I don't think archiving images would be that expensive. For one, I
have found that most formats can be compressed quite substantially
using simple, standard procedures like bzip2. If optimized, raw
images won't take up that much space. Also, initially, only those
images that have been used to obtain phases and to refine finally
deposited structures could be archived. If the average structure
takes up 20GB of space, 5,000 structures would be 1TB, which fits on
a single hard drive for less than $400. If the community thinks this
is a worthwhile endeavor, money should be available from granting
agencies to establish a central repository (e.g., at the RCSB).
Imagine what could be done with as little as $50,000. For large
detectors, binning could be used, but giving current hard drive
prices and future developments, that won't be necessary. Best - MM
On Aug 16, 2007, at 9:13 AM, Phil Evans wrote:
> What do you count as raw data? Rawest are the images - everything
> beyond that is modellling - but archiving images is _expensive_!
> Unmerged intensities are probably more manageable
>
> Phil
>
>
> On 16 Aug 2007, at 15:05, Ashley Buckle wrote:
>
>> Dear Randy
>>
>> These are very valid points, and I'm so glad you've taken the
>> important step of initiating this. For now I'd like to respond to
>> one of them, as it concerns something I and colleagues in
>> Australia are doing:
>>>
>>> The more information that is available, the easier it will be to
>>> detect fabrication (because it is harder to make up more
>>> information convincingly). For instance, if the diffraction data
>>> are deposited, we can check for consistency with the known
>>> properties of real macromolecular crystals, e.g. that they
>>> contain disordered solvent and not vacuum. As Tassos Perrakis has
>>> discovered, there are characteristic ways in which the standard
>>> deviations depend on the intensities and the resolution. If
>>> unmerged data are deposited, there will probably be evidence of
>>> radiation damage, weak effects from intrinsic anomalous
>>> scatterers, etc. Raw images are probably even harder to simulate
>>> convincingly.
>>
>> After the recent Science retractions we realised that its about
>> time raw data was made available. So, we have set about creating
>> the necessary IT and software to do this for our diffraction data,
>> and are encouraging Australian colleagues to do the same. We are
>> about a week away from launching a web-accessible repository for
>> our recently published (eg deposited in PDB) data, and this should
>> coincide with an upcoming publication describing a new structure
>> from our labs. The aim is that publication occurs simultaneously
>> with release in PDB as well as raw diffraction data on our
>> website. We hope to house as much of our data as possible, as well
>> as data from other Australian labs, but obviously the potential
>> dataset will be huge, so we are trying to develop, and make
>> available freely to the community, software tools that allow
>> others to easily setup their own repositories. After brief
>> discussion with PDB the plan is that PDB include links from
>> coordinates/SF's to the raw data using a simple handle that can be
>> incorporated into a URL. We would hope that we can convince the
>> journals that raw data must be made available at the time of
>> publication, in the same way as coordinates and structure
>> factors. Of course, we realise that there will be many hurdles
>> along the way but we are convinced that simply making the raw data
>> available ASAP is a 'good thing'.
>>
>> We are happy to share more details of our IT plans with the
>> CCP4BB, such that they can be improved, and look forward to
>> hearing feedback
>>
>> cheers
------------------------------------------------------------------------
--------
Mischa Machius, PhD
Associate Professor
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353
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