Parallel and Cloud-Based Analysis of Omics Data: Modelling and Simulation in Medicine

High throughput experimental platforms and diagnostic equipments available in clinical settings and in research laboratories, such as magnetic resonance imaging, microarray, mass spectrometry and next-generation sequencing, are producing an increasing volume of clinical and omics data. Moreover, Electronic Patients Records (EPRs), eHealth systems, personal mobile sensors and Social Networks are collecting an overwhelming volume of health and life style data that may be integrated with clinical data and more and more is used for the real-time monitoring of patient's health. This poses new issues in terms of secure data storage, effective models for data integration, efficient algorithms for data analysis, new models for health monitoring, that may be addressed, among the others, using high performance computing solutions. Parallel computing and Cloud Computing may offer efficient and scalable solutions in an orthogonal way. In fact, parallel, bioinformatics software, that exploit off-the-shelf high performance computers, may be used to preprocess and analyze omics data at a lower layer, for instance to highlight genetic variation associated with complex diseases. On the other hand, Cloud Computing offers large scale data storage, data sharing services, on-demand anytime and anywhere access to resources and applications, for the realization of elastic and scalable applications and services. Motivated by the increasing use of parallel computing and cloud computing in life sciences, in this paper we survey both parallel bioinformatics algorithms for the parallel preprocessing and statistical and data mining analysis of omics data, as well as Cloud-based healthcare and biomedicine services and systems for large scale applications. Moreover, the paper underlines main issues and problems related to the use of such platforms for the storage and analysis of health data, with special focus to the security and privacy of patients data, that are particularly important in fields such as personalized medicine. Finally, the paper presents some case studies about the parallel and distributed modelling and simulation in medicine and biology.