Databases

An I/O device driver for bioinformatics tools: the case for BLAST

R. Campos Mauro and Lifschitz, S., An I/O device driver for bioinformatics tools: the case for BLAST, vol. 4, pp. 563-570, 2005.

There are many bioinformatics tools that deal with input/output (I/O) issues by using filing systems from the most common operating systems, such as Linux or MS Windows. However, as data volumes increase, there is a need for more efficient disk access, ad hoc memory management and specific page-replacement policies. We propose a device driver that can be used by multiple applications. It keeps the application code unchanged, providing a non-intrusive and flexible strategy for I/O calls that may be adopted in a straightforward manner.

BNDb - Biomolecules Nucleus Database: an integrated proteomics and transcriptomics database

A. C. Faria-Campos, Gomes, R. R., Moratelli, F. S., Rausch-Fernandes, H., Franco, G. R., and Campos, S. V. A., BNDb - Biomolecules Nucleus Database: an integrated proteomics and transcriptomics database, vol. 6. pp. 937-945, 2007.

Proteomics correspond to the identification and quantitative analysis of proteins expressed in different conditions or life stages of a cell or organism. Methods used in proteomics analysis include mainly chromatography, two-dimensional electrophoresis and mass spectrometry. Data generated in proteomics analysis vary significantly, and to identify a protein it is often necessary to perform a series of experiments, comparing its results to those found in proteomics databases.

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