Daniel Machado

I think spontaneous does not cover all cases. There could simply be reactions that are known (or supposed) to occur, but the respective protein has not been identified. I guess...

Hi Pedro, CarveMe matches input sequences to an internal protein database that connects BiGG genes to BiGG reactions. The integration with eggnog-mapper required adding BiGG gene identifiers as an additional...

Hi Pedro, Sorry for the late reply as well. By default CarveMe is expecting a TSV file generated with diamond. If you generate the columns in the same order as...

Hi Zoey, Yes it is possible to run CarveMe inside a docker container. I have done it with cplex. Unfortunately we don't get the same results when running CarveMe with...

Hi Antoine, Sorry for the late reply. I have an automated benchmark for gram-positive and gram-negative bacteria but not for cyanobacteria. So it is possible that during the last manual...

That's strange. Can you give more details on that? What part of the model is invalid SBML ?

I think the "boundary" attribute became mandatory recently, and we have not updated the SBML output to comply with that. But anyway that attribute is not used by cobrapy or...

Ok, thanks for clarifying that.

Sorry for the late reply. Can you send me the SBML file?

cdanielmachado at gmail