Crystallography Online: the website of the International Union of Crystallography

Dear Colleagues,

   I just got the reviews on the MEDSBIO proposal we submitted last year.
In view of the reviews themselves and recent events, it seems worthwhile
to submit a revised proposal for the 25 June 2007 proposal cycle.  The
purpose of this message is to see who wishes to be a collaborator in
that revised proposal.

   Let me briefly address the reviews.  They ranged from very good down to
good.  The issues raised against are appended below, but the real issues
we need to address are from recent events -- the growing use of imgCIF
and the change in attitudes towards preservation of raw experimental
data.  Clearly, within a few years, we, as a community, will have to
have an agreed, organized approach to the archiving and exchange of
raw data in structural biology.

I suggest the following revised goals for MEDSBIO

The goals of the MEDSBIO consortium are to

   1.  Create a collaborative environment in which to resolve
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; and

   2.  In cooperation with the major existing archives
in structural biology, the major journal publishers in structural
biology, the relevant government and international organizations
and the major vendors in structural biology to contribute to
the evolving effort to define a mechanism to preserve all raw
experimental data in structural biology for future reference; and

   3.  To maintain an archive of documentation on standards and
proposals for ontologies, software, hardware specifications, web
templates and other documentation related to such protocols; and

   4.  To maintain an archive of open source software and links to
closed source software related to such protocols; and

   5.  To 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.

   The MEDSBIO activities for which funding is needed include
funds to organize and run 1-2 workshops per year, funds for
student staff to acquire, organize and disseminate data
formats and software and funds to develop software to fill
gaps in this infrastructure, especially in creating open
source interface and translation software among formats.

These efforts are primarily focused on the fine details of data
acquisition, of managing raw data in hardware and software in ways
that conserve resources, of providing the fully elaborated data
format specifications and robust interchange software that will
enable archiving and interchange.  These are issues that users of this
data often gloss over or do not consider at all.  For the users, data
derived from the raw data, e.g. structure factors derived from
pixel-by-pixel photon counts are the primary data, to be provided by
"black-box" systems.  For an archive the messy details of subtle
differences among substantially similar data representations may
be serious inconveniences hindering worthwhile efforts at making
data indices and feeding databases.   MEDSBIO is concerned with
issues in the innards  of those black boxes and the valid scientific
reasons for these subtle differences.

   The MEDSB

     Comments please.

      Regards,
        Herbert

    "...The promise of developing new algorithms for analyzing data was
nice, but there were no specifics as to how this would be done.

"Although the proposal mentioned many kinds of data, in the end the
proposal was for X-ray crystallographic data. This is not a proposal
for a depository for raw data. A similar group is already established
with 3 workshops already planned. There were no plans for
implementation or carrying through the ideas from the workshops to
practice. ...

"Taken together, the observations that the group was already
interacting, the fact that the data collection (in whatever form it
would take) was just that, not a way to foster new research, and the
limited general interest all dampened the panel's enthusiasm."

...

"Why is there no contribution toward support from vendors?"

...

"It is hard to tell exactly what science will be done as a result of
the proposal, it seems more like some workshops will be held and
people will be encouraged to talk with one another, but that is
already being done in other formats."

...

"The proposal is timely, but there is no real detail on how the goals
of the project will be achieved. There is a lot of information on
what is being done elsewhere by the individual collaborators and
other investigators, and it has to be assumed that the planned
workshops and meetings will help the consortium consolidate and focus
its efforts as it relates to meeting the needs of the community. In
addition, little effort is focused on the current formats being used
for NMR, cryo-electron microscopy (cryo-EM) and image reconstructed
data, or muon spin research and how this information will be
documented or interfaced, as was the a premise at the beginning of
the proposal. If this consortium really wants to "serve" the
structural biology field as a whole, there really should also be
discussions on how to archive documentation on data acquisition and
storage protocols for these and also solution scattering techniques.
Clearly this would be an even larger undertaking than the
crystallographic data that became the main focus of this proposal.

However, even after having said the above, these groups of
collaborators are the ideal investigators to take on this task of
creating the forum such as the MEDSBIO since they are the most
experienced with the issues involved.

-- 
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  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

                  +1-631-244-3035
                  yaya at dowling.edu
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