Dear All,
I would just like to add to Enrico's mention of ISPyB. This LIMS
system will log all your data collected at the beamline (experimental
parameters, screening images, data sets, edge scans, xrf spectra,
crystal snapshots etc) automatically and is stored indefinitely. Your
colleagues can also follow data collections in real time by logging on
from their home labs. In addition, you can upload large amounts of
information on your samples (acronym, space group, pin barcode etc) to
the data base that can be recovered at the beamline through MXCuBE and
the sample changer, tying all data collections to this information. You
can also track your dewars to and from the ESRF using it - even
receiving an email when it reaches the beamline. It has recently delved
into the world of data analysis, as you can rank crystals against each
other using a number of criteria. For those not in an exclusive
relationship with the ESRF, you will be glad to hear it is also
available at Diamond and I believe will be at PETRAIII.
Cheers, Matt
Some links:
ISPyB:
http://www.esrf.eu/UsersAndScience/Experiments/MX/How_to_use_our_beamlines/ISPYB
Sample tracking:
http://www.esrf.eu/UsersAndScience/Experiments/MX/How_to_use_our_beamlines/ISPYB/ispyb-dewar-tracking
Ranking:
http://www.esrf.eu/UsersAndScience/Experiments/MX/How_to_use_our_beamlines/ISPYB/ispyb-sample-ranking
Enrico Stura wrote:
Knowing where all the important files are is really all that is
needed. Sofistication can come later.
I would welcome a CCP4 database-assisted data archive system.
Here is my contribution to the discussion:
I agree with Paul Paukstelis that getting users to use any
database-assisted data archive system
is the biggest obstacle. I have had problems with compliance with my
system, where all that the student
has to do is to provide file and directory names each Friday to keep
the database up to date.
It is a simple html based access system where through hyperlinks one
can access the data anywhere
where it is stored. Users need only provide the directories names of
where the various pieces
of data are stored within the accessible network and the data manager
(any HTML competent individual)
can then set-up the links to the main control platform (start-up html
page).
The advantage of such system is that it is platform independent and
needs only a well configured browser.
It is backward compatible with any old data.
George Pelios may want to consider an automated system where mosflm,
scala and all subsequent
programs contribute to create and update a raw data retrieval file on
the basis of the files
they have used. When the project is finished a backup program should
be able to retrieve
all such files to be stored in a consolidated manner for transfer to a
long term storage server.
A brief description of the system I use for synchrotron data collection:
========================================================================
Prior to the synchrotron trip, each sample taken to the synchrotron is
entered in a table that represents its position in
the puck with hyperlinks to a file describing its position in the
crystallization tray (this file will have hyperlinks
to crystallization and all prior preparation steps).
As data is collected a short comment (resolution and number of frames
is included if data has been
collected) as the data is transfered in the home lab a link to the
directory where the data is
stored is then added.
To give an idea of data quality Mosflm and gimp screen capture are
used to create a jpg of
the first data image (with the frame filename added) which is stored
in the same directory as
the raw data frames. This image is accessed when clicking on the comment.
Compliance with the system can be checked by clicking on comments
other than "not tested".
It is all manual but is not very time consuming once the initial html
templates have been
set up. Still I am looking foward to a simple CCP4 designed system
that can do something similar
automatically.
I would also recommend looking at ispyb implemented at the ESRF which
is also web based:
www.esrf.eu/UsersAndScience/Experiments/MX/Software/ispyb
Enrico.
--
Matthew Bowler
Structural Biology Group
European Synchrotron Radiation Facility
B.P. 220, 6 rue Jules Horowitz
F-38043 GRENOBLE CEDEX
FRANCE
===================================================
Tel: +33 (0) 4.76.88.29.28
Fax: +33 (0) 4.76.88.29.04
http://www.esrf.fr/UsersAndScience/Experiments/MX/
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