A Cloud Infrastructure for Optimization of a Massive Parallel Sequencing Workflow

Massive Parallel Sequencing is a term used to describe several revolutionary approaches to DNA sequencing, the so-called Next Generation Sequencing technologies. These technologies generate millions of short sequence fragments in a single run and can be used to measure levels of gene expression and to identify novel splice variants of genes allowing more accurate analysis. The proposed solution provides novelty on two fields, firstly an optimization of the read mapping algorithm has been designed, in order to parallelize processes, secondly an implementation of an architecture that consists of a Grid platform, composed of physical nodes, a Virtual platform, composed of virtual nodes set up on demand, and a scheduler that allows to integrate the two platform

Virtual Environment for Next Generation Sequencing Analysis

Next Generation Sequencing technology, on the one hand, allows a more accurate analysis, and, on the other hand, increases the amount of data to process. A new protocol for sequencing the messenger RNA in a cell, known as RNA- Seq, generates millions of short sequence fragments in a single run. These fragments, or reads, can be used to measure levels of gene expression and to identify novel splice variants of genes. The proposed solution is a distributed architecture consisting of a Grid Environment and a Virtual Grid Environment, in order to reduce processing time by making the system scalable and flexibl

Optimizing Splicing Junction Detection in Next Generation Sequencing Data on a Virtual-GRID Infrastructure

The new protocol for sequencing the messenger RNA in a cell, named RNA-seq produce millions of short sequence fragments. Next Generation Sequencing technology allows more accurate analysis but increase needs in term of computational resources. This paper describes the optimization of a RNA-seq analysis pipeline devoted to splicing variants detection, aimed at reducing computation time and providing a multi-user/multisample environment. This work brings two main contributions. First, we optimized a well-known algorithm called TopHat by parallelizing some sequential mapping steps. Second, we designed and implemented a hybrid virtual GRID infrastructure allowing to efficiently execute multiple instances of TopHat running on different samples or on behalf of different users, thus optimizing the overall execution time and enabling a flexible multi-user environmen

On the stability of some isoperimetric inequalities for the fundamental tones of free plates

We provide a quantitative version of the isoperimetric inequality for the fundamental tone of a biharmonic Neumann problem. Such an inequality has been recently established by Chasman adapting Weinberger's argument for the corresponding second order problem. Following a scheme introduced by Brasco and Pratelli for the second order case, we prove that a similar quantitative inequality holds also for the biharmonic operator. We also prove the sharpness of both such an inequality and the corresponding one for the biharmonic Steklov problem

Strong existence and uniqueness of the stationary distribution for a stochastic inviscid dyadic model

We consider an inviscid stochastically forced dyadic model, where the additive noise acts only on the first component. We prove that a strong solution for this problem exists and is unique by means of uniform energy estimates. Moreover, we exploit these results to establish strong existence and uniqueness of the stationary distribution

Comparison between adenosine triphosphate bioluminescence and aerobic colony count to assess surface sanitation in the hospital environment

Background: Adenosine triphosphate bioluminescence produced by the firefly luciferase has been successfully introduced to verify cleaning procedures in the food industry according to the Hazard Analysis Critical Control Point program. Our aim was to evaluate the reliability of bioluminescence as a tool to monitor the effectiveness of sanitation in healthcare settings, in comparison with the microbiological gold standard. Methods: 614 surfaces of various material were randomly sampled in Policlinico University Hospital units in Palermo, Italy, to detect adenosine triphosphate bioluminescence and aerobic colony count. Linear regression model and Pearson correlation coefficient were used to estimate the relationship between the two variables of the study. Results: Aerobic colony count median was 1.71 colony forming units/cm2 (interquartile range = 3.8), whereas adenosine triphosphate median was 59.9 relative light units/cm2 (interquartile range = 128.3). Pearson coefficient R2 was 0.09. Sensitivity and specificity of bioluminescence test with respect to microbiology were 46% and 71%, whereas positive predictive value and negative predictive value were 53% and 65%, respectively. Conclusion: According to our results, there seemed to be no linear correlation between aerobic colony count and adenosine triphosphate values, suggesting that current bioluminescence technology has not any proportional relationships with culturable microbes contaminating environmental surfaces in health-care settings

Geometric bounds for the magnetic Neumann eigenvalues in the plane

We consider the eigenvalues of the magnetic Laplacian on a bounded domain Ω of R2 with uniform magnetic field β>0 and magnetic Neumann boundary conditions. We find upper and lower bounds for the ground state energy λ1 and we provide semiclassical estimates in the spirit of Kröger for the first Riesz mean of the eigenvalues. We also discuss upper bounds for the first eigenvalue for non-constant magnetic fields β=β(x) on a simply connected domain in a Riemannian surface. In particular: we prove the upper bound λ