Metabolic maps

The giant Mycobacterium tuberculosis genome has a large central area that is presently empty, save for a few molecular models. That is not for lack of potential content ideas and I'm presently pondering how best to represent metabolism in the M. tuberculosis bioscape (as I call it until I can think of a better name).

The pathways in the image above are from an Open Access paper from Palsson's lab and go with a metabolic model they published recently. The chequerboard in the background is a touchpos-based menu; the image next to it is a one-prim representation of the 4-prim map my avatar is standing on.

Many of the images in the Palsson paper are large and getting them into SL is going to take some work. I'd like to be able to hack the SVG they come in but suspect I may have to settle for raster image format. Using QuickTime or HTML would also be nice but there are limitations in terms of the number of media URLs.

The Palsson model presently contains 661 genes catalysing 939 reactions and is presumably a subset of what the real bug can do with its 3800-odd genes, though admittedly not all encoding enzymes. From an educational perspective, completeness at a fine-grained level is not a major issue though making connections between genome and metabolome.

At a basic level, the exercise of mapping the gene id onto the unrelated enzyme abbreviation on the metabolic map makes a useful point regarding naming and databases. The gene markers on the genome can rez physics-based prims representing proteins. These can be taken into inventory and used to decorate the metabolic map.

So far as the TB build is concerned, I think we are looking at a proof-of-concept within a proof-of-concept so I shall start with just a few pathways in the first instance.