Quilt plots. Like heat maps, only…heat maps

Stephen tweets:

A "quilt plot"

A “quilt plot”

Quilt plots. Sounds interesting. The link points to a short article in PLoS ONE, containing a table and a figure. Here is Figure 1.

If you looked at that and thought “Hey, that’s a heat map!”, you are correct. That is a heat map. Let’s be quite clear about that. It’s a heat map.

So, how do the authors justify publishing a method for drawing heat maps and then calling them “quilt plots”?
Read the rest…

Genomic analysis of Pseudoalteromonas tunicata

Some years ago, I provided advice and a little analysis for a group at UNSW studying marine bacteria. It’s nice to see that they remembered me:

Thomas, T., Evans, F.F., Schleheck, D., Mai-Prochnow, A., Burke, C., Penesyan, A., Dalisay, D.S., Stelzer-Braid, S., Saunders, N., Johnson, J., Ferriera, S., Kjelleberg, S. and Egan, S. (2008).
Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment.
PLoS ONE 3:e3252.

If correlating genomic features with microbial physiology is your thing, go and check it out. The article is open access, for your pleasure – as are five of my last six efforts, I just noticed.

A small achievement

Moving to a new group and a new project is always difficult. However, one of the better aspects of being a bioinformatician is that you can often contribute to other projects – which can be a bonus when your own are not progressing so well.

I’m happy to announce:

Thakur, A.S., Robin, G., Guncar, G., Saunders, N.F.W., Newman, J., Martin, J.L. and Kobe, B. (2007). Improved Success of Protein Crystallization Sparse Matrix Screening with Heterogeneous Nucleating Agents. PLoS ONE 2:e1091. Open Access

My contribution was very minor; some writing and a little statistical evaluation (although the method that I had in mind didn’t make it to the final version). The take-home message is: if your protein won’t crystallise, try throwing some dried seaweed into the mix! It’s not ground-breaking stuff but it’s solid enough, so we decided it was ideal for PLoS ONE, which gives us the added warmth and fuzziness of supporting OA publishing.