World Community Grid Message Board Posts
HPF 2 progress Report February 2006
There are a few things to report this month. If you have any
questions about this stuff put the questions up as a post on the
forum and we'll try to answer them soon.
News item #1:
We've posted some results (just some pictures of proteins from HPF2)
for all you volunteers to check out. We've tested and retested the
code and the resulting proteins and we can officially say that the
beginning is over for HPF2 and now we're in the "extended
crunching" stage...somewhere after mile 1 and somewhere well before
mile 26.
Check these picture of HPF2 structures out again... The discerning eye
will notice something fishy about these pictures, guess what is wrong
(think about the difference between HPF1 and HPF2). So this is sort
of a pop quiz. Check out the pictures and then see if you can guess
what is missing...
Answer
News item #2:
We have received proteins from our collaborators in Seattle working
on pregnancy malaria. These proteins are proteins that Patrick
Duffy's lab has identified as possibly important in this
particularly bad type of malaria (Plasmodium). Paul Shannon is one of
the Bioinformatics scientists working with us on this project, he's
looked for proteins that are: 1. The right size or have pieces/
domains the right size for Rosetta 2. Are unregulated/over-expressed
during the type of malaria they study in Duffy's lab and 3. Not easy
to annotate with other methods (unknown proteins). For more info on
this lab's overall effort follow this link (where the need to look
at these proteins was brought to our attention see:
http://www.sbri.org/research/duffy.asp
. Each time we look at a new set of
proteins I'll try to put up an update. Before this we were looking
at proteins from the Key organisms for this study, but this new set
jumps the queue, as they are directly relevant to this research
group. For a reminder of the three main disease related sets of
proteins we will be crunching on this project see:
http://homepages.nyu.edu/~rb133/wcg/thread_9681.html
Extra news item:
We have published another paper based off the HPF results. This paper
will appear soon in PLoS biology. I'll let you know as soon as we
have a web-express type link. The copy-editing phase has another week
or two to go. In any case Lars Malmstrom. Mike Riffle, Dave Baker and
I are happy to be done with the writing. The data is available via a
web portal that Mike and Lars made that also serves up lots of other
data-types from the UW yeast resource center. We're also happy that
we can continue on to the next paper, focusing on the next release of
the data. We'll start writing this next paper asap. In any case
more on this next paper (in a chain of papers directly resulting from
HPF1 & 2) when I have a link!
Goodnight for now,
And thanks for crunching.
