Silvio Waschina

The gapfilling algorithm was updated on the cobrar branch. The key was indeed to reduce the bound violation tolerance in cases where an optimal solution returned by the initial pFBA...

Yes, the master branch still relies on the sybil packages. Since the fix involved quite some changes in the gapfilling algorithm, I just made the changes to the "cobrar" branch...

Sorry for getting back to the issue this late. In the end, the problem was simply because Nickel (Ni2+) was missing from the gut medium. Nickel is part of the...

Hi @cmkobel , It is great to see gapseq on conda! Thank you! As @jotech already said, we are currently trying to get rid of all sybil-related code and dependencies....

Hi @cmkobel A quick update: We are nearly there with the first [cobrar](https://github.com/Waschina/cobrar) release. We are currently replacing sybil with cobrar in the gapseq code on a separate [branch](https://github.com/jotech/gapseq/tree/cobrar) and...

The first stable cobrar version is released: https://github.com/Waschina/cobrar/releases/tag/v0.1.0 A bioconda recipe for cobrar has a pull request, which awaits a review before a potential merge: https://github.com/bioconda/bioconda-recipes/pull/50354 Meanwhile, I am working...

"cobrar" is now on bioconda. However, I will need to release an update, because I noticed that infeasible LPs were not well-handled in v0.1.0.

I'd suggest to wait until I updated cobrar to v0.1.1. I'm running final tests.

Hi @cmkobel The release is out. Feel free to let us know if there is anything we can talk about regarding the bioconda package. Thank you!

Could you report the output of `./gapseq test`?