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CCP4BB  June 2009

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Subject:

Survey: crystallography lab LIMS

From:

"Lesburg, Charles" <[log in to unmask]>

Reply-To:

Lesburg, Charles

Date:

Tue, 2 Jun 2009 15:57:32 -0400

Content-Type:

text/plain

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Hi all,

I would like to compile a summary of what sorts of software that labs,
departments, or individual crystallographers are using to track their
experimental work.  Of course, whatever responses I receive will be
summarized and reposted to the ccp4bb.  Hopefully, this can benefit us
all.

More specifically, I am interested in finding a system that includes the
following concepts (no order intended), and integrates them together in
order to save time:

* track ongoing crystallizations/cocrystallizations/soaks
* ability to manage inventories (plasmids, compounds, protein supply,
trays, frozen crystals, etc.)
* multi-user with authentication and authorization
* web-based (ideally; to allow broad access to experimental data without
having to install software)
* data reporting/data mining
* integratability (is that a word?) with or functionality as some sort
of electronic lab notebook
* include information on the project, construct, sample handling, data
collection and processing stats, and ideally include some sort of
structure deposition
* integration with other lab automation hardware --
solution/screen-makers, crystallization robots, imagers, sample-changers
* integration with other software -- design of followup screens,
refinement pipelines, etc.
* ability to search based on target sequence
* "chemical-awareness", meaning that ligands are handled robustly and
searchable using 2D tools
* can deal with complexes beyond protein:ligand interactions (e.g.
protein:protein, protein:protein:ligand, protein:nucleic acid:ligand,
etc...)
* ability to manage experimental rationale/justifications -- that is,
why I am doing what I'm doing.

If you use or know of a system that does something like this or even a
portion of it, I would like to include it in the summary, even if it is
for internal use and not available to the greater community.

Some examples I found on the web include (again, in no particular
order):

* Xtaldb (http://jurand.med.virginia.edu/xtaldb/)
* CLIMS (http://clims.med.monash.edu.au:8027/)
* XRAYDB (Bosch et al. unpublished?)
* XtalBase (http://www.xtalbase.net)

Are systems used by the various structural genomics initiatives
available to the public?  Even if not, it would be great if they could
be included in the summary as well.

Sincerely,

Chip Lesburg
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