The Real Protein Structure Viewer
March 20, 2008
One of my bosses (Bette Korber)
has a workshop
coming up (in Banff - but she didn't invite me along :( )
where she wanted to be able to show off some new stuff.
As it happens, much of her new stuff is projects I have been doing.
So she wanted the mosaic vaccine design tool suite
and my protein sequence structure feature viewer
to be put on the public HIV server right away.
So, there they are, even though the protein viz thing isn't really finished.
When Bette says 'jump', everybody tries to see who can jump the highest.
We really need a better name for that protvis thing.
The mosaic vaccine thing is also pretty cool,
although I only wrote part of that set of tools.
is that you can design vaccines for badass hyper-variable viruses
like HIV and Ebola by making artificial proteins that are a
kind of 'super-combination' of pieces of the real virus's proteins.
The trick is in how you distill the real proteins -
it's a pretty sweet idea, and it just might work, too.
Did I mention before that It Is Cool to be working on a cure for AIDS?
The Protein Structure Viewer
Feb. 3, 2008
a copy of a tool I'm building for
the team I work with
at the lab.
There's also a link in the sidebar at the right.
I'll keep my copy as similar as I can, but by the time I'm done with
this tool, it will be hooked in to the infrastructure of the HIV
website in ways I can't emulate here. So my local version will be more
of a demo, and won't do all the cool stuff that the real thing will do.
When the real one goes live, I'll probably put a link to it here too.
In the meantime, if you know anything about biochemistry, the demo here
is already fairly interesting.
It uses Jmol,
a nice java applet for viewing molecules.
But I've added a little magic of my own,
to make the tool useful for AIDS/HIV researchers.
Users will be able to bring a set of sequences, perhaps newly sequenced
from a patient of interest, and align it to a reference sequence we
have and an HIV protein sequence for which we have solved the structure.
The tool shows a 3-D graphic of our protein, and shows them how and
where the sequence(s) they bring are different from it.
The part that will be of interest, we think, is that users can then
select parts of this sequence and the tool will 'highlight' the
corresponding amino acids in the protein in the graphic, immediately.
They can see which physical parts of the protein are affected by
mutations in their sequences, compared to the reference and protein
Try it out, if you are interested in that kind of thing.
A Little of That Ol' Dynamic Content
Jan. 21, 2008
Well, it continued to bother me that I was 'blogging',
but I was doing it backward.
I just can't seem to get with the anti-chronological-order thing.
So I decided I'd have it both ways.
Click on the '[switch to (other) order view]' link above
to reverse the order of my posts.
Those of us from the (really) old school who prefer to read things
from past to future, older to newer, can still do so.
You youngsters can read things the new way.
OK, OK. I realize that the entire point of blog ordering
is so that you impatient folks can read the very latest stuff
without having to do anything - no clicking, no scrolling.
So I suppose it would be pointless to leave my text in chronological
order, even though I like it better that way.
Us more patient oldsters don't mind a click to get things the way we
want them, so I'll make the upside-down order the default. Happy?
Dec. 9, 2007
I have discovered the mysterious enlightenment of
And I want one.
I stumbled across a reference to the Gömböc in
a NYT article;
part of a page on noteworthy scientific advancements of 2007.
This is a beautiful example of mathematics given form,
and that form then transcending its arid origins to become art.
This is a mono-monostatic object,
i.e. one with but a single stable equilibrium orientation.
Actually, it's pretty easy to make an object like this (think Weebles),
but this is the first known example of one that is
convex and homogeneous (no ballast).
Or it was thought to be, until someone noticed that certain types
of turtles have shells that are quite close to this shape:
It seems that the shape makes it pretty easy for these turtles to
turn themselves back upright if they are turned over.
Other kinds use the ancient art of turtle-fu:
This, and other arcana related to the mysterious Gömböc, can be found
Code pulling together
Oct. 29, 2007
OK - fairly major update to the site structure...
I decided to move to a php-based template system.
This will make it easier to expand the site while keeping a consistent
look, and of course easier to change that look across the site if I like.
Slightly more complicated to work with, of course - but I've had
with this sort of thing, so it's not bad.
Besides, it also opens lots of possibilities for interesting dynamic
content. Now that I've said that, I'll probably feel obligated to
do some of that, though...
Nov. 3, 2007
I dug into some alternative ways to get my column heights to work
the way I wanted - that 'one problem' I mentioned earlier.
Found a pretty comprehensive
of various ways to solve the problem on the
Front-Page CSS Wiki.
I'm going with 'Solution A'
(padding excess / negative margin compensation / overflow:hidden cut)
and crossing my fingers, because I don't want to use faux columns -
too many things would have to be changed. Sounds like the only
disadvantage is that I can no longer safely use anchor links in my
text - something I probably wouldn't do anyway.
So now the attentive site viewer (so far that will basically be me)
will notice that the text on
no longer has a scroll bar - the page now extends to accomodate all
of the text.
As does this page, now that I've got more stuff on it.
I've just noticed that I'm updating this page in old-school anti-blog
order, that is, chronologically.
Not much content yet
Oct. 27, 2007
I'm learning a bunch about CSS and stuff, so I'm concentrating on
the site layout and structure. I don't want to be stuck with something
I don't like maintaining, so I'm not adding lots of material until I
get things the way I want them.
Stuff may well change while I work through this part. I've already
gone through a couple of versions. This was, in fact, an experimental
layout, to see if I could make it work - so far, it has only one
problem I haven't been able to lick. 'Course, I haven't tested it in
any browsers except Firefox and IE.
One remote test with Safari on a Mac...which is to say that my dad
has now seen the site.