Comments on: TARDIS for the Storage of X-ray Diffraction Images http://www.P212121.com/2009/07/19/tardis-for-the-storage-of-x-ray-diffraction-images/ Protein Crystallography there is an Easier Way Wed, 18 Jan 2012 10:14:22 -0500 http://wordpress.org/?v=2.8.5 hourly 1 By: Sean http://www.P212121.com/2009/07/19/tardis-for-the-storage-of-x-ray-diffraction-images/comment-page-1/#comment-1066 Sean Tue, 21 Jul 2009 02:33:18 +0000 http://www.P212121.com/?p=2821#comment-1066 Paul, Good points and questions. I don't know if RCSB has any interest or funding to support this type of database. The funding issue will definitely come into play, if everyone starts submitting their data sets. However, TARDIS has been around for at least two years and only has 33 data sets so far. I believe part of the reason for creating the database is to help ensure quality structures are deposited. The raw data would be helpful in cases in which there is a question about if the structure is correct. I wonder, if at some point in the future, journals will require deposition of the raw images. My personal interest in the database is to have data sets to learn on then compare with what has been submitted to the PDB (for example, I don't have access to any S phasing data sets nor a good MIR). Paul,

Good points and questions. I don’t know if RCSB has any interest or funding to support this type of database.

The funding issue will definitely come into play, if everyone starts submitting their data sets. However, TARDIS has been around for at least two years and only has 33 data sets so far.

I believe part of the reason for creating the database is to help ensure quality structures are deposited. The raw data would be helpful in cases in which there is a question about if the structure is correct. I wonder, if at some point in the future, journals will require deposition of the raw images.

My personal interest in the database is to have data sets to learn on then compare with what has been submitted to the PDB (for example, I don’t have access to any S phasing data sets nor a good MIR).

]]> By: Paul http://www.P212121.com/2009/07/19/tardis-for-the-storage-of-x-ray-diffraction-images/comment-page-1/#comment-1064 Paul Mon, 20 Jul 2009 15:25:58 +0000 http://www.P212121.com/?p=2821#comment-1064 I have mixed feelings about this. First, I think it would make more sense that the RCSB (and associated PDB organizations) handle raw data storage and depositions, otherwise things might become fragmented. Second, although I think overall this is a good idea, are the current validation tools so poor that we can't already highlight suspicious structures (yes, there are rare exceptions, but probably no more common than other types of data banks)? Shouldn't we focus time and money on ensuring quality structures are deposited to begin with rather than expecting the end user to figure out the good versus the bad? Finally, how many other areas of the life sciences go to such efforts with declaring all their data (I've never seen raw chromatograms for DNA sequences deposited in SwissProt)? I personally feel that the cost might outweigh the benefit for this. I have mixed feelings about this. First, I think it would make more sense that the RCSB (and associated PDB organizations) handle raw data storage and depositions, otherwise things might become fragmented. Second, although I think overall this is a good idea, are the current validation tools so poor that we can’t already highlight suspicious structures (yes, there are rare exceptions, but probably no more common than other types of data banks)? Shouldn’t we focus time and money on ensuring quality structures are deposited to begin with rather than expecting the end user to figure out the good versus the bad? Finally, how many other areas of the life sciences go to such efforts with declaring all their data (I’ve never seen raw chromatograms for DNA sequences deposited in SwissProt)? I personally feel that the cost might outweigh the benefit for this.

]]> By: Buckle structural bioinformatics group » TARDIS article on P212121 http://www.P212121.com/2009/07/19/tardis-for-the-storage-of-x-ray-diffraction-images/comment-page-1/#comment-1063 Buckle structural bioinformatics group » TARDIS article on P212121 Mon, 20 Jul 2009 03:26:32 +0000 http://www.P212121.com/?p=2821#comment-1063 [...] The crystallography blog P212121 have posted an article on TARDIS  entitled “TARDIS for the Storage of X-ray Diffraction Images“. [...] [...] The crystallography blog P212121 have posted an article on TARDIS  entitled “TARDIS for the Storage of X-ray Diffraction Images“. [...]

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