carveme

carveme copied to clipboard

Hi @cdanielmachado, Are there any updates on [Carveme 2.0](https://github.com/cdanielmachado/carveme/issues/158#issuecomment-1202330836) and the universal models for eukaryotes, fungi and yeast? Thanks in advance.

rhernandvel

Incomplete cyanobacteria universe - lacks photosynthesis related reactions

1

Hi, I was trying to model the metabolism of a cyanobacteria species using the cyanobacteria universe file. However, I encountered some unexpected results. Upon examining the file "carveme/data/generated/universe_cyanobacteria.xml.gz," I noticed...

GediminasA

Hello , I was finally able to run the gapfill method in carveme but im curious to know where are the output files located. I already have the output model...

AzizBenA

Multi-process processing error

1

when I use "carve -r ./*.faa ......"，an error occurred： AttributeError: Can't pickle local object 'main..f' It shows that in CarveMe's code, there is a problem that cannot be serialized during...

green34567

HI, After running `carve Bsubtilis_168.faa --universe bacteria --gapfill M9 --mediadb media_db.tsv -v`, I noticed differences between the XML output and the example files provided on the CarveMe GitHub page. Figure...

xuetingyue

My model has more than 400 unbalanced reactions and I dont know why is this, trying to solve them manually takes an enormous amount of time, is there a way...

AnnyMais03

Traceback (most recent call last): File "/home/chencong/anaconda3/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper status = _inner_run() File "/home/chencong/anaconda3/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run return self.run(options, args) File "/home/chencong/anaconda3/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 67, in wrapper return...

ChenCongZ

Inconsistencies between reactions in universe file and in model generated from it

2

Hi I'm using a curated universe file and I noticed some changes in the model generated from it, specifically changes in chemical formulas. Is this related to the optimization method...

Brunokemon