Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

Narrowband IoT: from the end device to the cloud. An experimental end-to-end study

This thesis is about a novel study and experimentation of a Cloud IoT application, communicating over a NB-IoT Italian network. So far there no been presented studies, which are about the interactions between the NB-IoT network and the cloud. This thesis not only fill this gap but also shows the use of Cognitive Services to interact, through the human voice, with the IoT application. Compared with other types of mobile networks, NB-IoT is the best choice

Massive Non-Orthogonal Multiple Access for Cellular IoT: Potentials and Limitations

The Internet of Things (IoT) promises ubiquitous connectivity of everything everywhere, which represents the biggest technology trend in the years to come. It is expected that by 2020 over 25 billion devices will be connected to cellular networks; far beyond the number of devices in current wireless networks. Machine-to-Machine (M2M) communications aims at providing the communication infrastructure for enabling IoT by facilitating the billions of multi-role devices to communicate with each other and with the underlying data transport infrastructure without, or with little, human intervention. Providing this infrastructure will require a dramatic shift from the current protocols mostly designed for human-to-human (H2H) applications. This article reviews recent 3GPP solutions for enabling massive cellular IoT and investigates the random access strategies for M2M communications, which shows that cellular networks must evolve to handle the new ways in which devices will connect and communicate with the system. A massive non-orthogonal multiple access (NOMA) technique is then presented as a promising solution to support a massive number of IoT devices in cellular networks, where we also identify its practical challenges and future research directions.Comment: To appear in IEEE Communications Magazin

Demonstrating Immersive Media Delivery on 5G Broadcast and Multicast Testing Networks

This work presents eight demonstrators and one showcase developed within the 5G-Xcast project. They experimentally demonstrate and validate key technical enablers for the future of media delivery, associated with multicast and broadcast communication capabilities in 5th Generation (5G). In 5G-Xcast, three existing testbeds: IRT in Munich (Germany), 5GIC in Surrey (UK), and TUAS in Turku (Finland), have been developed into 5G broadcast and multicast testing networks, which enables us to demonstrate our vision of a converged 5G infrastructure with fixed and mobile accesses and terrestrial broadcast, delivering immersive audio-visual media content. Built upon the improved testing networks, the demonstrators and showcase developed in 5G-Xcast show the impact of the technology developed in the project. Our demonstrations predominantly cover use cases belonging to two verticals: Media & Entertainment and Public Warning, which are future 5G scenarios relevant to multicast and broadcast delivery. In this paper, we present the development of these demonstrators, the showcase, and the testbeds. We also provide key findings from the experiments and demonstrations, which not only validate the technical solutions developed in the project, but also illustrate the potential technical impact of these solutions for broadcasters, content providers, operators, and other industries interested in the future immersive media delivery.Comment: 16 pages, 22 figures, IEEE Trans. Broadcastin

Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli.

A significant obstacle in training predictive cell models is the lack of integrated data sources. We develop semi-supervised normalization pipelines and perform experimental characterization (growth, transcriptional, proteome) to create Ecomics, a consistent, quality-controlled multi-omics compendium for Escherichia coli with cohesive meta-data information. We then use this resource to train a multi-scale model that integrates four omics layers to predict genome-wide concentrations and growth dynamics. The genetic and environmental ontology reconstructed from the omics data is substantially different and complementary to the genetic and chemical ontologies. The integration of different layers confers an incremental increase in the prediction performance, as does the information about the known gene regulatory and protein-protein interactions. The predictive performance of the model ranges from 0.54 to 0.87 for the various omics layers, which far exceeds various baselines. This work provides an integrative framework of omics-driven predictive modelling that is broadly applicable to guide biological discovery

A quadri-dimensional approach for poor performance prioritization in mobile networks using Big Data

Abstract The Management of mobile networks has become so complex due to a huge number of devices, technologies and services involved. Network optimization and incidents management in mobile networks determine the level of the quality of service provided by the communication service providers (CSPs). Generally, the down time of a system and the time taken to repair [mean time to repair (MTTR)] has a direct impact on the revenue, especially on the operational expenditure (OPEX). A fast root cause analysis (RCA) mechanism is therefore crucial to improve the efficiency of the operational team within the CSPs. This paper proposes a quadri-dimensional approach (i.e. services, subscribers, handsets and cells) to build a service quality management (SQM) tree in a Big Data platform. This is meant to speed up the root cause analysis and prioritize the elements impacting the performance of the network. Two algorithms have been proposed; the first one, to normalize the performance indicators and the second one to build the SQM tree by aggregating the performance indicators for different dimensions to allow ranking and detection of tree paths with the worst performance. Additionally, the proposed approach will allow CSPs to detect the mobile network dimensions causing network issues in a faster way and protect their revenue while improving the quality of the service delivered