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Dear ccp4bb, cnsbb and O communities,
I would like to officially announce
X T A L B A S E
a new powerful web-based crystallization and crystallography data
management system. The homepage of XtalBase is
http://www.xtalbase.net
XtalBase allows designing, manageing and documenting crystallization
experiments and organizes a variety of data like coordinates, data
collections, data sets, publications etc. The program is operated via
a web browser and consists of a series of php scripts, which access a
MySQL database. XtalBase is free and can be downloaded from
http://www.xtalbase.net.
The core features of XtalBase are:
* XtalBase integrates a compounds database containing physicochemical
data of a large number of compounds used in crystallization.
* Every user maintains his/her own stocks database with freely
defined concentration, volumina etc.
* The identity of compounds and stocks is maintained in the design
and evaluation of crystallization experiments. It is therefore
possible to correlate drop composition and success rates and to share
this information with other users.
* Crystallization experiments are designed individually, in series or
by random.
* Crystallization plates can be copied from a large number of
predefined commercially available screenings.
* Crystallization plates are assigned to projects.
* The program hosts a browsable and searchable 1:1 copy of the BMCD
(Biological molecule crystallization database:
http://wwwbmcd.nist.gov:8080/bmcd/bmcd.html, not included in download
package).
* The dimensions of crystallization plates can be freely chosen.
* The number of drops per well can be freely chosen.
* Drops can be defined by adding stock volumes or by setting final
concentrations.
* The program displays recipes for all stocks used in the plate and
the stock volumes needed for the plate.
* Drop concentrations, pipetting recipes and observation sheets can
be displayed in a ready-to-print layout.
* Observations can be documented in form of free text (per drop and
per plate), scores and pictures.
* Users can calculate an estimate of success of a given drop
composition based on data from the BMCD, all users who have recorded
observations within the program or of a particular project. This
estimate of success can be used when new conditions are generated by
random.
* The user can view plate and project summaries with some success
statistics over the drops within a plate/project.
* XtalBase can be easily configured such that any kind of data or
groups of data can be stored in the system. Interfaces to access,
browse, search, and import these data are instantly available.
* The currently managed data comprise: protein batches,
compounds/stocks, crystallization plates, solutions, data
collections, data sets, coordinates, refinement cycles, publications.
* All data stored in the database can be searched via a unified
search interface. The search interface allows searching in all or
only specific fields of a database entry. Search terms can be
concatenated by logical 'AND', 'OR' and can also be negated ('NOT').
* Data can be imported from text files with help of importer
templates.
* Plate data can be imported from text files, which are formatted in
one of two possible formats.
* Data can be exported using freely defined export templates.
* It is possible via mouse-click to run external executables and
provide these executables with data from the database. The output of
these executables can be either displayed or parsed by an importer
and fed back into specific fields of the database. For example,
XtalBase can be configured such that - on mouse-click - an external
program is invoked that would determine the sequence from a pdb file
and produce an output, from which the sequence is reimported into the
database.
* Users can share their data either with other specific users, with
the user group, they belong to, or with all other registered users.
* The program administrator has full control over who can view what
data.
* Upgrade to a more recent version always preserves all data and
personal settings.
* XtalBase has a built-in messageing facility, which can be used to
send messages to specific users, all members of a group or all
registered users.
* A help text system provides context-related help throughout the
program.
Any constructive feedback is highly welcome.
With best regards,
Winfried Meining
-------------------------------------------
Dr. Winfried Meining
Karolinska Institutet
Department of Biosciences and Nutrition, NOVUM
Center for Structural Biochemistry
S-14157 Huddinge, Sweden
Tel.: +46-(0)8-6083-336
Fax : +46-(0)8-6089-290
http://www.csb.ki.se/xray/wim/
