The big little things: the colour of genes, default tracks, words.

I was thinking about the web design process for e50 - our new web interface due out in July (definitely will be late July). We're at the stage now where Fiona is going to be asking users their preferences for all the "little things" which make no difference to technical aspects of the web site but make a pretty big difference to the useability. Like, for example, how do we colour our genes? This is a long standing debate where everyone has an opinion and everyone's opinion is right - at least for them. (only 2 colours, and the colours should distinguish manually annotated genes from automatic says one person. No - use the whole spectrum of colours, and make sure we distinguish non-coding RNA genes from pseudogenes from protein coding genes and indicate which ones have orthologs - to mouse. No to rat. No - instead of that use GO functional catagories to colour genes. Or the number of non coding SNPs. Or the gene-wide omega value from the dn/ds measurement)

Sometimes people look at this debate and say that this is a clear area for user defined colours. Which is sort of true for 10 seconds, but - not really. Firstly most users are not going to get around to changing options - partly due to the fact they have better things to do (like design experiments and run them!), partly because this sort of configuration is just a bit too geeky and partly because, to be honest, if they are into configuring things we'd like them first off to work out which tracks that would like displayed (more on this below), and colouring genes should be low on their list. Secondly we want to provide a scheme which feels natural to the most number of people. Hence a rather long series of options to choose from currently being proposed.

The same argument goes for default tracks. (I can't imagine not having SNPs on my display! I can't imagine not having the ESTs switched on!). Everyone has an opinion and everyone is right. Here it is clear we've got to make sensible default decisions (which are also heavily, heavily speed optimised - sadly the new Collections framework wont be ready for SNPs for 50, which is annoying, as really we want SNP density these days in human, but all the other obvious default tracks are pretty well optimised, including some funky scaling stuff to get the continuous basepair comparative genomics measure to come back sensibly when you are zoomed out). But then our main task it to get the user to explore as the "wouldn't it be nice to see xxxx, I wonder if Ensembl has it" with configuration system which is very enticing, but not in the way, and importantly for the non-expert user, not completely overwhelming. In our e50 design means more hierarchy in the options so they can be grouped (itself a bit of pain to handle - we've got alot of tracks), and a nice "light box" effect over the display which reassures you that (a) the thing that you were looking at wont disappear (b) the display will come back quickly. I think we're on the right path here for the configuration, but we still have decide on the default tracks (for me the only obvious one is "Genes").


Finally we've got the mundane business of which words do we use for each of our "pagelet" displays. (our new pagelets are very nice, and in our latest round of testing, >50% of the in-the-lab biologists liked not only the pagelets, but a specific layout of them. less than 10% preferred the current ensembl display). So - we need one or two words to describe "A graphical representation of a phylogenetic tree of a gene with duplication nodes marked". Hmmm. "Gene Tree". Or "Phylogenetic Tree"? (phylogenetic is a bit of a long word, and might get in the way of the menu...). What about "a text based alignment of resequenced individuals with the potential to mark up some features of interest". Is this - "resequencing alignment" or "individual alignment" or "individuals".



If you'd like to take part in this, email survey@ebi.ac.uk (perhaps cc'd to Xose - xose@ebi.ac.uk) to make sure you are on our list. Ideally we'd like you to be wet-lab biologists. We have alot of in-house or near-in-house opinions from bioinformaticians, and in anycase, bioinformaticians are happier to explore configurations etc. Its the researcher who will be visiting us - say - once or twice a month which we think is the main user to optimise for (again, more frequent users we hope will explore configuration to match things perfectly for them).



More on other e50 topics soon - speed, the importance of chocolate in bribing web developers and the end game for e50!