Biological Modelling and Parallel Simulation Theory
Nature is extremely complex and not still completely explored. The biological activities of living beings are complex and radically interconnected. Only an exhaustive understanding of the organisms’ internal machinery can give a chance to abstract and focus them coherently. Thus, a well-structured model can be simulated to provide new insights about the "possible" behaviours of the phenomenon under examination. A central problem lies in the fact that most of the models nowadays existing have intractable sizes, thereby resulting suitable neither for any manually conducted analysis routine nor for the existing automatic simulation routines. Parallel simulation algorithms aim at overcoming this issue. Two classes of algorithms are worth investigating: the one concerning the multiple replication of the same trajectory in parallel (MRiP) and the other related to the concurrent simulation of the same trajectory through many cooperating processors (SRiP). The last is a relatively recent research area that involves three interesting intersecting areas (graph partitioning, simulated local time synchronization and time warping).
Orchestration of Bio-Services and Cloud Computing
Web Services technology is beginning to emerge as a de facto standard for integrating disparate applications and systems. In addition, the integration between web services and existing applications is becoming a standard approach to form more meaningful business processes: the Workflows. A Workflow Management System enacts business processes described in a process description language to easily automate and manage business processes that cross enterprises, platforms and application boundaries. Cloud computing has recently enjoyed great success because of its ability of transparently putting in communication different services on different platforms. Through it, the user can ignore any problem linked to the hardware administration and fully devote to the design and functionality of the service.
Bio-Data Handling and Storing
Every day, laboratories output vast amounts of raw data. Pre-processing treatments have been ad-hoc made with the aim to extract the information present in raw data from the inevitable noise introduced by the user inaccuracy as well as by the measurement tools. However, data (even in their cleaned form) remain in an unstructured form. Thus, considering the enormous growing of data, giving them a structure and storing them in appropriate repositories are becoming more and more urgent needs. Standard languages for biology (e.g. mzData, SBML, etc) exist.
Bio-Network Topology Analysis
Biological systems are characterized by a large number of interacting entities whose dynamics is described by a number of reaction equations. Such systems have been largely represented as network and widely studied as far as their topological properties are connected. Some properties like: chemicals centrality, fragmentation, essentiality, path redundancy, structure robustness, connectivity, etc. have been the object of many studies and keep on fascinating many scientists and their research. Of particular interest were the topological properties of the dependency graph (graph of dependency of biological reactions), whose properties are still mostly obscure.