GCP - Bioinformatics - Web Services

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BioCASE Installation

The BioCASE software can be downloaded from this page and documentation can be found in this page.

The BioCASE provider software runs on any CGI compliant web server and supports any database for whiuch there is a Python library, for detailed instructions please refer to the official installation guide.

The steps needed to install this system are:

  • Download the provider software.
  • Set-up a virtual directory in your web server that points to BioCASE's www directory.
  • Install the latest Python version.
  • Configure your web server to use Python as a CGI.
  • Run the setup configuration script.

Once you have completed these steps you should be able to see the main page of your biocase installation.

The next thing you should do is install the third party libraries that are required, if your installation is "localhost/biocase" then you can directly try http://localhost/biocase/utilities/testlibs.cgi. Here you wiull see the list of installed and not yet installed libraries that are needed by BioCASE to operate, a list of libraries to work with your particular database engine and the status of the directories that need to be writeable by the web server.

Once you have completed this step you are ready to configure your server. In this process you will create the data sources, describe the database structure and map your database to XML schemas.

Data sources are end points from which you will publish your databases via web services using common XML schema formats. You normally will create one datasource per database, or per database view; the latter means that if you are publishing several datasets from the same database and you intend to publish these datasets separately it is a good idea to set-up one data source per data set.

Describing the database structure means identifying the table primary keys, foreign keys and table aliases. This step is done once per dataset.

Mapping the database means linking elements of an XML schema to database fields, so that the stored data can be represented in an XML structure. Which XML schemas to use depend on which audiences you want to serve, please refer to the schema documentation page.

For more detailed instructions and training examples please refer to the configuration page.


Please provide feedback on the design, suggested features or problems and errors you might discover to Milko A. Skofic at Bioversity International.


Subprogramme Leader Theo van Hintum, Wageningen,
theo.vanhintum@wur.nl




WEB SERVICES
Welcome

Technology
BioCASE
BioMOBY
TAPIR


Installation
BioCASE
BioMOBY
TAPIR

Schemas
Documentation

Providers
Data sources



GENERAL LINKS

Bioinformatics homepage
GCP Bioinformatics links
GCP Bioinformatics Brochures