Website Update: A New Graphical User Interface to EMBOSS

EMBOSS, the European Molecular Biology Open Software Suite is a collection of over 150 bioinformatics programs. It provides individual applications for retrieval, editing, and analysis of nucleotide and peptide sequences. It also includes software for analysing protein structure. Distributed under the GNU General Public License software agreements [6], all programs are available, free of charge, to all academic or commercial users. EMBOSS brings together programs from various sources including the EMBOSS development team, individuals and members of the EMBnet community. To mark the fifth anniversary of EMBOSS, an exciting new graphical user interface (GUI), ‘Jemboss’, has been launched. Written at the HGMPRC, in collaboration with the core EMBOSS development team, it has been designed to appeal to a broad base of research biologists wishing to utilise the computational analysis applications that EMBOSS offers. Jemboss is a Java application and has been designed to run on UNIX workstations, proprietary PC operating systems or indeed any Java enabled platform. This user-friendly interface dispenses with the requirement for training in UNIX or operating EMBOSS programs via a command line. It may therefore be used by biological scientists with the minimum of computing experience. A server for the new interface, accessible to registered HGMP users, has been set up at the EMBOSS web site [5]. It is also linked from the ‘Bioinformatics Applications’ menu on the HGMP site. Jemboss will function in client-server mode allowing many users to run their analyses remotely. The Jemboss interface window (the client) is launched on the users’ workstations. Analyses are then run on the HGMP machines and the results returned to the local screen. This has been achieved using the Simple Object Access Protocol (SOAP) [1], a new advance in Internet Communication Technology designed specifically to circumvent firewall restrictions. This, therefore, allows the user access to the EMBOSS applications whilst still maintaining the security of the server computer. SOAP manages this by using HyperText Transfer Protocol (HTTP), which is the protocol used to transfer data on the World Wide Web. Jemboss is also incorporated into the general EMBOSS distribution, packaged together with all the EMBOSS applications. System administrators who provide a local copy of EMBOSS on their site therefore also have the opportunity of making the GUI available to local users. In this standalone mode it will access and run a local copy of the EMBOSS programs, the programs are called directly and there is no need for the SOAP calls. Comparative and Functional Genomics Comp Funct Genom 2002; 3: 75–78. DOI: 10.1002 / cfg.136