Further developments towards a genome-scale metabolic model of yeast

Paul D Dobson, Kieran Smallbone, Daniel Jameson, Evangelos Simeonidis, Karin Lanthaler, Pnar Pir, Chuan Lu, Neil Swainston, Warwick B Dunn, Paul Fisher, Duncan Hull, Marie Brown, Olusegun Oshota, Natalie J Stanford, Douglas B Kell, Ross D King, Stephen G Oliver, Robert D Stevens and Pedro Mendes

BMC Systems Biology. 2010;4:145

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Background

To date, several genome-scale network reconstructions have been used to describe the metabolism of the yeast Saccharomyces cerevisiae, each differing in scope and content. The recent community-driven reconstruction, while rigorously evidenced and well annotated, under-represented metabolite transport, lipid metabolism and other pathways, and was not amenable to constraint-based analyses because of lack of pathway connectivity.

Results

We have expanded the yeast network reconstruction to incorporate many new reactions from the literature and represented these in a well-annotated and standards-compliant manner. The new reconstruction comprises 1102 unique metabolic reactions involving 924 unique metabolites - significantly larger in scope than any previous reconstruction. The representation of lipid metabolism in particular has improved, with 234 out of 268 enzymes linked to lipid metabolism now present in at least one reaction. Connectivity is emphatically improved, with more than 90% of metabolites now reachable from the growth medium constituents. The present updates allow constraint-based analyses to be performed; viability predictions of single knockouts are comparable to results from in vivo experiments and to those of previous reconstructions.

Conclusions 

We report the development of the most complete reconstruction of yeast metabolism to date that is based upon reliable literature evidence and richly annotated according to MIRIAM standards. The reconstruction is available in the Systems Biology Markup Language (SBML) and via a publicly accessible database (http://www.comp-sys-bio.org/yeastnet/).

On Meetings and Conferences

"I think you might do something better with the time," Alice said, "than wasting it in asking riddles that have no answers."

A quote that often pops into my head in meetings and at conferences.

Alice in Wonderland, Lewis Carroll (1865)

Masters Courses - We are not amused

Remember graduation day? Your Mum getting all emotional? Wearing a suit, a cloak and a stupid hat in the middle of summer? The photographer giving you a piece of PVC pipe to hold instead of your degree certificate?

Queen Victoria, who dished out many a university charter.

"I'm not happy" - that was her catchphrase.

Then what? For me it was a career in academic research - I never wanted to do anything else. I was fortunate, I found a PhD position without first doing a Masters. I've met a lot of Masters students, ranging from the clearly talented to the nearly useless. Not all of these people want a career in research, which is a good job because I wouldn't trust some of them to sit the right way on the toilet, never mind work in a laboratory. How do these people get on their courses?