Design and implementation of a testbed for data distribution management

Data Distribution Management (DDM) is a core part of High Level Architecture standard, as its goal is to optimize the resources used by simulation environments to exchange data. It has to filter and match the set of information generated during a simulation, so that each federate, that is a simulation entity, only receives the information it needs. It is important that this is done quickly and to the best in order to get better performances and avoiding the transmission of irrelevant data, otherwise network resources may saturate quickly. The main topic of this thesis is the implementation of a super partes DDM testbed. It evaluates the goodness of DDM approaches, of all kinds. In fact it supports both region and grid based approaches, and it may support other different methods still unknown too. It uses three factors to rank them: execution time, memory and distance from the optimal solution. A prearranged set of instances is already available, but we also allow the creation of instances with user-provided parameters. This is how this thesis is structured. We start introducing what DDM and HLA are and what do they do in details. Then in the first chapter we describe the state of the art, providing an overview of the most well known resolution approaches and the pseudocode of the most interesting ones. The third chapter describes how the testbed we implemented is structured. In the fourth chapter we expose and compare the results we got from the execution of four approaches we have implemented. The result of the work described in this thesis can be downloaded on sourceforge using the following link: https://sourceforge.net/projects/ddmtestbed/. It is licensed under the GNU General Public License version 3.0 (GPLv3).

Implementazione ed analisi di un framework basato su Cloud per la valutazione di algoritmi di data Distribution Management

Il Data Distribution Management (DDM) è un componente dello standard High Level Architecture. Il suo compito è quello di rilevare le sovrapposizioni tra update e subscription extent in modo efficiente. All'interno di questa tesi si discute la necessità di avere un framework e per quali motivi è stato implementato. Il testing di algoritmi per un confronto equo, librerie per facilitare la realizzazione di algoritmi, automatizzazione della fase di compilazione, sono motivi che sono stati fondamentali per iniziare la realizzazione framework. Il motivo portante è stato che esplorando articoli scientifici sul DDM e sui vari algoritmi si è notato che in ogni articolo si creavano dei dati appositi per fare dei test. L'obiettivo di questo framework è anche quello di riuscire a confrontare gli algoritmi con un insieme di dati coerente. Si è deciso di testare il framework sul Cloud per avere un confronto più affidabile tra esecuzioni di utenti diversi. Si sono presi in considerazione due dei servizi più utilizzati: Amazon AWS EC2 e Google App Engine. Sono stati mostrati i vantaggi e gli svantaggi dell'uno e dell'altro e il motivo per cui si è scelto di utilizzare Google App Engine. Si sono sviluppati quattro algoritmi: Brute Force, Binary Partition, Improved Sort, Interval Tree Matching. Sono stati svolti dei test sul tempo di esecuzione e sulla memoria di picco utilizzata. Dai risultati si evince che l'Interval Tree Matching e l'Improved Sort sono i più efficienti. Tutti i test sono stati svolti sulle versioni sequenziali degli algoritmi e che quindi ci può essere un riduzione nel tempo di esecuzione per l'algoritmo Interval Tree Matching.

Potential effect of marine traffic on white-beaked dolphin (Lagenorhynchus albirostris) distribution and behaviour in Faxaflói Bay, southwest Iceland

Faxaflói bay is a short, wide and shallow bay situated in the southwest of Iceland. Although hosting a rather high level of marine traffic, this area is inhabited by many different species of cetaceans, among which the white-beaked dolphin (Lagenorhynchus albirostris), found here all year-round. This study aimed to evaluate the potential effect of increasing marine traffic on white-beaked dolphins distribution and behaviour, and to determine whether or not a variation in sighting frequencies have occurred throughout years (2008 – 2014). Data on sightings and on behaviour, as well as photographic one, has been collected daily taking advantage of the whale-watching company “Elding” operating in the bay. Results have confirmed the importance of this area for white-beaked dolphins, which have shown a certain level of site fidelity. Despite the high level of marine traffic, this dolphin appears to tolerate the presence of boats: no differences in encounter durations and locations over the study years have occurred, even though with increasing number of vessels, an increase in avoidance strategies has been displayed. Furthermore, seasonal differences in probabilities of sightings, with respect to the time of the day, have been found, leading to suggest the existence of a daily cycle of their movements and activities within the bay. This study has also described a major decline in sighting rates throughout years raising concern about white-beaked dolphin conservation status in Icelandic waters. It is therefore highly recommended a new dedicated survey to be conducted in order to document the current population estimate, to better investigate on the energetic costs that chronic exposure to disturbances may cause, and to plan a more suitable conservation strategy for white-beaked dolphin around Iceland.

Stochastic modeling of bacterial protein domains distribution to predict horizontal gene transfer

In questo elaborato, abbiamo tentato di modellizzare i processi che regolano la presenza dei domini proteici. I domini proteici studiati in questa tesi sono stati ottenuti dai genomi batterici disponibili nei data base pubblici (principalmente dal National Centre for Biotechnology Information: NCBI) tramite una procedura di simulazione computazionale. Ci siamo concentrati su organismi batterici in quanto in essi la presenza di geni trasmessi orizzontalmente, ossia che parte del materiale genetico non provenga dai genitori, e assodato che sia presente in una maggiore percentuale rispetto agli organismi più evoluti. Il modello usato si basa sui processi stocastici di nascita e morte, con l'aggiunta di un parametro di migrazione, usato anche nella descrizione dell'abbondanza relativa delle specie in ambito delle biodiversità ecologiche. Le relazioni tra i parametri, calcolati come migliori stime di una distribuzione binomiale negativa rinormalizzata e adattata agli istogrammi sperimentali, ci induce ad ipotizzare che le famiglie batteriche caratterizzate da un basso valore numerico del parametro di immigrazione abbiano contrastato questo deficit con un elevato valore del tasso di nascita. Al contrario, ipotizziamo che le famiglie con un tasso di nascita relativamente basso si siano adattate, e in conseguenza, mostrano un elevato valore del parametro di migrazione. Inoltre riteniamo che il parametro di migrazione sia direttamente proporzionale alla quantità di trasferimento genico orizzontale effettuato dalla famiglia batterica.

Ecological distribution of semi-demersal fishes in space and time on the shelf of Antalya Gulf

In this study we provide a baseline data on semidemersal fish assemblages and biology in a heterogeneous and yet less studied portion of the shelf of Antalya Gulf. The distribution of fish abundance in three transects subjected to different fisheries regulations (fishery vs non fishery areas), and including depths of 10, 25, 75, 125, 200 m, was studied between May 2014 and February 2015 in representative months of winter, spring, summer and autumn seasons. A total of 76 fish species belonging to 40 families was collected and semidemersal species distribution was analyzed in comparison with the whole community. Spatial distribution of fish was driven mainly by depth and two main assemblages were observed: shallow waters (10-25; 75 m) and deep waters (125-200 m). Significant differences among transects were found for the whole community but not for the semidemersal species. Analysis showed that this was due to a strong relation of these species with local environmental characteristics rather than to a different fishing pressure over transects. Firstly all species distribute according to the bathymetrical gradient and secondly to the bottom type structure. Semidemersal species were then found more related to zooplankton and suspended matter availability. The main morphological characteristics, sex and size distribution of the target semidemersal species Spicara smaris (Linnaeus, 1758), Saurida undosquamis (Richardson, 1848), Pagellus acarne (Risso, 1827) were also investigated.

Polychaete fauna of the Northwest Portuguese Coastal Shelf: ecology, diversity and distribution

Polychaetes are one of the larger groups of macroinvertebrates with more than 9000 species recognised, distributed worldwide. Thanks to the broad ecological adaptability and high abundaces, this taxon plays a leading role and is considered an important component of all benthic assemblages. Our knowledge about the West Iberian Coast polychaete fauna are scarce, and the only studies are recent. In this sense, the aim of this work was to investigate the composition and the spatial distribution of the polychaete fauna along the NW Portuguese Coastal Shelf, focusing on their relationship to environmental factors (depth, grain size, longitude and latitude) and to add new data to the existing biological dataset. A total of 39 sites were analysed, collected in an area of about 5665 km², between 20 and 150 m depth, distributed in a way to cover the overall grain size gradient. A total of 9352 specimens belonging to 41 families were found, and the analysis based on the abundance of polychaete species revealed five affinity groups: (a) nearshore medium sand characterised by Pisione parapari and Hesionura elongata; (b) very coarse sand that showed the highest abundance of Syllidae and was characterised by Protodorvillea kefersteini and Syllis garciai; (c) fine sand dominated by Spiophanes bombyx and Glycera tridactyla; (d) very fine sand with Nepthys assimilis and Amage sp. and the highest abundance of Paraonidae; (d) mud characterised by Labioleanira yhleni and Ampharete finmarchica. The combination of the environmental variables and the biological data, done with BIOENV routine, demonstrated that depth, grain size and fine contents were the best related with the biological data (rho=0.598). In general, the results agree with the composition and the spatial distribution of the polychaete fauna in other parts of the world; further polychaete assemblages related to mud sediments were firstly recorded in the Northwestern Portuguese Coastal Shelf.