SeWeR: a customizable and integrated dynamic HTML interface to ...

BIOINFORMATICS APPLICATIONS NOTE

Vol. 17 no. 6 2001 Pages 577–578

SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics services Malay Kumar Basu Centre for Cellular and Molecular Biology, Hyderabad 500007, India Received on August 25, 2000; revised on January 30, 2001; accepted on March 2, 2001

ABSTRACT Summary: Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser. Availability: The web version of SeWeR can be freely accessed from http://www.bioinformatics.org/sewer/ or http://iubio.bio.indiana.edu/webapps/SeWeR/, and also from several mirror sites all over the world (a full listing is available on the SeWeR web page). It can also be downloaded under GNU General Public License from ftp://iubio.bio.indiana.edu/molbio/analyze/sewer.zip. Contact: [email protected]

The plethora of bioinformatics services available on the World Wide Web necessitates the integration of these services in a seamless interface. Three such freely available interfaces are Baylor College of Medicine (BCM) search launcher (http://dot.imgen.bcm.tmc.edu:9331/; Smith et al., 1996), ORBIT (Bellgard et al., 1999) and The Biology Workbench (http://workbench.sdsc.edu/; Subramaniam, 1998). But each of these approaches is either greatly dependent on server-side processing of data or requires installation of software environments like Perl or Java. On one hand, dependency on server-side processing of data makes software like this difficult to port to another server architecture. On the other hand, installation of a software environment and compilation of source code to customize or to extend particular software is beyond the capabilities of casual users, and therefore, restrict the use of such services to experts. Sequence analysis using Web Resources (SeWeR) is a versatile software that addresses all the above-mentioned limitations. SeWeR is implemented to make use of the ubiquitous presence of a new generation of web-browsers that are amenable to programming in JavaScript. Together with Cascading Style Sheets (CSS; see http://www.w3c. org/), a set of document-formatting rules, JavaScript can be used to generate sophisticated user interfaces and can c Oxford University Press 2001


turn a static HTML page into a truly interactive webapplication. Dynamic HTML (DHTML; Goodman, 1998) has the added advantage of being completely independent of any additional software environment like Perl or Java. A browser is enough to run a DHTML application, which is considerably faster than Java applets. The choice of DHTML also enables SeWeR to transparently access the existing service without any change of the existing server architecture of a particular service. SeWeR does all its computation on the client browser making it capable of running as a stand-alone application from within the browser. Use of DHTML also makes SeWeR capable of being hosted from a web site. SeWeR presents an integrated uniform interface to commonly used services in bioinformatics, such as nucleic acid and protein sequence retrieval and analysis, PCR related analysis, sequence alignment, database searching, protein structure prediction, sequence format conversion, sequence assembly, etc. (see SeWeR web site for details). It also supplies all the advanced options of a particular service. Certain common tasks like retrieving a sequence from a database or a PubMed search are quickly performed from the top navigation panel. A typical search page is shown in Figure 1 (in this case ‘Database Searches’). All the services can be accessed through a common query form. The form provides access to the help page of the selected service and also the advanced options of the selected service. The user, after completing the option form, can also customize the form by clicking on the ‘customize’ button, which opens up a new window with a form dynamically generated with all the chosen options already filled in. This customized page can be saved locally. The user does not need to fill in the options of a customized page. If a remote service is not already supported by SeWeR, the user can incorporate the service in SeWeR in ‘Customization section’. The user has to supply the HTML page of the service, SeWeR target page and some simple information such as the URL of the service, help-page URL, program name etc. SeWeR intelligently parses the HTML page and seamlessly incorporates the service in SeWeR. 577

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Fig. 1. Screen dump showing the option menu. The program chosen is BLAST.

SeWeR also provides a set of simple sequence manipulation tools locally. At present, the implemented tools are a program to inverse-complement and another to ‘clean’ a DNA sequence. The latter is a script written to get rid of number, line-breaks, spaces and other characters from the sequence. A special feature of SeWeR is the use of Bookmarklets (see http://developer.netscape.com/ docs/manuals/communicator/jsguide/misc.htm). These are small JavaScript codes that can be executed from a personal toolbar that can be very useful. Although used quite often in web development, these codes were rarely used in bioinformatics. At present the only web site in bioinformatics where bookmarklets are used is EBI SRS server (Zdobnov et al., 2000). SeWeR offers two bookmarklets as prototypes. One for the retrieving sequence from GeneBank and the other one for PubMed query. In conclusion, SeWeR is a prototype interface written entirely in JavaScript that is cross-platform, extendable, customizable and easy to use. It provides several levels of customization of the interface according to the user skilllevels and his needs. The structure of SeWeR is highly amenable for batch processing and automation and allows the most efficient use of web-based sequence analysis. 578

ACKNOWLEDGEMENTS I gratefully acknowledge facilities provided by CCMB. I am grateful to Dr Don Gilbert, Indiana University for his careful insight and critical comments on the manuscript and also for nurturing SeWeR. I thank Dr Malay K. Ray, Dr S. Shivaji, members of Bioinformatics.org, Uma and Powrnima. I was recipient of CSIR fellowship for my PhD during the development of SeWeR. REFERENCES Bellgard,M.I., Hiew,H.L., Hunter,A. and Wiebrands,M. (1999) ORBIT: an integrated environment for user-customized bioinformatics tools. Bioinformatics, 15, 847–851. Goodman,D. (1998) Dynamic HTML, the Definitive Reference. O’Reilly. Smith,R.F., Wiese,B.A., Wojzynski,M.K., Davison,D.B. and Worley,K.C. (1996) BCM search launcher—an integrated interface to molecular biology data base search and analysis services available on the World Wide Web. Genome Res., 6, 454–462. Subramaniam,S (1998) The biology workbench—a seamless database and analysis environment for the biologist. Proteins, 32, 1–2. Zdobnov,E.M., Lopez,R., Apweiler,R. and Etzold,T. (2000) The EBI SRS server—recent developments. Proceedings of the German Conference on Bioinformatics, pp. 139–147.