Yeast-GEM visualization?

[forxhunter]

Hi, I am wondering if anyone has already created a visualization map with tools like Escher or DD-DeCaF. I am currently interested in doing so on yeast-GEM 9, it would be better if I can start on someone's legacy work

[edkerk]

To my knowledge, there is no active development around Yeast-GEM visualization. DD-DeCaF is no longer functional, MetabolicAtlas has some yeast maps, but these are mostly suited for overlaying omics data, it it not well-suited for flux data. The maps are available here as SVG, and it appears like they are based on the SBGN/SBML files here, but I'm uncertain if this is correct. There is also this outdated effort.

Please feel free to reach out for further discussions, as a good visualization map would be extremely valuable.

[forxhunter]

To my knowledge, there is no active development around Yeast-GEM visualization. DD-DeCaF is no longer functional, MetabolicAtlas has some yeast maps, but these are mostly suited for overlaying omics data, it it not well-suited for flux data. The maps are available here as SVG, and it appears like they are based on the SBGN/SBML files here, but I'm uncertain if this is correct. There is also this outdated effort.

Please feel free to reach out for further discussions, as a good visualization map would be extremely valuable.

Hi, edkerk, I am just working on building up a pathways map based on yeast-gem 9. There is one paper published by Jen Nielsen visualized yeast-gem 8.3.4 with celldesigner. https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/full/10.1002/bit.27943.

Based on this, I am currently working on naming those reactions and metabolites not showing up in kigg database and try to build up separete pathway maps in escher for yeast-GEM9.0.1.

[forxhunter]

I can show you my works once they are done. By the way, there are roughly 600 reactions not included in the yeast-GEM 9.0.0, which I can acquire from iMM904 or iND750.

is there a reason? Or should I ask how you summrize all the reactions into the yeast-GEM