Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics

The BITS2011 meeting, held in Pisa on June 20-22, 2011, brought together more than 120 Italian researchers working in the field of Bioinformatics, as well as students in Bioinformatics, Computational Biology, Biology, Computer Sciences, and Engineering, representing a landscape of Italian bioinformatics research

Why High-Performance Modelling and Simulation for Big Data Applications Matters

Modelling and Simulation (M&S) offer adequate abstractions to manage the complexity of analysing big data in scientific and engineering domains. Unfortunately, big data problems are often not easily amenable to efficient and effective use of High Performance Computing (HPC) facilities and technologies. Furthermore, M&S communities typically lack the detailed expertise required to exploit the full potential of HPC solutions while HPC specialists may not be fully aware of specific modelling and simulation requirements and applications. The COST Action IC1406 High-Performance Modelling and Simulation for Big Data Applications has created a strategic framework to foster interaction between M&S experts from various application domains on the one hand and HPC experts on the other hand to develop effective solutions for big data applications. One of the tangible outcomes of the COST Action is a collection of case studies from various computing domains. Each case study brought together both HPC and M&S experts, giving witness of the effective cross-pollination facilitated by the COST Action. In this introductory article we argue why joining forces between M&S and HPC communities is both timely in the big data era and crucial for success in many application domains. Moreover, we provide an overview on the state of the art in the various research areas concerned

Understanding the retinal basis of vision across species

The vertebrate retina first evolved some 500 million years ago in ancestral marine chordates. Since then, the eyes of different species have been tuned to best support their unique visuoecological lifestyles. Visual specializations in eye designs, large-scale inhomogeneities across the retinal surface and local circuit motifs mean that all species' retinas are unique. Computational theories, such as the efficient coding hypothesis, have come a long way towards an explanation of the basic features of retinal organization and function; however, they cannot explain the full extent of retinal diversity within and across species. To build a truly general understanding of vertebrate vision and the retina's computational purpose, it is therefore important to more quantitatively relate different species' retinal functions to their specific natural environments and behavioural requirements. Ultimately, the goal of such efforts should be to build up to a more general theory of vision

On Fine Stochastic Simulations of Liposome-Encapsulated PUREsystem™

The PURESystem™(for short: PS) is a defined set of about 80 different macromolecular species which can perform protein synthesis starting from a coding DNA. To understand the processes that take place inside a liposome with entrapped PS, several simulation approaches, of either a deterministic or stochastic nature, have been proposed in the literature. To correctly describe some peculiar phenomena that are observed only in very small liposomes (such as power-law distribution of solutes and supercrowding effect), a stochastic approach seems necessary, due to the very small average number of molecules contained in these liposomes. Here we recall the results reported in other works published by us and by other Authors, discussing the importance of a stochastic simulation approach and of a fine description of the system: both these aspects, in fact, were not properly acknowledged in such previous papers

Experimental evidences suggest high between-vesicle diversity of artificial vesicle populations: Results, models and implications

In the past years, artificial cellular models for origins-of-life research and synthetic biology have been extensively studied. At this aim, solute-filled lipid vesicles (liposomes) are widely used. Several evidences have been collected about the capture of water-soluble chemicals, the mechanism of vesicle self-reproduction, and the course of (bio)chemical reactions in the vesicle lumen. Among the several fascinating questions which emerged from these studies, here we focus on a peculiar feature, namely, the fact that a spontaneous heterogeneity of vesicle structure often emerges. In other words, vesicle populations created in the laboratory by classical batch methods include very ‘diverse’ vesicles with respect to size, morphology, and – importantly – solute content. The consequences of this between-vesicle diversity are shortly discussed