Unable to run cameo design API

[SiYeon-Ju]

Hi, I tried to run a example of design API (https://cameo.bio/08-high-level-API.html). But, i had no results. What should I do?

############################################ [ Python Ver 3.7.14 in Google Colab] !pip install cameo !pip install cobra==0.17.0

import cameo import cobra from cameo import api from cameo.parallel import MultiprocessingView

mp_view = MultiprocessingView() api.design.options.max_pathway_predictions = 4 api.design.options.heuristic_optimization_timeout = 30 report = api.design(product = 'vanillin', view = mp_view) ###############################################

Starting searching for compound vanillin Found 1 compounds that match query 'vanillin' Predicting pathways for product vanillin in Saccharomyces cerevisiae (using model iMM904). ERROR:cameo.strain_design.pathway_prediction.pathway_predictor:No pathway could be predicted. Terminating pathway predictions. ERROR:cameo.strain_design.pathway_prediction.pathway_predictor:None (time_limit) Optimizing 0 pathways

[carrascomj]

Not an expert on the high level design API, but it seems like your computer hit the timeout.

You can try either changing the timeout (you set it to 30 as in the documentation) or the linear programming solver. Different underlying linear programming solvers need more or less time to run the simulations, and, of course, it also depends on your hardware.