I really like the front page mock-up, much cleaner and less confusing. Couple of things resolving weirdly on my browser (FireFox, Linux) though: I can't see the box you type the text into on the front page, and the tree view is a bit distorted, all the filter boxes too big, can't see top of the term names. But I guess these are the sort of things we'd sort out later?
an idea - can we make the tree browser so when you click a term, it opens the branch below, rather than taking you to term details, and at the end of each term, we have a little icon that says (genes) or (details) or something? This should stop people clicking the high level terms so often...?
Another little thing, can we have a mouse-over for the pie chart icons?
I like this a lot. The design is much cleaner and easier to read than previously. I love that the results open in the same page and not in a smaller new window as before. I'm using Firefox, but the only display problem I see is with the Gene Product Filter boxes extending too far to the right in the left menu bar. On the front search page the 'Query by Sequence' is in bold whereas the 'Browse GO' and 'Advanced Query' are not - is this intentional? I can see that highlighting the search results in blue is less offensive to the eye, but I kind of feel it's too much blue, so the highlights aren't very obvious - maybe another colour to contrast with the blue but not give you a headache - light grey??