Cool - we've found our volunteer!!
On 26/10/2011 17:28, Jacob Keller wrote:
Is anyone seriously questioning whether we should archive the images
used for published structures? That amount of space is trivial, could
be implemented just as another link in the PDB website, and would be
really helpful in some cases. One person could set it up in a day! You
could just make it a policy: no images, no PDB submission, no
publishing!
Jacob
On Wed, Oct 26, 2011 at 11:15 AM, Gloria Borgstahl<gborgst...@gmail.com> wrote:
I just want to jump in to state that I am ALL FOR the notion of
depositing the images that go with the structure factors and the
refined structure.
Through the years, I have been interviewing folks about the strange
satellite diffraction they saw, but ignored,
used the mains that they could integrate and deposited that structure,
does not help me to
justify the existance of modulated protein crystals to reviewers.
But if I could go and retrieve those images, and reanalyze with new methods.
Dream come true. Reviewers convinced.
On Wed, Oct 26, 2011 at 10:59 AM, Patrick Shaw Stewart
<patr...@douglas.co.uk> wrote:
Could you perhaps use the principle of "capture storage" that is used by
wild-life photographers with high-speed cameras?
The principle is that the movie is written to the same area of memory,
jumping back to the beginning when it is full (this part is not essential,
but it makes the principle clear). Then, when the photographer takes his
finger off the trigger, the last x seconds is permanently stored. So you
keep your wits about you, and press the metaphorical "store" button just
after you have got the movie in the can so to speak
Just a thought
Patrick
On Wed, Oct 26, 2011 at 2:18 PM, John R Helliwell<jrhelliw...@gmail.com>
wrote:
Dear Frank,
re 'who will write the grant?'.
This is not as easy as it sounds, would that it were!
There are two possible business plans:-
Option 1. Specifically for MX is the PDB as the first and foremost
candidate to seek such additional funds for full diffraction data
deposition for each future PDB deposiition entry. This business plan
possibility is best answered by PDB/EBI (eg Gerard Kleywegt has
answered this in the negative thus far at the CCP4 January 2010).
Option 2 The Journals that host the publications could add the cost to
the subscriber and/or the author according to their funding model. As
an example and as a start a draft business plan has been written by
one of us [JRH] for IUCr Acta Cryst E; this seemed attractive because
of its simpler 'author pays' financing. This proposed business plan is
now with IUCr Journals to digest and hopefully refine. Initial
indications are that Acta Cryst C would be perceived by IUCr Journals
as a better place to start considering this in detail, as it involves
fewer crystal structures than Acta E and would thus be more
manageable. The overall advantage of the responsibility being with
Journals as we see it is that it encourages such 'archiving of data
with literature' across all crystallography related techniques (single
crystal, SAXS, SANS, Electron crystallography etc) and fields
(Biology, Chemistry, Materials, Condensed Matter Physics etc) ie not
just one technique and field, although obviously biology is dear to
our hearts here in the CCP4bb.
Yours sincerely,
John and Tom
John Helliwell and Tom Terwilliger
On Wed, Oct 26, 2011 at 9:21 AM, Frank von Delft
<frank.vonde...@sgc.ox.ac.uk> wrote:
Since when has the cost of any project been limited by the cost of
hardware? Someone has to implement this -- and make a career out of it;
thunderingly absent from this thread has been the chorus of volunteers
who
will write the grant.
phx
On 25/10/2011 21:10, Herbert J. Bernstein wrote:
To be fair to those concerned about cost, a more conservative estimate
from the NSF RDLM workshop last summer in Princeton is $1,000 to $3,000
per terabyte per year for long term storage allowing for overhead in
moderate-sized institutions such as the PDB. Larger entities, such
as Google are able to do it for much lower annual costs in the range of
$100 to $300 per terabyte per year. Indeed, if this becomes a serious
effort, one might wish to consider involving the large storage farm
businesses such as Google and Amazon. They might be willing to help
support science partially in exchange for eyeballs going to their sites.
Regards,
H. J. Bernstein
At 1:56 PM -0600 10/25/11, James Stroud wrote:
On Oct 24, 2011, at 3:56 PM, James Holton wrote:
The PDB only gets about 8000 depositions per year
Just to put this into dollars. If each dataset is about 17 GB in
size, then that's about 14 TB of storage that needs to come online
every year to store the raw data for every structure. A two second
search reveals that Newegg has a 3GB hitachi for $200. So that's
about $1000 / year of storage for the raw data behind PDB deposits.
James
--
Professor John R Helliwell DSc
--
patr...@douglas.co.uk Douglas Instruments Ltd.
Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
Directors: Peter Baldock, Patrick Shaw Stewart
http://www.douglas.co.uk
Tel: 44 (0) 148-864-9090 US toll-free 1-877-225-2034
Regd. England 2177994, VAT Reg. GB 480 7371 36
