0.22.1
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_COBRApy/eccb9db64e44b41e026708957f12983e4bb1a24a/biosimulators.json
specificationsP…
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I ran this:
```julia
model = load_model(joinpath("modelfiles", "e_coli_core.json"))
fva_mins, fva_maxs = flux_variability_analysis_dict(
model,
Gurobi.Optimizer;
bounds = objective…
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This repository is ~400 MB including the git tree.
I am wondering if the developers have a way to access the cases without cloning the repo? Like an API?
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We want to drastically speed up fontmake: https://github.com/googlei18n/fontmake/issues/367
Other than switching booleanOperations to something vector-based and fast (https://github.com/typemytype/…