Comments made by J. N. Enrique, ph.D.
Comments made by J. N. Enrique, ph.D.
I really found GEMSiRV as a very complete and interesting tool for metabolic reconstructions.
I really found GEMSiRV as a very complete and interesting tool for metabolic reconstructions.
Despite that by using models that you provide, the importing step was very straight forward; the greatest difficulty that I have found during the testing process has been to import no-standard models to GEMSiRV. I was unable to import successfully some models. Especially difficult was to import the recent model of Chlamydomonas published by our group and one of my unpublished models. After to use extensively “TextReplacer” I could import them, but some of the compartments were not recognizes by GEMSiRV. Specifically, the thylakoid was replaced by cytoplasm in all the attempts that I did. As consequence, I couldn't evaluate these models. I know that this is a critical step due the different source of the available models, but I’m wondering why I always found problems in models having thylacoid “[u]”.
Despite that by using models that you provide, the importing step was very straight forward; the greatest difficulty that I have found during the testing process has been to import no-standard models to GEMSiRV. I was unable to import successfully some models. Especially difficult was to import the recent model of Chlamydomonas published by our group and one of my unpublished models. After to use extensively “TextReplacer” I could import them, but some of the compartments were not recognizes by GEMSiRV. Specifically, the thylakoid was replaced by cytoplasm in all the attempts that I did. As consequence, I couldn't evaluate these models. I know that this is a critical step due the different source of the available models, but I’m wondering why I always found problems in models having thylacoid “[u]”.
In summary, I think although additional algorithms could be included for the refinement process, GEMSiRV, together GBKPaser and MrBac will be an very useful tool in order to accelerate the metabolic reconstruction process.
In summary, I think although additional algorithms could be included for the refinement process, GEMSiRV, together GBKPaser and MrBac will be an very useful tool in order to accelerate the metabolic reconstruction process.
Comments made by Y. H. Chen, ph.D.
Comments made by Y. H. Chen, ph.D.
