On the question of what is "trivial" I would argue that deposition of the raw diffraction images is not - for a few simple reasons:
- if I deposit structure factors with my model it is very straightforward to run an analysis tool which will confirm that model and I/F belong together. Without a pretty respectable amount of data reduction it will be impossible to demonstrate that the images belong to the structure being deposited. - I am fortunate in that the only data I need to curate is that kindly provided to me by friendly crystallographers. The amount is such that it resides comfortably on 8 firewire disks as the primary resource. I still however need to keep a spreadsheet as to *where* to find a certain data set. This is not insurmountable but is a measurable amount of work. "The hardware required to store all those data, even in a highly redundant way, is clearly trivial." No I think I have to agree with Kim on this one - it is not trivial. Setting up even a modest RAID array costs real money and takes real time. Setting one up with a guaranteed quality of service (uptime, bandwidth, disaster recovery) capable of storing the images which directly contributed to every deposition would be very expensive. Now, if the people who collected that data could find a "place on the web" to store the compressed images, and deposit a link to where they can be found, that would be ace. People who are interested in the results can go fetch the images - since probably only ~ 5 people would actually download them this would not be too bandwidth intensive. If that place on the web dies - well hopefully they still have them on firewire or on DVD ... Now the main difference with this would be to move the images from being something inconveniently large which usually we don't share to something inconveniently large we usually make available to those who are interested. From the replies to the list in this discussion you could probably figure out who *is* interested, and it is not world+dog. This shift of burden would turn it from something which would require a huge grant proposal which would almost certainly not get funded to a 1% increase in the cost of the structure solution for the lab in question and peace of mind for the community at large. I for one would be happy to write a few scripts which will compress batches of images, write the index pages, compute the md5sums so we know that the data are ok and generally put together a toolbox for curating images on the web. So we end up with... You want to argue with my structure - well, here are the frames, *you* solve it. Can't really argue with that. Again, just MHO. Cheers, Graeme -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Mischa Machius Sent: 17 August 2007 15:07 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Depositing Raw Data Since there are several sub-plots in that mammoth thread, I thought branching out would be a good idea. I think working out the technicalities of how to publicly archive raw data is fairly simple compared to the bigger picture. 1. Indeed, all the required meta-data will need to be captured just like for refined coordinates. This will be an additional burden for the depositor, but it's clearly necessary, and I do consider it trivial. Trivial, as in the sense of "straightforward", i.e., there is no fundamental problem blocking progress. As mentioned, current data processing software captures most of the pertinent information already, although that could be improved. I am sure that the beamlines, diffraction-system manufacturers and authors of data- processing software can be convinced to cooperate appropriately, if the community needs these features. 2. More tricky is the issue of a unified format for the images, which would be very helpful. There have been attempts at creating unified image formats, but - to my knowledge - they haven't gotten anywhere. However, I am also convinced that such formats can be designed, and that detector manufacturers will have no problems implementing them, considering that their detectors may not be purchased if they don't comply with requirements defined by the community. 3. The hardware required to store all those data, even in a highly redundant way, is clearly trivial. 4. The biggest problem I can see in the short run is the burden on the databank when thousands of investigators start transferring gigabytes of images, all at the same time. 5. I think the NSA might go bonkers over that traffic, although it certainly has enough storage space. Imagine, they let their decoders go wild on all those images. They might actually find interesting things in them... So, what's the hold-up? Best - MM On Aug 17, 2007, at 3:23 AM, Winter, G (Graeme) wrote: > Storing all the images *is* expensive but it can be done - the JCSG do > this and make available a good chunk of their raw diffraction data. > The > cost is, however, in preparing this to make the data useful for the > person who downloads it. > > If we are going to store and publish the raw experimental measurements > (e.g. the images) which I think would be spectacular, we will also > need to define a minimum amount of metadata which should be supplied > with this to allow a reasonable chance of reproduction of the results. > This is clearly not trivial, but there is probably enough information > in the harvest and log files from e.g. CCP4, HKL2000, Phenix to allow > this. > > The real problem will be in getting people to dig out that tape / dvd > with the images on, prepare the required metadata and "deposit" this > information somewhere. Actually storing it is a smaller challenge, > though this is a long way from being trivial. > > On an aside - firewire disks are indeed a very cheap way of storing > the data. There is a good reason why they are much cheaper than the > equivalent RAID array. They fail. Ever lost 500GB of data in one go? > Ouch. ;o) > > Just MHO. > > Cheers, > > Graeme > > -----Original Message----- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of > Phil Evans > Sent: 16 August 2007 15:13 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] The importance of USING our validation tools > > 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
