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I think I can speak from experience on the topic of archiving image data. I have ~40,000 DVD-R disks in my office. This represents: 6 years of data collection at ALS 8.3.1 60 TB of data (>99% of everything collected, 2 copies) 10,000 data sets 318 PDB entries $4000 of media The purposes of this archive are: 1) an "eternal" off-site backup for users of ALS 8.3.1 2) a potential source of "interesting" data sets for methods developers I define "interesting" as: a data set from a known structure that cannot be solved by conventional methods. After all, if you are developing new methods then data that can be solved by existing methods is of limited utility. However, it is also difficult to develop and test a new algorithm if you don't know what the "right answer" is. For this reason, I think the most useful data sets to make available are the "early" data sets from a structure project (the ones you couldn't solve). Almost by definition, these are the most relevant data sets for developing new methods. We all would like to get a structure solved sooner than later. The problem is getting permission. Yes, it is perhaps "legal" for me to give away people's data if they were collected at a DOE facility (without a proprietary research agreement in place). However, I would like to keep the few friends I have. It is important to clear such transactions with the scientist who collected the data. The difficulty is in connecting 10,000 image data sets to one of 40,000 PDB entries (which are generally deposited 1-2 years after data collection) and then connecting interested parties to one of 500 users who collected the data. This is not an insurmountable logistics problem, but I'm afraid it is going to take me a while to do it all in my "spare time". IMHO we do not need a universal image format, we need WELL DOCUMENTED image formats! Once that is done, then writing a converter to-and-from imgCIF and any other format will be possible, and then imgCIF can start to take hold. I believe a pivotal step toward a universal image format is to have every generator of images (beamlines, diffractometer manufacturers, etc.) make a lysozyme data set available in a very public place. Preferably with instructions on how to process it properly. I will now volunteer the following web page as the place to put all these example data sets (for now). To put my money where my mouth is: A lysozyme data set from ALS 8.3.1 is available here: http://bl831.als.lbl.gov/example_data_sets/ WRT archiving in general, I think it also important to point out that RAID only protects you against the total failure of one (or maybe two) hard disk drives. RAID does NOT generally protect against anything else, such as failures of RAID controller cards, flaky drive cables, bad sectors or other "subtle" drive failures, filesystem corruption, power surges, disgruntled sysadmins, etc. I have experienced all of these. So, even if your stuff is on a RAID, always backup often. I chose DVD-R because it is the cheapest media with a long rated shelf-life (~100 years if you don't leave them in the sun). That, and our astronomer colleagues (who also have the problem of storing large amounts of digital image data) chose DVD-R as the storage medium for Sky Survey 2 a few years back. I recently checked on the prices of alternative media. Here is what I came up with: media price source lifetime DVD-R $0.056/GB ( $0.25 / 4.5 GB ) 100 year? LTO-3 $0.063/GB ( $50 / 800 GB ) 3-5 year LTO-2 $0.063/GB ( $25 / 400 GB ) 3-5 year DLTIV $0.200/GB ( $16 / 80 GB ) 3-5 year HDD $0.424/GB ( $318 / 750 GB ) 3-5 year BD-R $0.640/GB ( $16 / 25 GB ) 100 year? CD-R $0.771/GB ( $0.54 / 0.7 GB ) 100 year? 8mm $1.000/GB ( $2.50 / 2.5 GB ) 3-5 year ZIP $16.00/GB ( $4 / 0.25 GB ) 3-5 month floppy $90.28/GB ( $0.13 / 1.44 MB ) 3-5 min clay $2700./GB ( $.3/lb 1 bit/mm^3) >30,000 y Note that hard disk drives cost 10x more than DVD-R. Blu-Ray disks (BD-R) are more expensive than hard drives! Storing all this data on hard drives would cost ~$50k, with an additional $5k/year for the 2 GB/hr we routinely collect. Storing all the data from all 30 PX beamlines in the world would amount to ~$150k/year of hard drives. The ~100 year lifetime of optical "-R" media has, of course yet to be proved historically. Early CDs did have a problem that the glue used for the label was slightly acid and corroded the aluminum reflective layer that encodes the data (which, BTW, is directly under the label!). Modern media no longer have this problem, and there are watchdog agencies you can find with google that simulate the long-term effects of time on any media you like. I can certainly say I have had problems with worn-out DVD-R drives starting to make bad disks that pass verification in the writer but not in a low-end reader. It seems that the solution to this is to try reading the disk back in a good DVD-R writer drive. One must balance media lifetime with cost. The longest proved storage lifetime of any media is clay tablets. In fact, the lifetime of data stored with this medium is perhaps the definition of "recorded history". I estimate that the maximum practical data density on clay tablets would be 1 bit represented by an 0.5 mm diameter pit in the wet clay, spaced on a 1x1 mm grid in a slab 1 mm thick. However, this thickness is probably pushing it if you want the media to stand up to 30 millenia of earthquakes and global warming. Note that I have only estimated the cost of the media, not the kiln to fire it or the subsequent FTEs to curate the archive. The problem I have now is similar. I have 40,000 DVDs with progressively sketchier computerized records of what is on them as I go back in time. (In the beginning, I was burning them all myself and printing out sticky labels from a Word document). It is perhaps relevant to mention here that this project is essentially unfunded. I have twice applied for grants to make the image archive accessible to the methods development community, but no luck. I mention this here because I think it relevant to point out that the cost of curating a public data base far exceeds the cost of the storage medium you use. I also have a question: It would seem LTO-3 or maybe the upcoming LTO-4 is not a bad short-term alternative to DVD-R? Anybody out there have experience with one of these tape drives? I would really appreciate the input. -James Holton MAD Scientist Winter, G (Graeme) wrote: >Hi, > >On the question of a "uniform format" for this data, I believe that >imgCIF has been working towards this end for a number of years. As a >very vocal supporter of this I would like to say that this is an ideal >archival format for the following reasons: > > - the terms are clearly defined (or are currently in the process of >such) > - the images are compressed, typically by a factor of 2-3 > - some data reduction packages (Mosflm, XDS) can read them in this >compressed form > >Now, I would be telling lies if I said that this was all finished but I >think it is fair to say that this is already a long way down the path. >As soon as I am convinced that you can go losslessly to and from imgCIF, >and the data reduction programs will give precisely the same results, I >will convert thus freeing up 5 firewire disks. > >For more information on this take a look at medsbio.org. > >Cheers, > >Graeme > >-----Original Message----- >From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of >Mischa Machius >Sent: 17 August 2007 15:07 >To: [log in to unmask] >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:[log in to unmask]] On Behalf Of >>Phil Evans >>Sent: 16 August 2007 15:13 >>To: [log in to unmask] >>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 > >