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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Basidiomycete fungi model #158

Open shacharje1 opened 2 years ago

shacharje1 commented 2 years ago

Hi Daniel, I was wondering if you think ill be able to use your package to create a metabolic model for Basidiomycete fungi?

And if not could you recommend a different tool to use?

Thank you very much, Shachar.

franciscozorrilla commented 1 year ago

Hi Shachar,

As outlined in the original publication, CarveMe was developed for the reconstruction of prokaryotic organisms. To reconstruct fungi models you would have to generate your own yeast universal model as described in the advanced usage documentation. We are currently working on CarveMe 2.0 and hope to provide additional specialized universal model templates, such as one for fungi. Daniel also has this repo with 36 yeast strains that you may find interesting.

For now I would recommend you to check out the Chalmers SysBio Github page, where they host and actively develop yeast models, perhaps you may find this repo useful as well.

You could also try using the RAVEN toolbox to reconstruct your particular species' model from homology using a well curated template. We outline such a method in this recent protocol paper.

Best wishes, Francisco

shacharje1 commented 1 year ago

Hi Francisco, Thank you very much! I will check these resources. All the best, Shachar

‫ב-2 באוג׳ 2022, בשעה 13:56, ‏‏Francisco Zorrilla @.***> כתב/ה:‬

 Hi Shachar,

As outlined in the original publication, CarveMe was developed for the reconstruction of prokaryotic organisms. To reconstruct fungi models you would have to generate your own yeast universal model as described in the advanced usage documentation. We are currently working on CarveMe 2.0 and hope to provide additional specialized universal model templates, such as one for fungi. Daniel also has this repo with 36 yeast strains that you may find interesting.

For now I would recommend you to check out the Chalmers SysBio Github page, where they host and actively develop yeast models, perhaps you may find this repo useful as well.

You could also try using the RAVEN toolbox to reconstruct your particular species' model from homology using a well curated template. We outline such a method in this recent protocol paper.

Best wishes, Francisco

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