BioUML server

BioUML server is a Java application that is started as servlet on J2EE compatible server (Tomcat server is being used).

Architecture of BioUML server

Like BioUML workbench it also uses Eclipse runtime to manage plug-ins that provide different services. The main services provided by BioUML server are:

• database service - provides information about database and secure access to it,
• access service - provides access to databases (read/write),
• diagram service - provides protocol to read/write diagram and all diagram elements during one HTTP request,
• Lucene service - provides full text search and its configuration,
• query service - provides indexed search for a database,

BioUML server supports access to different types of databases, such as:

• relational databases (for example, Ensembl database that is available as MySQL dump)
• text databases (for exampe, KEGG/Ligand database)
• XML databases (for example, databases in BioPAX or SBML formats)
• databases available via web services (for example, SABIO-RK database)