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Databases |
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Databases |
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Mutagenesis Screen
MEPD: Medaka Expression Pattern Database
Genetic Map
This database keeps track of all data in the screen from raw data until publication. The resolution of the database is one single egg. Information can be traced back from a mutant until the very first embryo in the screen displaying this phenotype.
Technicians
who collect the eggs in the morning enter egg numbers and their
identity (F2-family and cross number). Clutch identity and date of
egg lay is entered by a barcode reader. Their phenotype is examined
by researchers in the following days. The phenotype of an embryo can
be described by a list of structure-feature patterns (eg.
tectum=malformed), by text-comments and by pictures. This phenotype
description can be entered for several embryonic stages. Phenotype
description is been done online. Computers are equipped with a
microscopes and cameras. Pictures can be submitted immediately
through web interfaces.
A web search interface is provided, which allows to select for almost any parameter. One can search for affected structure or feature, for date of egg lay or screening, for name of the screener or for F2-family name. The search result page provides the user with all available information.
Having the complete screening data in a database format offers the opportunity to evaluate otherwise time consuming statistical calculations. In our screen a statistics is evaluated every night regarding screened families and genomes, phenotypes per genome and others.
The database is located in Kyoto on an IBM RS6000 running an AIX operating system. The database software is IBM DB2. The web server is WebSphere. Data exchange with the database is done using Java-Servlets. This architecture enables access to the database from any computer running a web browser. Screens could run in separated laboratories using a common database.
This database keeps information about the expression of genes and their sequences within the developing embryo. Expression patterns of ESTs at different embryonic stages are stored as picture files and as description. The description is hierarchically organized from crude (e.g. mesoderm - endoderm) till fine. Text comments, category (e.g. specific, ubiquitous) and expression strength complete the pattern description. Go to MEPD.
The database is located in Kyoto on an IBM RS6000 running an AIX operating system. The database software is IBM DB2. The web server is WebSphere. Data exchange with the database is done using Java-Servlets. This architecture enables access to the database from any computer running a web browser. Screens could run in separated laboratories using a common database.
Submission of sequences and pictures can be done by web interfaces or if many have to be submitted at once by scripts. Descriptions of the expression pattern can be entered by an interface.
A web search interface is provided, which allows to select for many parameter. One can search for stained structures, expression strength or blast a sequences with the blastn algorithm.
Sequences in this database are clustered and blast results are stored within the database and updated daily.
The genetic map database is not located on this server. For more information click here.
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Databases |
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