Dear Gerard,
I think that a major achievement of this online debate will have been
to actually get you to carry out a constructive analysis (an impressive one,
I will be the first to say) of this question, instead of dismissing it right
away. It is almost as great an achievement as getting the Pope to undergo
psychoanalysis! (I am thinking here of the movie "Habemus Papam".)
It is very useful to have the facts and figures you mention for the
costs of full PDB officialdom for the storage of raw data. I think one could
describe the first stage towards that, in the form I have been mentioning as
the "IUCr DDDWG pilot project", as first trying to see how to stop those raw
images from disappearing, pending the mobilisation of more resources towards
eventually putting them up in five-star accommodation (if they are thought
to be earning their keep). I am again hopeful that anticipated difficulties
at the five-star stage (with today's cost estimates) will not stop us from
trying to do what is possible today in this pilot project, and I also hope
that enough synchrotrons and depositors will volunteer to take part in it.
The extra logistical load on checking that submitted raw images sets do
correspond to the deposited structure should be something that can be pushed
down towards the synchrotron sources, as was mentioned for the proper
book-keeping of "metadata", as part of keeping tidy records linking user
project databases to datasets, and towards enhancements in data processing
and structure determination pipelines to keep track of all stages of the
derivation of the deposited results from the raw data. Not trivial, but not
insuperable, and fully in the direction of more automation and more
associated record keeping. This is just to say that it needs not all land on
the PDB's shoulders in an initially amorphous state.
In any case, thank you for devoting so much time and attention to this
nuts-and-bolts discussion when there are so many tempting forms of high
octane entertainment around!
With best wishes,
Gerard (B.)
--
On Fri, Oct 28, 2011 at 11:02:46PM +0200, Gerard DVD Kleywegt wrote:
> Hi all,
>
> It appears that during my time here at Cold Spring Harbor, I have missed a
> small debate on CCP4BB (in which my name has been used in vain to boot).
>
> I have not yet had time to read all the contributions, but would like to
> make a few points that hopefully contribute to the discussion and keep it
> with two feet on Earth (as opposed to La La Land where the people live who
> think that image archiving can be done on a shoestring budget... more about
> this in a bit).
>
> Note: all of this is on personal title, i.e. not official wwPDB gospel. Oh,
> and sorry for the new subject line, but this way I can track the replies
> more easily.
>
> It seems to me that there are a number of issues that need to be separated:
>
> (1) the case for/against storing raw data
> (2) implementation and resources
> (3) funding
> (4) location
>
> I will say a few things about each of these issues in turn:
>
> -----------
>
> (1) Arguments in favour and against the concept of storing raw image data,
> as well as possible alternative solutions that could address some of the
> issues at lower cost or complexity.
>
> I realise that my views carry a weight=1.0 just like everybody else's, and
> many of the arguments and counter-arguments have already been made, so I
> will not add to these at this stage.
>
> -----------
>
> (2) Implementation details and required resources.
>
> If the community should decide that archiving raw data would be
> scientifically useful, then it has to decide how best to do it. This will
> determine the level of resources required to do it. Questions include:
>
> - what should be archived? (See Jim H's list from (a) to (z) or so.) An
> initial plan would perhaps aim for the images associated with the data used
> in the final refinement of deposited structures.
>
> - how much data are we talking about per dataset/structure/year?
>
> - should it be stored close to the source (i.e., responsibility and costs
> for depositors or synchrotrons) or centrally (i.e., costs for some central
> resource)? If it is going to be stored centrally, the cost will be
> substantial. For example, at the EBI -the European Bioinformatics
> Institute- we have 15 PB of storage. We pay about 1500 GBP (~2300 USD) per
> TB of storage (not the kind you buy at Dixons or Radio Shack, obviously).
> For stored data, we have a data-duplication factor of ~8, i.e. every file
> is stored 8 times (at three data centres, plus back-ups, plus a
> data-duplication centre, plus unreleased versus public versions of the
> archive). (Note - this is only for the EBI/PDBe! RCSB and PDBj will have to
> acquire storage as well.) Moreover, disks have to be housed in a building
> (not free!), with cooling, security measures, security staff, maintenance
> staff, electricity (substantial cost!), rental of a 1-10 Gb/s connection,
> etc. All hardware has a life-cycle of three years (barring failures) and
> then needs to be replaced (at lower cost, but still not free).
>
> - if the data is going to be stored centrally, how will it get there? Using
> ftp will probably not be feasible.
>
> - if it is not stored centrally, how will long-term data availability be
> enforced? (Otherwise I could have my data on a public server until my paper
> comes out in print, and then remove it.)
>
> - what level of annotation will be required? There is no point in having
> zillions of files lying around if you don't know which
> structure/crystal/sample they belong to, at what wavelength they were
> recorded, if they were used in refinement or not, etc.
>
> - an issue that has not been raised yet, I think: who is going to validate
> that the images actually correspond to the structure factor amplitudes or
> intensities that were used in the refinement? This means that the data will
> have to be indexed, integrated, scaled, merged, etc. and finally compared
> to the deposited Fobs or Iobs. This will have to be done for *10,000 data
> sets a year*... And I can already imagine the arguments that will follow
> between depositors and "re-processors" about what software to use, what
> resolution cut-off, what outlier-rejection criteria, etc. How will
> conflicts and discrepancies be resolved? This could well end up taking a
> day of working time per data set, i.e. with 200 working days per year, one
> would need 50 *new* staff for this task alone. For comparison: worldwide,
> there is currently a *total* of ~25 annotators working for the wwPDB
> partners...
>
> Not many of you know that (about 10 years ago) I spent probably an entire
> year of my life sorting out the mess that was the PDB structure factor
> files pre-EDS... We were apparently the first people to ever look at the
> tens of thousands of structure factor files and try to use all of them to
> calculate maps for the EDS server. (If there were others who attempted this
> before us, they had probably run away screaming.) This went well for many
> files, but there were many, many files that had problems. There were dozens
> of different kinds of issues: non-CIF files, CIF files with wrong headers,
> Is instead of Fs, Fcalc instead of Fobs, all "h" equal to 0,
> non-space-separated columns, etc. For a list, see:
> http://eds.bmc.uu.se/eds/eds_help.html#PROBLEMS
>
> Anyway, my point is that simply having images without annotation and
> without reprocessing is like having a crystallographic kitchen sink (or bit
> bucket) which will turn out to be 50% useless when the day comes that
> somebody wants to do archive-wide analysis/reprocessing/rerefinement etc.
> And if the point is to "catch cheaters" (which in my opinion is one of the
> weakest, least-fundable arguments for storage), then the whole operation is
> in fact pointless without reprocessing by a "third party" at deposition
> time.
>
> -----------
>
> (3) Funding.
>
> This is one issue we can't really debate - ultimately, it is the funding
> agencies who have to be convinced that the cost/benefit ratio is low
> enough. The community will somehow have to come up with a stable, long-term
> funding model. The outcome of (2) should enable one to estimate the initial
> investment cost plus the variable cost per year. Funding could be done in
> different ways:
>
> - centrally - e.g., a big application for funding from NIH or EU
>
> - by charging depositors (just like they are charged Open Access charges,
> which can often be reclaimed from the funding agencies) - would you be
> willing to pay, say, 5000 USD per dataset to secure "perpetual" storage?
>
> - by charging users (i.e., Gerard Bricogne :-) - just kidding!
>
> Of course, if the consensus is to go for decentralised storage and a
> DOI-like identifier system, there will be no need for a central archive,
> and the identifiers could be captured upon deposition in the PDB. (We could
> also check once a week if the files still exist where they are supposed to
> be.)
>
> -----------
>
> (4) Location.
>
> If the consensus is to have decentralised storage, the solution is quite
> simple and very cheap in terms of "centralised" cost - wwPDB can capture
> DOI-like identifiers upon deposition and make them searchable.
>
> If central storage is needed, then there has to be an institution willing
> and able to take on this task. The current wwPDB partners are looking at
> future funding that is at best flat, with increasing numbers of depositions
> that also get bigger and more complex. There is *no way on earth* that
> wwPDB can accept raw data (be it X-ray, NMR or EM! this is not an exclusive
> X-ray issue) without *at least* double the current level of funding (and
> not just in the US for RCSB, but also in Japan for PDBj and in Europe for
> PDBe)! I am pretty confident that this is simply *not* going to happen.
>
> [Besides, in my own humble opinion, in order to remain relevant (and
> fundable!) in the biomedical world, the PDB will have to restyle itself as
> a biomedical resource instead of a crystallographic archive. We must take
> the structures to the biologists, and we must expand in breadth of coverage
> to include emerging hybrid methods that are relevant for structural cell
> (as opposed to molecular) biology. This mission will be much easier to fund
> on three continents than archiving TBs of raw data that have little or no
> tangible (i.e., fundable) impact on our quest to find a cure for various
> kinds of cancer (or hairloss) or to feed a growing population.]
>
> However, there may be a more realistic solution. The role model could be
> NMR, which has its own global resource for data storage in the BMRB. BMRB
> is a wwPDB partner - if you deposit an NMR model with us, we take your
> ensemble coordinates, metadata, restraints and chemical shifts - any other
> NMR data (including spectra and FIDs) can subsequently be deposited with
> BMRB. These data will get their own BMRB ID which can be linked to the PDB
> ID.
>
> A model like this has advantages - it could be housed in a single place,
> run by X-ray experts (just as BMRB is co-located with NMRFAM, the national
> NMR facility at Madison), and there would be only one place that would need
> to secure the funding (which would be substantially larger than the
> estimate of $1000 per year suggested by a previous poster from La La Land).
> This could for instance be a synchrotron (linked to INSTRUCT?), or perhaps
> one of the emerging nations could be enticed to take on this challenging
> task. I would expect that such a centre would be closely affiliated with
> the wwPDB organisation, or become a member just like BMRB. A similar model
> could also be employed for archiving raw EM image data.
>
> -----------
>
> I've said enough for today. It's almost time for the booze-up that kicks
> off the PDB40 symposium here at CSHL! Heck, some of you who read this might
> be here as well!
>
> Btw - Colin Nave wrote:
>
> "(in increasing order of influence/power do we have the Pope, US president,
> the Bond Market and finally Gerard K?)"
>
> I'm a tad disappointed to be only in fourth place, Colin! What has the Pope
> ever done for crystallography?
>
> --Gerard
>
> ******************************************************************
> Gerard J. Kleywegt
>
> http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
> ******************************************************************
> The opinions in this message are fictional. Any similarity
> to actual opinions, living or dead, is purely coincidental.
> ******************************************************************
> Little known gastromathematical curiosity: let "z" be the
> radius and "a" the thickness of a pizza. Then the volume
> of that pizza is equal to pi*z*z*a !
> ******************************************************************
--
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