Put up a list of awesome metabolic engineering tools somewhere?

[bdelepine]

Hello everyone!

I was thinking about last COBRApy meeting and more specifically about how difficult it is to onboard people to use the right computational metabolic engineering tools (master students that end up asking the same questions on the Google Group, but also wet-lab researchers that don't know which tools to use, etc.). I wonder if we could improve that by putting up something like an awesome list of metabolic engineering resources. We could refer to this list in COBRAPy doc and README in an attempt to redirect the exploration of new users.

Of course, we would need to discuss the scope of the list (only Python? only GEM-related? only those maintained en the last X years? etc.).

Below a quick showcase of what I have in mind:

Learning resources

• Palsson lectures on systems biology
• Metabolic modeling for cell factory engineering

Genome-scale models repositories

• BiGG Models

WebGUI to reconstruct GEM

• MetaNetX
• ModelSEED
• MetExplore

Metabolic network visualisation tools

• Escher
• MetExploreViz
• Cytoscape with cy3sbml app

GEM simulation software

• COBRA for MATLAB, COBRApy
• CAMEO
• OptFlux
• Caffeine

Yet another category

• More items

What do you think? Would you expect it to be useful for newcomers?

[Midnighter]

I don't have the bandwidth right now to add to your list but in general I think it's a great idea. As you mention, it will help to set the scope of the list early on.