Validation aside, access to raw data is also helpful for method
development (eg integration and scaling algorithms), on which we all
rely.
Ashley
On 17/08/2007, at 1:04 AM, Santarsiero, Bernard D. wrote:
Sorry, I think it's a waste of resources to store the raw images. I
think
we should trust people to be able to at least process their own
data set.
Besides, you would need to include beamline parameters, beam position,
detector distances, etc. that may or may not be correct in the image
headers. I'm all for storage and retrieval of a primary intensity data
file (I or F^2 with esds).
Bernie Santarsiero
On Thu, August 16, 2007 9:46 am, Mischa Machius wrote:
Hmm - I think I miscalculated, by a factor of 100 even!... need more
coffee. In any case, I still think it would be doable. Best - MM
On Aug 16, 2007, at 9:30 AM, Mischa Machius wrote:
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
--------------------------------------------------------------------
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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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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
*NOTE* My new tel. no: (03) 9902 0269
Ashley Buckle Ph.D
NHMRC Senior Research Fellow
The Department of Biochemistry and Molecular Biology
School of Biomedical Sciences, Faculty of Medicine &
Victorian Bioinformatics Consortium (VBC)
Monash University, Clayton, Vic 3800
Australia
http://www.med.monash.edu.au/biochem/staff/abuckle.html
iChat/AIM: blindcaptaincat
skype: ashley.buckle
Tel: (613) 9902 0269 (office)
Tel: (613) 9905 1653 (lab)
Fax : (613) 9905 4699
