SparkBLAST: scalable BLAST processing using in-memory operations.

BACKGROUND: The demand for processing ever increasing amounts of genomic data has raised new challenges for the implementation of highly scalable and efficient computational systems. In this paper we propose SparkBLAST, a parallelization of a sequence alignment application (BLAST) that employs cloud computing for the provisioning of computational resources and Apache Spark as the coordination framework. As a proof of concept, some radionuclide-resistant bacterial genomes were selected for similarity analysis. RESULTS: Experiments in Google and Microsoft Azure clouds demonstrated that SparkBLAST outperforms an equivalent system implemented on Hadoop in terms of speedup and execution times. CONCLUSIONS: The superior performance of SparkBLAST is mainly due to the in-memory operations available through the Spark framework, consequently reducing the number of local I/O operations required for distributed BLAST processing.

IntegraEPI: a Grid-based epidemic surveillance system.

The proposal of new analytical techniques has guided innovative methodological developments in public health interventions. The goal of this work is show advances in the development of a large scale system for space-time visualization, monitoring, modeling and analysis of epidemic data using a Grid platform. The resulting virtual laboratory, dubbed IntegraEPI, is expected to provide better epidemic forecasting and to define better strategies to fight the spread of a disease, in which new population-level interventions could be evaluated and iteratively refined using computational simulations, with tangible benefits for real-world epidemic prevention and control efforts.

PDA for health professionals: can you deal with that?

Personal digital assistants (PDAs) are being increasingly used on the health field, however, there are not many papers guiding a PDA-software development process concerning its usability in health field. This paper presents our experience dealing with PDAs regarding some elements of usability. We have shown that if simple yet extremely important points are to be observed before and during the development process, usability on PDA software can be greatly improved.