TARDIS for the Storage of X-ray Diffraction Images
I have been able to get some details about TARDIS, which was mentioned in the comments of the post:Do we need an X-ray Diffraction Image Data Bank?.
A number of tools for TARDIS are coming online in the near future. The tools are being designed so that labs can install the repository software at no cost on a basic PC server that will allow the deposition of images with minimal annotation (5 or 6 lines of text describing the experiment).
If your server is on their network, TARDIS will be able to locate your data and make it available to everyone. They are open to having anyone who wants to deposit images before the tools are released to contact them and they will deposit the images on the server for you. I have been told that the tools are going to be lightweight and easy solution to the problem. I am looking forward to their release!
Although not explicitly stated, it looks like the server will be open to anyone in the world that wishes to deposit their images. I have been watching the site for about 6 weeks and have noticed that no new structures have been deposited. I hope that with the release of these deposition tools that the number of data sets will greatly increase.
Buckle structural bioinformatics group » TARDIS article on P212121
July 19th, 2009 at 10:26 PM #
[...] The crystallography blog P212121 have posted an article on TARDIS entitled “TARDIS for the Storage of X-ray Diffraction Images“. [...]
Paul
July 20th, 2009 at 10:25 AM #
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.
Sean
July 20th, 2009 at 9:33 PM #
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).