Henning Redestig

Implement better errors

4

Once fixed in optlang, use the better errors in `get_solution` etc to avoid the catch-alls

all public objects should be accessible via `import .. from cobra` or predictably one of the few submodules. Go through the package and ensure that everything that should be supported...

msdtc failing with mcr.microsoft.com/mssql/server:2019-CTP3.2-ubuntu

9

I run docker 18.09.6 on centos 7 and followed the instructions for setting [MSDTC capable SQL Server](https://docs.microsoft.com/en-us/sql/linux/sql-server-linux-configure-msdtc-docker?view=sql-server-ver15) to serve an application that relies on MSDTC. That application cannot connect to...

Implement optstoic http://www.nature.com/articles/srep16009 Apply to previously generated heterologous pathways from pathway predictor / optstrain

trouble reverting reaction changes

1

test_reactions_in_group_become_blocked_if_one_is_removed fails when rolling back changes to the model due variable not being properly removed

_From @hredestig on January 10, 2017 15:1_ Original paper: http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1003378 Used very effectively in http://www.sciencedirect.com/science/article/pii/S1096717616300350 Kristian has already done some work towards this goal https://github.com/biosustain/cameo/blob/master/cameo/flux_analysis/structural.py _Copied from original issue: DD-DeCaF/scrum#37_

``` python from cameo import models model_orig = models.bigg.iJO1366 py = product_yield(model.reactions.EX_thr__L_e, model.reactions.EX_glc__D_e) optswap = CofactorSwapOptimization(model=model, objective_function=py) optswap.run(max_evaluations=2000, max_size=2) ``` gives a plot that never shows up instead we get...

Iteration happen over all residue tokens of the tokenized sequence (first index 1). The corresponding residue in `sequence` exludes the start token so `i - 1`.

scaling of gecko model

4

without a directly reproducible example, I note that upper bounds for protein draw reactions are often very small. With both cplex and glpk I have noted that this causes numerical...

Wheels for macos python 3.11

1

Hi, Would you care to make wheels for macosx and python 3.11 please? When installing from source I sadly get ``` error: subprocess-exited-with-error × Running setup.py install for edlib did...