Touche! But alas, I have no access to the PDB's server, so... JPK
On Wed, Oct 26, 2011 at 11:54 AM, Frank von Delft <frank.vonde...@sgc.ox.ac.uk> wrote: > 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 >>>> >>>> >> >> > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *******************************************
