I must "say" that there were some emails exchanged between me and Gerard
later, in which I pointed out that I wasn't against deposition of images
(data frames). In fact, if SR sources kept user's data there would be
one more structure from here in the PDB: HDD failure here, the data on a
mirror HDD but the company in charge of maintenance erased the data
frames and data processing statistics by accident. For a trypanosomal
enzyme there is no chance that I can ever get funding now to replicate
the work (protein production and purification, crystallisation, data
collection) so that "Table 1" could be produced for a manuscript.
However, my email to the bb was provocative - I admit I was doing this
willingly - to write that in such harsh funding times someone could
start a career, get some small grant, enough to clone produce purify
crystallize and collect a first data set. And then find him or herself
without funding for X years (success rate = less than 10% these days).
If this person then gets scooped by whoever, end of a promising career.
Unfortunately, such a prospect doesn't seem to be science fiction any
more nowadays. I hope this clears things. I wanted to be provocative and
point out the difficulties we are all facing wrt funding so that we
shouldn't set up a system that may result in killing careers. Our
politicians do not need any help from us on that I think.
Fred.
Gerard Bricogne wrote:
> Dear Remy,
>
> You are right, and I was about to send a message confessing that I had
> been rash in my response to Fred's. Another person e-mailed me off-list to
> point out that sometimes a structure can be quickly solved, but that doing
> all the rest of the work involved in wrapping that structure into a good
> biological story for publication can take a very long time, and that it
> would be wrong for a SR source's forced disclosure policy to start imposing
> deadlines on that process. I entirely agree with both of you and admit that
> I reacted too quickly and with insufficient thought to Fred's message.
>
> However, as you point out yourself, this issue is related to a
> different question (SR sources' disclosure policy towards all data collected
> on their beamlines) from the original one that started this thread
> (deposition of raw images with the pdb entries they led to). The two topics
> became entangled through the idea of prototyping an approach to the latter
> by tweaking the storage and access features involved in the former.
>
> Many thanks to you and to the other correspondent for picking up and
> correcting my error. This however leaves the main topic of this thread
> untouched.
>
>
> With best wishes,
>
> Gerard.
>
> --
> On Fri, Oct 28, 2011 at 01:38:29PM +0200, Remy Loris wrote:
>
>> Dear Gerard,
>>
>> I cannot agree. Last year my group published a paper in Cell which
>> contained a structure for which the native data were collected at a
>> synchrotron around 1997. Various reasons contributed to the long lag period
>> for solving this structure, but basically it all came down to money needed
>> to do the work. Equally I am sure there are other cases for which a first
>> good native data set is a breakthrough you wish to protect rather than hand
>> it out to anyone who might potentially scoop you after you have put lots of
>> money and effort into the project.
>>
>> Therefore: Images corresponding to structures I deposit in the PDB: No
>> problem. That is what we do with processed data as well. But images of
>> unsolved structures, I don't see why that should be enforced or done
>> automatically by synchrotrons. Nobody deposits processed data without an
>> accompanying structure either.
>>
>> I do agree that one could be given the option to deposit interesting data
>> with which he/se will not continue for whatever reason. But this should be
>> optional, and a clear consensus should emerge within the community as how
>> the original producers of the data have to be acknowledged if these data
>> are used and the results published by another team, especially if the use
>> of that particular dataset is crucial for the publication.
>>
>> Remy Loris
>> Vrije Universiteit Brussel and VIB
>>
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