carveme

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Hey @cdanielmachado, I have found an error when CPLEX is not used as the default solver (also reported in this [closed issue](https://github.com/cdanielmachado/carveme/issues/175)). It seems due to this single line: https://github.com/cdanielmachado/carveme/blob/766291005915cc51e8eebb3bd0bfff2dcb03cdc0/carveme/__init__.py#L14...

Robaina

hi, Recently I have been using Carveme to construct a metabolic model for a single microbial genome. However, the nutrient component (Bis(2-ethylhexyl) phthalate, chemical formula: C24H38O4) I am using does...

microbial-cookie

Hi, are there any example codes used for carveme reconstructions that I might be able to look at? Thank you!

parsanayyara

Hi, I am using carveme on a cluster but it is using all available cores and I would like to set it so that it uses less cores. How can...

stephane-wang

Inconsistencies in metabolite charges on pre-generated universe files.

1

Hi, I have been using carveme to generate metabolic reconstructions of bacterial isolates and testing them with memote. In the "Charge Balance" test, memote is routinely flagging ~200 reactions with...

Gscorreia89

Is it possible to add this to bioconda so it can include all of the dependencies in an environment such as diamond?

jolespin

Gapfilling using a curated sbml?

1

Hello, Is it possible to gapfill using another GEM? I know that its possible to reconstruct based on another gem but could we use one to gapfill? Thanks. :-D

pushing2

I am working on building a probiotic model, and I want to use CarveMe to quickly build a probiotic model. I try the Carveme software and use the cmd "carve...

Dodolove725

example command meets with format mistak in py3

1

Hi Everybody, I tried to run Carveme on my Jupyter notebook with py3 kernel, as the document shows it's now support python 3.6. I installed the package through the command...

Chenjlin28

I've been generating models from a range of bacterial isolates using my own custom media with the gapfill and init flags. Full command is: `carve --dna --output --gapfill MRS --init...

ryan-boobybiome