[IUCr Home Page] [MEDSBIO]

| IUCr Home Page | CIF Home Page | CBF | NeXus |
| BioSync | MEDSBIO list | MEDSBIO list archive | Meetings |
| Make a Submission to the MEDSBIO web site |

Consortium for Management of Experimental Data in Structural Biology
Second imgCIF workshop (new series)
at BNL on Thursday 24 May 2007
in conjunction with the 2007 Joint NSLS and CFN Users' Meeting

Synchrotron Image-Data Format Workshop

Herbert J. Bernstein, yaya at dowling dot edu
Robert M. Sweet, sweet at bnl dot gov
Sponsored by DOE under grant ER64212-1027708-0011962, NSF under grant DBI-0610407 and NIH under grant 1R13RR023192-01A1.

Workshop Report

The pace of data collection and the volume of data collected at synchrotron beam lines is increasing. The ACA Data, Standards, and Computing Committee is spearheading an effort to improve the efficiency of the handling and storage of these data by encouraging the adoption of common data formats and standard software interfaces. The goal of this is firstly to have the data be self defining, therefore equally accessible to data-reduction and -visualization codes. The second goal, for the purposes of secure archiving, is to provide robust internal documentation of the source of the data.

The first imgCIF/CBF workshop took place at Brookhaven National Laboratory in 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 were created, are available on the web, and are described in Volume G of the IUCr International Tables for Crystallography. Now the community should adopt a consensus standard for management of data at synchrotron beam lines, and to make it easier for users to process data taken from various beam lines. Also, as our science evolves, new concepts will be considered: possibilities include NeXus and XML.

The first workshop in the new series on "Management of Synchrotron Image Data: imgCIF File System and Beyond", was held on 22 July 2006 as part of the 2006 ACA meeting in Honolulu, Hawaii. That workshop concluded that that was "the right time for more widespread use of imgCIF ... [and that] SR sources should start writing imgCIF image files as soon as possible, employing the imgCIF dictionary already adopted by the IUCr Committee on the Maintenance of the CIF Standard (COMCIFS) and published on the web and in International Tables Volume G.] " [from the report of the workshop, see http://www.medsbio.org/meetings/ACA_2006_WK02_Report.html].

Subsequent to the Hawaii workshop intensive work was started in response to these recommendations. Both the imgCIF dictionary and the supporting software library were reviewed and, after meetings at SLS and ESRF, extended. See SLS_report.html and ESRF_report.html for more information on those meetings. The work continued in collaboration with members of the community (see the imgCIF mailing list http://www.iucr.org/iucr-top/cif/cbf/imgcif-l/.

In light of this activity a workshop on data formats for synchrotron image data was held after the NSLS/CFN meeting on 24 May 2007 at BNL in the Biology Department. Topics discussed included proposed extensions to imgCIF, the use of NeXus, progress on software and the status of imgCIF at Diamond and at SLS. The workshop was organized by Herbert J. Bernstein of Dowling College and Bob Sweet of Brookhaven National Laboratory. Because Bob Sweet could not attend, John Skinner of BNL filled in for Bob Sweet at the workshop itself.

The topics for the workshop were:

Participants, left to right: G. Todorov,
J. Skinner, C. Nielsen, J. Steinbrener, D. O'Brien, Q. Guo (standing), I. Awuah Asiamah (seated),
J. Jemilawon, N. Darakev, [not visible: G. Darakev, J. Westboook],
F. Bernstein, A. Howard, N. Sauter, [behind the camera: H. Bernstein]

The workshop was attended by 15 participants and began with a brief welcome and introduction by Herbert Bernstein. The particpants then introduced themselves. This was followed by talks by John Skinner of Brookhaven National Laboratory, Andy Howard of IIT, John Westbrook of Rutgers, Chris Nielsen of ADSC, Nick Sauter of Lawrence Berkeley National Laboratory, Jan Steinbrener of the State University of New York at Stony Brook, and by Herbert Bernstein of Dowling College. The remainder of the meeting was devoted to open discussion of the issues raised in the presentations and tutorials to clarify both the dictionary and the software.

The discussion was wide-ranging and constructive. The overall impression was of an acceptance of the need to be able to use imgCIF in the PX world, and to work out sensible interfaces to other approaches to synchrotron image data management (e.g. hdf5 and NeXus).

The major action items agreed to at the workshop were:

(The pre-workshop agenda and charge is at http://www.medsbio.org/meetings/BNL_May07_imgCIF_Workshop.html)

The agenda for the workshop as held was

8:30 am	Breakfast

9:00 am Welcome and introduction to the workshop    H. J. Bernstein, Dowling
                                                      [imgCIF dic,
                                                       CBFlib man]

9:10 am Participants introduce themselves:  

9:20 am "Data Management at the NSLS PXRR Beamlines"
                                                    J. Skinner, BNL

9:40 am "imgCIF, Robotics and Remote Access"          A. Howard, IIT

10:00 am "Harvesting Data Collection Information for
         Protein Data Bank Depositions"             J. Westbrook, Rutgers
10:20 am (how we log the information related to the
         experiment)                                C. Nielsen, ADSC

10:40 am Break

11:00 am "Use of the CBF Library in the Context of 
         Real-Time Image Analysis"                  N. Sauter, LBNL   

11:20 am "Theory of a unified field: standard file
        formats and subroutine libraries for
        diffraction imaging"                        J. Steinbrener, USB
11:40 am "The current status of the imgCIF dictionary
        and related software -- a work in progress"
                                                    H. Bernstein, Dowling
12:00 pm Discussion and plans for the afternoon

12:15 pm Lunch.
      Note: those with a general interest in the subject
      are welcome to stay for the afternoon technical

1:00  pm Technical discussions

2:30  pm Break

3:00  Further discussion and conclusions

      At 4 pm, A. Howard, N. Sauter, H. Bernstein and F. Bernstein
      adjourned for continued informal discussions in a more
      comfortable setting.
The main points discussed at the workshop were:


Name Affiliation Email address
Isaac Awuah Asiamah Dowling College catskill1331 at yahoo dot com
Frances C. Bernstein Bernstein + Sons fcb at bernstein-plus-sons dot com
Herbert J. Bernstein Dowling College yaya at bernstein-plus-sons dot com
Nikolay Darakev Dowling College darakevn at gmail dot com
Georgi Darakev Dowling College darakevg at gmail dot com
Quanzhong Guo BNL qguo at bnl dot gov
Andy Howard IIT howard at iit dot edu
John Jemilawon Dowling College damie225 at gmail dot com
Chris Nielsen ADSC cn at adsc-xray dot com
Daniel T. O'Brien Dowling College dto2 at dowling dot edu
Nicholas K. Sauter LBL nksauter at lbl dot gov
John Skinner BNL skinner at bnl dot gov
Jan F Steinbrener USB steinbre at xray1.physics.sunysb dot edu
Georgi Todorov Dowling College terahz at geodar dot com
John Westbrook Rutgers jwest at rcsb.rutgers dot edu

A. Howard, N. Sauter J. Westbrook, F. Bernstein, A. Howard

J. Steinbrener, J. Lemilawon, N. Darakev, J. Westbrook, F. Bernstein, A. Howard

J. Skinner, G. Todorov, C. Nielsen, J. Steinbrener, D. O'Brien,
A. Awuah Asiamah, J. Jemilawon, N. Darakev, J. Westbrook (partially visible), A. Howard
Q. Guo, J. Skinner

Travel arrangements

For the convenience of participants, forms to be used for travel reimbursement requests are here.


Our thanks to Brookhaven National Laboratory for the use of their facilities, in particular to Kathryn Folkers, Salvatore Sclafani, John Skinner and Bob Sweet for their hospitality and hard work, to Nayyarson's Food Service, especially to Ray Hernandez, for food service that worked unobtrusively and to the U.S. Department of Energy, the U. S. National Science Foundation and the U. S. National Institutes of Health for funding used to make this workshop series possible.