Consortium for Management of Experimental Data in Structural Biology

MEDSBIO Goals:The goals of the MEDSBIO consortium are to resolve collaboratively the interface issues among multiple structural biology data management protocols, including imgCIF, NeXus, vendor data formats, instrument control and signaling protocols, local and remote experiment control protocols, etc. with the objective of making the collection, transfer and archiving of data for experiments in structural biology as efficient as practicable; maintain an archive of documentation on standards and proposals for ontologies, software, hardware specifications, web templates and other documentation related to such protocols; maintain an archive of open source software and links to closed source software related to such protocols; maintain a archive of samples and test cases related to such protocols; run annual workshops on issues relating to such protocols; contribute open source software to fill gaps in the infrastructure related to such protocols; gather and where necessary create curricular material to assist in training experimenters in issues related to such protocols. more ...

Data Formats:There are many data formats in experimental structural biology. Each instrument, each control system, and software package may have a different format.

imgCIF/CBF: Building on earlier work by Andy Hammersley on a crystallographic binary format for images, the first imgCIF/CBF workshop took place at the Brookhaven National Laboratory 20-22nd October 1997 and proposed a format combining support for an efficient binary representation of images with a fully CIF-compliant ASCII equivalent. An imgCIF/CBF dictionary and software to support the format have been produced and are available on the web at

http://www.iucr.org/iucr-top/cif/imgcif/index.html

and have been included in Volume G of the IUCr International Tables for Crystallography [Bernstein, Hammersley 2005] [Bernstein 2005] [Hammersley, Bernstein, Westbrook 2005] [Bernstein, Ellis 2005]. The program mosflm [Powell 2001] in the CCP4 software suite has handled the imgCIF/CBF format for half a decade and the program PDB_EXTRACT [Westbrook et al. 2003] will harvest the experimental setup from imgCIF/CBF. more ...

NeXus: "NeXus is a data format for the exchange of neutron and synchrotron scattering data between facilities and user institutions. It has been developed by an international team of scientists and computer programmers from neutron and X-ray facilities around the world. The NeXus format uses the hierarchical data format (HDF) that is portable, binary, extensible and self-describing. The NeXus format defines the structure and contents of these HDF files in order to facilitate the visualization and analysis of neutron and X-ray data. In addition, an application program interface (API) [was] produced in order to simplify the reading and writing of NeXus files. The details of the format are available at http://www.neutron.anl.gov/NeXus/" ---[Klosowski et al. 1998]. more...

The Interaction between imgCIF and NeXus: The Diamond group is adopting imgCIF/CBF for their MX beam lines, but is also considering NeXus for the future [Ashton et al. 2005] [and see below]. The imgCIF effort should it easier for users to process data taken from various beam lines. The NeXus effort should provide data management at multiple beamlines that produces consistent imgCIF data for users to take to their home institutions. Therefore, it is important to resolve the fine details of the interaction between NeXus and imgCIF. This is a non-trivial task, involving mappings between the NeXus tree-oriented structure and the imgCIF table-oriented structure, extending the ontologies for both data and metadata to concordances.

Under Construction