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- A computational tool for peptide mass fingerprintingPublication . al-hawri, eman; Anjos, António dos; Pearson, GarethProtein identification using Mass Spectrometry (MS) is essential in the study of proteomics. Two popular techniques are used in the identification: Tandem Mass Spectrometry (MS/MS) and Peptide Mass Fingerprinting (PMF), which is considered in this work. PMF is widely used in the proteomics field. It is faster and more economic when compared to MS/MS. This work focuses on the development of a computational tool for protein identification using PMF data. The main objective for any PMF tool is to identify the correct protein (if it exists) by searching a peak list, produced by MS, against a protein database. However, one of the great challenges to these tools is related to the size of the databases that result in many random matches. In fact, the main difference between these tools is the scoring method which is responsible of minimizing these random matches. Therefore, a review of PMF tools and their scoring methods is presented and discussed. There are many tools on the Internet (both commercial or academic) for PMF protein identification using public databases. These tools do not offer a locally installable version, and do not allow the use of in-house databases, a feature that is of great importance to biologists who work on non-model systems. In contrast, the tool developed in this work is free, can be installed locally, and can be used with both public and local databases. Additionally, it supports different sorts of protein modifications and contaminants suppression, features that are not available by some of the existing tools. A new scoring method is proposed and incorporated in the proposed tool. The proposed tool is compared with two of the most popular software packages (commercial and academic), showing a good accuracy and being very competitive with the most popular and robust commercial software (Mascot). The developed prototype is platform-independent and is very easy to install. To allow users to work and interact with the system in an easy-to-use environment, a friendly graphical user interface is developed to allow them to manage their files very efficiently. In addition, it can work with single or multiple query files to support different work scales. The features this new tool offers make it an important assist to the biological laboratories concerning the PMF task.
- Network coding for reliable wireless sensor networksPublication . al-hawri, eman; Correia, N.; Barradas, ÁlvaroWireless sensor networks are used in many applications and are now a key element in the increasingly growing Internet of Things. These networks are composed of small nodes including wireless communication modules, and in most of the cases are able to autonomously con gure themselves into networks, to ensure sensed data delivery. As more and more sensor nodes and networks join the Internet of Things, collaboration between geographically distributed systems are expected. Peer to peer overlay networks can assist in the federation of these systems, for them to collaborate. Since participating peers/proxies contribute to storage and processing, there is no burden on speci c servers and bandwidth bottlenecks are avoided. Network coding can be used to improve the performance of wireless sensor networks. The idea is for data from multiple links to be combined at intermediate encoding nodes, before further transmission. This technique proved to have a lot of potential in a wide range of applications. In the particular case of sensor networks, network coding based protocols and algorithms try to achieve a balance between low packet error rate and energy consumption. For network coding based constrained networks to be federated using peer to peer overlays, it is necessary to enable the storage of encoding vectors and coded data by such distributed storage systems. Packets can arrive to the overlay through any gateway/proxy (peers in the overlay), and lost packets can be recovered by the overlay (or client) using original and coded data that has been stored. The decoding process requires a decoding service at the overlay network. Such architecture, which is the focus of this thesis, will allow constrained networks to reduce packet error rate in an energy e cient way, while bene ting from an e ective distributed storage solution for their federation. This will serve as a basis for the proposal of mathematical models and algorithms that determine the most e ective routing trees, for packet forwarding toward sink/gateway nodes, and best amount and placement of encoding nodes.
- Design of network coding based reliable sensor networksPublication . Al-hawri, Eman; Correia, Noélia; Barradas, A.Network coding can be very useful in achieving a balance between energy efficiency and end-to-end packet error in sensor networks, particularly if only a subset of the nodes act as encoding nodes. In this article, a mathematical model and a heuristic algorithm are proposed to plan for the best placement of encoding nodes while ensuring reliability. These approaches are also able to address scenarios where sensor networks, using different gateways, are federated. In this case a distributed storage system is required to ensure the recovery of packets when related coded packets arrive to the different gateways. The experimental results show that the adequate number and placement of encoding nodes can be effectively determined, significantly enhancing the performance of constrained sensor networks using network coding. (C) 2019 Elsevier B.V. All rights reserved.
- RELOAD/CoAP P2P Overlays for Network Coding Based Constrained EnvironmentsPublication . Al-hawri, Eman; Correia, Noélia; Barradas, Álvaro; Camarinha-Matos, L. M.; Parreira-Rocha, M.; Ramezani, J.The Internet of Things will bring into the Internet all kinds of smart systems, which will be able to interact with each other. Therefore, applications relying on data sharing for collaboration will increase, and effective distributed solutions for data storage become necessary. This need led to the proposal of a CoAP Usage for RELOAD, a generic P2P protocol that accepts pluggable application layers (Usages). This allows P2P overlay networks to be built where constrained systems store their data and clients are able to retrieve it. Since many smart systems rely on wireless networks to communicate, where network coding can be used to reduce packet error rate, P2P overlays should be prepared to store data from network coding based networks. More specifically, encoding vectors and encoded data must be stored, and a decoding service is required. In this article, we propose a CoAP Usage extension so that network coding based constrained networks can use RELOAD/CoAP P2P distributed storage.