Silvio Waschina

Thanks @nick-youngblut. I agree that a conda env yaml file would clean up the instructions. I'll update the conda instructions in January.

Hi Minghao Gong, thank you for you questions and for using gapseq! As pathway references, gapseq mainly uses the pathways described in MetaCyc. The pathways IDs are stated in the...

Hi Edoardo, I'll have a look at this case next week. What I usually do in such cases is to compare which reactions were gapfilled in each situation. Will let...

Hi Rodrigo, thank you for the feature request. Supporting protein-fasta as input is on our TODO lists, but we cannot say when we will be able to implement this, as...

It is now implemented. Please refer to #132

Hi Erique, could you provide some more detail on what you would like to achieve? Are you referring to the `gapseq medium` module to predict a gap-fill medium? At what...

Thank you very much for pointing out this issue. With the commit 82ff4ad1c5c5f9c2bba17693b7e43ee8839330c4 we should have a working sequence download again. It works in three steps: 1. Find UniprotKB IDs...

Hi, I'm afraid, that we can't get the additional columns exported to sbml. SBML has only limited and pre-defined columns of model, reaction and metabolite attributes that are exported. In...

Hi! Thank you for the suggestion and for using gapseq :) We are aware that the runtime is long compared to other tools such as carveme or modelseed. Currently, we...

With the latest changes, gapseq should be faster. Also, gapseq now allows users to specify the number of parallel processes. You can use the Option `-K 4` to use four...