Hi, I see the following error:

~\anaconda3\lib\site-packages\mewpy\simulation\cobra.py in
4 from cobra.core.model import Model
5 from cobra.core.solution import Solution
----> 6 from geckopy.gecko import GeckoModel
7 from cobra.flux_analysis import pfba, moma, room
8 from mewpy.simulation import SimulationMethod, SStatus

ModuleNotFoundError: No module named 'geckopy'

Thanks.

Hi, I encountered this error while trying to define a new reaction over/under expression problem instance.

TypeError Traceback (most recent call last)

Cell In [162], line 2
1 # run the optimization
----> 2 ea = EA(problem, max_generations= 100, visualizer=True)
3 final_pop = ea.run()

File ~\AppData\Local\Programs\Python\Python311\Lib\site-packages\mewpy\optimization_init_.py:154, in EA(problem, initial_population, max_generations, mp, visualizer, algorithm, **kwargs)
151 else:
152 engine = engines[engs[0]]
--> 154 return engine(problem, initial_population=initial_population, max_generations=max_generations, mp=mp,
155 visualizer=visualizer, algorithm=algorithm, **kwargs)

File ~\AppData\Local\Programs\Python\Python311\Lib\site-packages\mewpy\optimization\jmetal\ea.py:71, in EA.init(self, problem, initial_population, max_generations, mp, visualizer, algorithm, **kwargs)
69 self.ea_problem = JMetalKOProblem(self.problem, self.initial_population)
70 else:
---> 71 self.ea_problem = JMetalOUProblem(self.problem, self.initial_population)
72 self.crossover, self.mutation = self.ea_problem.build_operators()
73 self.population_size = kwargs.get('population_size', get_population_size())

TypeError: Can't instantiate abstract class JMetalOUProblem with abstract methods name, number_of_constraints, number_of_objectives, number_of_variables

Boa tarde,
Envio em anexo o modelo metabólico obtido pela app modelSeed na kbase, o qual segundo o FBA da plataforma indica um fluxo de biomassa de cerca de 19 em meio completo. Contudo, o mewpy indica "None" quando o objetivo definido é a biomassa.
M_formicicum_complete_media.SBML (1).zip

Hello!
I'm trying to build a tissue-specific model using the Gimme algorithm, but the resulting model cannot grow. I was looking at the test of Gimme, and they are incomplete for the build model option.

Can you help me with this?

Hi Vitor,

When I use the visualizer option I get the following error:

~/miniconda/miniconda3/envs/py36/lib/python3.6/site-packages/mewpy/optimization/ea.py in dominance_test(solution1, solution2, maximize)
    176     best_is_two = 0
    177 
--> 178     for i in range(len(solution1.fitness)):
    179         value1 = solution1.fitness[i]
    180         value2 = solution2.fitness[i]

AttributeError: 'KOSolution' object has no attribute 'fitness'

Hello. I installed mewpy through pip install- it installed the dependencies like cobra, but the modules for mewpy cannot be imported:

ModuleNotFoundError: No module named 'mewpy'

It is in my pip list, so I assume the problem's somewhere else?

This applies to all its modules, I reinstalled this package github, too, but it is not working yet.

Hi,

Following your tutorial for enzymatic constraints, I get error for loading GECKO model: "KeyError: 'model name must be one of ", using either the provided model in the repository or an external model. The path to the .xml file is also correct.

Thanks.

Hi Vitor,

Is there an option to simplify the solution pool after optimization? In the final population I often see many solutions with same fitness value and different number of knockouts.

Best regards,
Daniel

For the GKOProblem problem, it takes too long to calculate essential genes ( for iML1515 model), so why not just use the find_essential_genes function in the COBRApy, which gets results in seconds.

Hi, I see the following error message:

ImportError Traceback (most recent call last)
in
16
17 # build a new problem instance for enzymatic OU
---> 18 from mewpy.problems import GeckoROUProblem
19 problem = GeckoROUProblem(model, fevaluation=[
20 evaluator_1, evaluator_2], envcond=envcond)

ImportError: cannot import name 'GeckoROUProblem' from 'mewpy.problems' (C:\Users\anaconda3\lib\site-packages\mewpy\problems_init_.py)

Thanks.

Hi,

I wanted to ask what the numbers in front of reactions in the modification part actually mean?

I ran the example of OptRAM in the documentation (https://mewpy.readthedocs.io/en/latest/problems.html) and the examples in the code (the two codes are slightly different), both runs resulted in errors, what is the reason?

Hi, mewpy team! I have a problem running gene and reaction essentiality function. I used a GSM model with integrated transcriptomic data using RIPTiDe method. So, the analysis for initial model (without transcriptomics data) showes a list of essential genes and reactions but the list is blanked for the transcriptomics-guided model. Moreover, Cobrapy and Optflux functions for the same analysis returns non-zero list of genes/reactions for the last version of the model. In addition to that, the old mewpy version 0.1.11 found them too. Can you give a cue, where is a problem?
Thanks in advance for your reply!