BioUML server

BioUML server is a Java application that is started as servlet on J2EE compatible server (Tomcat server is being used). Like BioUML workbench it also uses [1] 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,

Architecture of BioUML server

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)