Silvio Waschina

The ModelSEED biochemistry database is very comprehensive and integrates several reaction and metabolite data sources, including MetaCyc (https://academic.oup.com/nar/article/49/D1/D575/5912569).

Hi Arianna, The workflow should be able to recognise that the input is a protein multifasta. Thus, something like the following should work: ```sh gapseq doall -K 16 ecoli.faa.gz ```...

Could you check the first log lines from the doall-call? It should look similar to this: ``` /tmp/tmp.UG83rhZH9N Protein fasta detected. Predicted taxonomy: Bacteria Checking updates for Bacteria /home/silvio/Software/gapseq/src/../dat/seq/Bacteria Reference...

Yes, this looks fine. It's the "FASTA-Reader: Ignoring invalid residues at position(s): On line" messages that worry me. It occurs in the transporter prediction script. Is there any line in...

Okay, thank you. The issue is most likely due to your gapseq version. There was a bug-fix in September 2022 (https://github.com/jotech/gapseq/commit/642549cdbd76bd2e71efc3f629781bae60da4834) in the protein fasta handling in the transporter prediction....

Hi Arianna, mhh, I am not sure what's happening here. Could you share all the logs or even the genome fasta file (if it is public)? When I can reproduce...

Hi, Just as an update: I have locally implemented a POST-based mapping from uniprot accessions to UniRef50/90. When testing, the POST-version was actually slower than the the GET method, that...

Uniprot queries and downloads should now be optimized and much faster.

Hi! I can confirm the issue with several AGORA2 models (version 2.01). In addition to the three points mentioned by @cdiener, some SBML parsers may fail to read specific models...

Hi @songmj86 the xml file is the genome-scale metabolic model in [SBML-format](https://sbml.org/documents/what-is-sbml/). To predict metabolite production you can read the xml file and use flux-balance-analysis using software packages such as...