Chen Liao

FBA solutions are different between Mackinac and Cobra

1

I generated a metabolic reconstruction using Mackinac and found that the objective values obtained between Mackinac (mackinac.optimize_modelseed_model) and Cobra (model.optimize()) are different. The former gives 1.66 while the latter gives...

Hi, I tried to run this pipeline and the first two steps work very well. However, it seems to get stuck there forever for the following line of codes (particularly...

KeyError: 'unclassified (taxid 0)'

2

When I run make_kreport.py, it generates the following error (KeyError: 'unclassified (taxid 0)'). Does anyone know what causes it? PROGRAM START TIME: 09-05-2020 13:40:52 >> STEP 1/4: Reading taxonomy kraken2_standard_09042020/mydb_taxonomy.txt......

Hi Rob, I have successfully installed PyFBA using python2. However, I failed to update to python3 after following the instructions (recompile pyglpk). The output is "SyntaxError: Missing parentheses in call...

I applied croissance to analyze growth curves of Pseudomonas aeruginosa grown on glycerol and the exponential phases identified by Croissance seem to include lag phases (and gives 0 lag time)....

Question on the parameter "correct_NA_tracer"

2

I recently encountered IsoCor and it fits my need so well! However, I am confused about the parameter **correct_NA_tracer** in the function _isocor.mscorrectors.LowResMetaboliteCorrector_. Suppose I want to correct the observed...