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cdanielmachado
CarveMe: genome-scale metabolic model reconstruction
When I build a model using the genome sequence of a single bacterium, the code I use is: 'carve genome.faa -o model.xml'. Why do I encounter the error 'Can't find...
Hi!, sorry if this is kind obvious but I'm having a hard time understanding how to create a customized universe model. According to the readme. > A script with some...
Hi! i want to start saying that CarveMe is a great tool for metabolical network reconstruction. By far it is the fastest and more user friendly than anything around. I...
Not super-important, but I suggest to rescale the biomass equations so they sum exactly to 1 :) The one for bacteria sums to 1.03
Hi, When I was using libSBML to read the model file created with CarveMe, I got multiple errors similar to the following error: 10773: (20623) Error A Species object must...
There are many issues with the compound formula. for example, in tnt (2 4 6 Trinitrotoluene), the formula should be C7H5N3O6, like in BIGG, but in Carveme it is ambiguous...
Hi Professor. I'm a newbie and I'm trying to construct a community metabolic model using carveme in order to analyze the metabolic characteristics of the community using smetana solver. I...
Hi, I have a problem installing CarveMe related to diamond. The version downloaded with conda (0.9.14) as recommended on the installation page returns the error: Error: Database was built with...
Using carveme v1.5.2. When the input proteome contains 2 or more very similar sequences, each of them well aligned (bitscore > 100) by Diamond on the same BiGG_gene (model.gene), only...
Using carveme v1.5.2. My opinion reading your code is that there is no real check whether a particular protein complex, as it is defined in a particular model for a...
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CarveMe: genome-scale metabolic model reconstruction