Dear James,
This is technically ingenious stuff.

Perhaps it could be applied to help the 'full archive challenge' ie containing many data sets that will never lead to publication/ database deposition?

However for the latter,publication/deposition, subset you would surely not 'tamper' with the raw measurements? 

The 'grey area' between the two clearcut cases  ie where eventually publication/deposition MAY result then becomes the challenge as to whether to compress or not? (I would still prefer no tampering.)

Greetings,
John

Prof John R Helliwell DSc 




On 24 Oct 2011, at 22:56, James Holton <[log in to unmask]> wrote:

> The Pilatus is fast, but or decades now we have had detectors that can read out in ~1s.  This means that you can collect a typical ~100 image dataset in a few minutes (if flux is not limiting).  Since there are ~150 beamlines currently operating around the world and they are open about 200 days/year, we should be collecting ~20,000,000 datasets each year.
> 
> We're not.
> 
> The PDB only gets about 8000 depositions per year, which means either we throw away 99.96% of our images, or we don't actually collect images anywhere near the ultimate capacity of the equipment we have.  In my estimation, both of these play about equal roles, with ~50-fold attrition between ultimate data collection capacity and actual collected data, and another ~50 fold attrition between collected data sets and published structures.
> 
> Personally, I think this means that the time it takes to collect the final dataset is not rate-limiting in a "typical" structural biology project/paper.  This does not mean that the dataset is of little value.  Quite the opposite!  About 3000x more time and energy is expended preparing for the final dataset than is spent collecting it, and these efforts require experimental feedback.  The trick is figuring out how best to compress the "data used to solve a structure" for archival storage.  Do the "previous data sets" count?  Or should the compression be "lossy" about such historical details?  Does the stuff between the spots matter?  After all, h,k,l,F,sigF is really just a form of data compression.  In fact, there is no such thing as "raw" data.  Even "raw" diffraction images are a simplification of the signals that came out of the detector electronics.  But we round-off and average over a lot of things to remove "noise".  Largely because "noise" is difficult to compress.  The question of how much compression is too much compression depends on which information (aka noise) you think could be important in the future.
> 
> When it comes to fine-sliced data, such as that from Pilatus, the main reason why it doesn't compress very well is not because of the spots, but the background.  It occupies thousands of times more pixels than the spots.  Yes, there is diffuse scattering information in the background pixels, but this kind of data is MUCH smoother than the spot data (by definition), and therefore is optimally stored in larger pixels.  Last year, I messed around a bit with applying different compression protocols to the spots and the background, and found that ~30 fold compression can be easily achieved if you apply h264 to the background and store the "spots" with lossless png compression:
> 
> http://bl831.als.lbl.gov/~jamesh/lossy_compression/
> 
> I think these results "speak" to the relative information content of the spots and the pixels between them.  Perhaps at least the "online version" of archived images could be in some sort of lossy-background format?  With the "real images" in some sort of slower storage (like a room full of tapes that are available upon request)?  Would 30-fold compression make the storage of image data tractable enough for some entity like the PDB to be able to afford it?
> 
> 
> I go to a lot of methods meetings, and it pains me to see the most brilliant minds in the field starved for "interesting" data sets.  The problem is that it is very easy to get people to send you data that is so bad that it can't be solved by any software imaginable (I've got piles of that!).  As a developer, what you really need is a "right answer" so you can come up with better metrics for how close you are to it.  Ironically, bad, unsolvable data that is connected to a right answer (aka a PDB ID) is very difficult to obtain.  The explanations usually involve protestations about being in the middle of writing up the paper, the student graduated and we don't understand how he/she labeled the tapes, or the RAID crashed and we lost it all, etc. etc.  Then again, just finding someone who has a data set with the kind of problem you are interested in is a lot of work!  So is figuring out which problem affects the most people, and is therefore "interesting".
> 
> Is this not exactly the kind of thing that publicly-accessible centralized scientific databases are created to address?
> 
> -James Holton
> MAD Scientist
> 
> On 10/16/2011 11:38 AM, Frank von Delft wrote:
>> On the deposition of raw data:
>> 
>> I recommend to the committee that before it convenes again, every member should go collect some data on a beamline with a Pilatus detector [feel free to join us at Diamond].  Because by the probable time any recommendations actually emerge, most beamlines will have one of those (or similar), we'll be generating more data than the LHC, and users will be happy just to have it integrated, never mind worry about its fate.
>> 
>> That's not an endorsement, btw, just an observation/prediction.
>> 
>> phx.
>> 
>> 
>> 
>> 
>> On 14/10/2011 23:56, Thomas C. Terwilliger wrote:
>>> For those who have strong opinions on what data should be deposited...
>>> 
>>> The IUCR is just starting a serious discussion of this subject. Two
>>> committees, the "Data Deposition Working Group", led by John Helliwell,
>>> and the Commission on Biological Macromolecules (chaired by Xiao-Dong Su)
>>> are working on this.
>>> 
>>> Two key issues are (1) feasibility and importance of deposition of raw
>>> images and (2) deposition of sufficient information to fully reproduce the
>>> crystallographic analysis.
>>> 
>>> I am on both committees and would be happy to hear your ideas (off-list).
>>> I am sure the other members of the committees would welcome your thoughts
>>> as well.
>>> 
>>> -Tom T
>>> 
>>> Tom Terwilliger
>>> [log in to unmask]
>>> 
>>> 
>>>>> This is a follow up (or a digression) to James comparing test set to
>>>>> missing reflections.  I also heard this issue mentioned before but was
>>>>> always too lazy to actually pursue it.
>>>>> 
>>>>> So.
>>>>> 
>>>>> The role of the test set is to prevent overfitting.  Let's say I have
>>>>> the final model and I monitored the Rfree every step of the way and can
>>>>> conclude that there is no overfitting.  Should I do the final refinement
>>>>> against complete dataset?
>>>>> 
>>>>> IMCO, I absolutely should.  The test set reflections contain
>>>>> information, and the "final" model is actually biased towards the
>>>>> working set.  Refining using all the data can only improve the accuracy
>>>>> of the model, if only slightly.
>>>>> 
>>>>> The second question is practical.  Let's say I want to deposit the
>>>>> results of the refinement against the full dataset as my final model.
>>>>> Should I not report the Rfree and instead insert a remark explaining the
>>>>> situation?  If I report the Rfree prior to the test set removal, it is
>>>>> certain that every validation tool will report a mismatch.  It does not
>>>>> seem that the PDB has a mechanism to deal with this.
>>>>> 
>>>>> Cheers,
>>>>> 
>>>>> Ed.
>>>>> 
>>>>> 
>>>>> 
>>>>> -- 
>>>>> Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
>>>>>                                               Julian, King of Lemurs
>>>>>