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 There is also this outdated effort.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 There is also this outdated effort.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

[mihai-sysbio]

There are many ways to draw pathway maps. In Metabolic Atlas we have chosen to prioritize quality and utility, i.e., maps should always have good resolution, which lead us to the SVG format, and utility, which meant maps should be also big when necessary. This meant that we have created our own compact SVG format, which can support multiple hundreds of reactions in a map. The downside has been that maps don't always look pretty, and they are also hard to edit.

For reference, the maps were initially worked on in this repo https://github.com/SysBioChalmers/yeast-maps, from which the final SVGs were copied to Metabolic Atlas.

@forxhunter could you shed more light on what is the desired output you are after? If you'd like to continue from the SVG maps in Metabolic Atlas, let me know.