BioTags: A JSP Tag Library for Bioinformatics Website Construction

Abstract

Today we are faced with a growing need for a rapid publishing of valuable biological information via internet. To fulfill the need, it is occasionally necessary to construct a small to middle scale website. Some of their pages may have to contain the dynamically generated response as a result of analysis tools such as BLAST, FASTA, etc. In most cases, such pages are written by script languages like Perl, Python or Ruby, or server-side script languages like PHP to make use of Common Gateway Interface (CGI) mechanism for generating dynamic contents. Here is a problem. To give the pages ability to run the analysis tool, one have to write a code to execute a native command. Thus there is a need for somewhat of programming skill. By using, however, the ‘tag extension’ capability specified in Java Server Pages 1.2 (JSP1.2) [6, 5, 3], there is no need to write any codes but to mark up content by XML-like tags. JSP is known as a content generation technology, and is built upon server-side Java technologies. So this makes it easy to design and port website contents. The tag set used in a JSP page is not fixed but extensible by importing additional libraries of custom tag. Currently there are a number of tag libraries available on-line [2, 4], but it seems there is no public tag library aimed at bioinformatical use. So we have developed the bioinformatics tag library: biotags.