Bioinformatics Web Portals

Bioinformatics Web Portals

Mario Cannataro (Università “Magna Græcia” di Catanzaro, Italy)
Copyright: © 2009 |Pages: 22
DOI: 10.4018/978-1-60566-098-1.ch016
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Bioinformatics involves the design and development of advanced algorithms and computational platforms to solve problems in biomedicine (Jones & Pevzner, 2004). It also deals with methods for acquiring, storing, retrieving and analysing biological data obtained by querying biological databases or provided by experiments. Bioinformatics applications involve different datasets as well as different software tools and algorithms. Such applications need semantic models for basic software components and need advanced scientific portal services able to aggregate such different components and to hide their details and complexity from the final user. For instance, proteomics applications involve datasets, either produced by experiments or available as public databases, as well as a huge number of different software tools and algorithms. To use such applications it is required to know both biological issues related to data generation and results interpretation and informatics requirements related to data analysis. Bioinformatics applications require platforms that are computationally out of standard. Applications are indeed (1) naturally distributed, due to the high number of involved datasets; (2) require high computing power, due to the large size of datasets and the complexity of basic computations; (3) access heterogeneous data both in format and structure; and finally (5) require reliability and security. For instance, applications such as identification of proteins from spectra data (de Hoffmann & Stroobant, 2002), querying of protein databases (Swiss-Prot), predictions of proteins structures (Guerra & Istrail, 2003), and string-based pattern extraction from large biological sequences, are some examples of computationally expensive applications. Moreover, expertise is required in choosing the most appropriate tools. For instance, protein structure prediction depends on proteins family, so choosing the right tool may strongly influence the experimental results.
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Literature Review

Shull, Russ and Basili (2000) defined six types of software defects that can be found in object-oriented designs: missing information, incorrect facts, inconsistent information, ambiguous information, extraneous information, and miscellaneous defects. Incorrect facts, inconsistent information, ambiguous information, and extraneous information refer to the model correctness, while missing information refers to completeness.

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