The design of Jemboss: a graphical user interface to EMBOSS

Bioinformatics. 2003 Sep 22;19(14):1837-43. doi: 10.1093/bioinformatics/btg251.


Design: Jemboss is a graphical user interface (GUI) for the European Molecular Biology Open Software Suite (EMBOSS). It is being developed at the MRC UK HGMP-RC as part of the EMBOSS project. This paper explains the technical aspects of the Jemboss client-server design. The client-server model optionally allows that a Jemboss user have an account on the remote server. The Jemboss client is written in Java and is downloaded automatically to a user's workstation via Java Web Start using the HTML protocol. The client then communicates with the remote server using SOAP (Simple Object Access Protocol). A Tomcat server listens on the remote machine and communicates the SOAP requests to a Jemboss server, again written in Java. This Java server interprets the client requests and executes them through Java Native Interface (JNI) code written in the C language. Another C program having setuid privilege, jembossctl, is called by the JNI code to perform the client requests under the user's account on the server. The commands include execution of EMBOSS applications, file management and project management tasks. Jemboss allows the use of JSSE for encryption of communication between the client and server. The GUI parses the EMBOSS Ajax Command Definition language for form generation and maximum input flexibility. Jemboss interacts directly with the EMBOSS libraries to allow dynamic generation of application default settings.

Results: This interface is part of the EMBOSS distribution and has attracted much interest. It has been set up at many other sites globally as well as being used at the HGMP-RC for registered users.

Availability: The software, EMBOSS and Jemboss, is freely available to academics and commercial users under the GPL licence. It can be downloaded from the EMBOSS ftp server:, Registered HGMP-RC users can access an installed server from:

MeSH terms

  • Computer Graphics*
  • Database Management Systems*
  • Databases, Factual*
  • Europe
  • Hypermedia
  • Information Storage and Retrieval / methods*
  • Internet
  • Local Area Networks
  • Molecular Biology / methods*
  • Programming Languages
  • Software Design*
  • User-Computer Interface*