This article gives an overview of approaches to developing web based tools for bioinformatics. It describes the alternatives at each layer of the system, including the data layer and sources of data, the application programming layer, the web layer, and bioinformatics tools and software libraries. The goal is to help prospective bioinformatics application developers (1) get started; (2) make good software technology choices, and; (3) have a map of how to put an entire bioinformatics web application together. Finally, the article discusses integration of disparate web applications.
The article describes some of the more popular tools for solving basic problems in DNA and protein sequence analysis, alignment, and searching. A brief background to the bioinformatics problems is presented and then a summary and comparison of the approaches and tools is given. Examples are given for Perl, Java, C, C#, PHP, and AJAX. I also discuss several of the open source bioinformatics libraries, including BioPerl and BioJava. The goal is the provide the reader with a guide to getting started with development of web based tools for bioinformatics and some of the factors to consider when developing web software for sequence analysis, alignment, and searching, including the use, environment, prerequisites, and summary of capabilities.
The intended audience is bioinformatics students and practitioners new to the area and starting on bioinformatics software development tasks. It should also help someone serious about building a bioinformatics web portal because it is a broad view of many different tools and technologies and considerations for the re-use of those tools.
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