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 <[log in to unmask]> 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
> <[log in to unmask]> 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 <[log in to unmask]>
>> 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
>>> <[log in to unmask]> 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
>>
>>
>>
>> --
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>>
>
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [log in to unmask]
*******************************************
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