MEMOIRE DE FIN D ETUDES ESIEA

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1 DE FIN D ETUDES ESIEA VisLab, SPS & ITEE Sensor Network Implemented on the Great Barrier Reef Réseau de capteurs implémenté sur la grande barrière de corail Par William Pagnon Jury : Jean-Baptiste Renard (parrain) Mr Durouchoux (président) Dr Nicole Bordes (chef de projet) Sigature parrain : Signature chef de projet : Date de soutenance : 23/08/2006 1

2 Table of Contents List of figures / Liste des Figures... 3 Acknowledgements / Remerciements... 5 Résumé... 6 Abstract... 8 Chapter Outline / Survole des Chapitres Stage Environment / Environement du Stage State of the Project at the Start of the Training Course / Etat d Avencement du Projet à l Arrivé du Stagiaire State of Art / Etat de l Art The Great Barrier Reef / La Grande Barrière de Corail The Coral and its Environment / Le Corail et son Environment The Scientific Communities Around the GBR / La Comunitée Scientific Autour de la GBC Method of Monitoring the Coral / Méthode de Surveillance du Corail What is Threatening the Great Barrier Reef? / Qu est-ce qui Menace la GBC? The Sensor Network and its Applications / Réseau de Capteurs et leur Applications The Sensors / les Capteurs Wireless Propagation Theory / Theorie de la Propagation sans Fil Google map API Technical Dimension of the Project / Dimension Technique du Projet Overview / Vue Generale Data used in the project / Données utilisées dans le projet Archived data / données archivées Live Data Capture / Capture de Données Temps Reel Project Architecture / Architecture de projet The Protocol / Le Protocole The Server / Le Serveur The Database / La base de Donées The GUI / L Interface Utilisateur The Console Mode / Le Mode Console Architecture of the Python Programs / Architecture des Programmes Python The Website / Le Site Web Example of Data mining Extraction Through the Presented System / Example d Extraction de données à travers ce System Conclusion of the Technical Part / Conclusion de la Partie Technique Human and Management Dimensions Internal to the Company / Dimension Humaine et Managerial interne à la companie Discussion References Annexes Annexe 1: Glossary Annexe 2: Colour Scale of HotSpot and DHW Annexe 3: Class from SensorNet_GUI.py with there function: Annexe 4: Classes from the other python program: Annexe 5: Package installation Annexe 6: Installation instruction: Annexe 7: website bookmarks used for the project Annexe 8: Example of python program, Class_com.py

3 List of figures Figure 1 : Station météorologique ou bouée sur le récif Davis, AIMS... 7 Figure 2 : weather station or buoy on Davies reef, photo courtesy of AIMS... 9 Figure 3 : internal architecture of the University of Queensland Figure 4 : Internal Human Structure Of The Vislab Laboratory Hierarchy Figure 5 : Architecture of QPSF Figure 6 : Presentation of the area (straight line) cover by the GBRMP [4] Figure 7 : Amount of COTS observed during the Broadscale Manta surveys [5] Figure 8 : Example of COTS specimen feed on coral [7] Figure 9 : Maximum temperature observed in the world after the El Nino phenomenon [9].. 22 Figure 10 : The Degree Heating per weeks observed for the last 90 days for the same period [9] Figure 11 : Maximum temperature observed nowadays [9] Figure 12 : The Degree Heating per weeks observed for the last 90 days nowadays [9] Figure 13 : Effect of degree heating per month over the past and the future on the coral (a) [5] Figure 14 : Effect of natural catastrophe per decade over the past and the future on the coral (b) [5] Figure 15 : Poster representing the different technologies involve in the Security network sensor project of US [12] Figure 16 : Cut of the tunnel view where a sensornet cable in optic fibber is installed [14] Figure 17 : graph of the sensor cable monitoring [14] Figure 18 : Thermocouple with its storage and communication system desired for the SensorNet project [11] Figure 19 : Representation of the method of faking electromagnetic waves for different frequencies from subrefraction (low frequencies) to trapping (high frequencies) [1] Figure 20 : Example of use of Google Map in the website developed during the project Figure 21 : Overview of the data streaming from buoys to final users Figure 22 : Map of the existing monitoring site on the GBR, PNG and West Australia Figure 23 : Weeder electronic board that capture data from thermocouple [17] Figure 24 : Scheme of the stream of the data from the thermocouple to the computer that simulate the buoy Figure 25 : Technical architecture of the SensorNet software project Figure 26 : Protocol of the network dialogue between the buoy and the server Figure 27 : Database scheme Figure 28 : Connexion panel of the GUI interface Figure 29 : Selection panel with the customised or assisted tool and its mouse interactive grid selection Figure 30 : Presentation of an example of graphic generated by the mouse interactive grid selection Figure 31 : 3D graphic selection and map of the GBR with buoys plot on from the latitude and longitude selected Figure 32 : Program architecture of the python programs Figure 33 : Website architecture Figure 34 : First part of the webpage displayed when all the options are selected Figure 35 : Second part of the web site with all the options selected Figure 36 : Full webpage generated for the case study Figure 37 : Graphic generated on the GUI for the case study Figure 38 : Saved picture file of the graph on PNG format for the case study

4 Figure 39 : Example of mathematical operation in SQL from the GUI Figure 40 : Graph from the website of the simulated buoy sensors for live data Figure 41 : graph from the GUI of the simulated buoy sensors for live data Figure 42 : zoom in of the graph from the GUI of the simulated buoy sensors for live data.. 53 Figure 43 : photo of Vislab with the Access Grid node environment with multi conversation and software utility running through 3 power wall projectors Figure 44 : presentation of the website used for archaeological data instead those of the GBR Figure 45 : example of the GUI used for archaeological data instead of those from GBR Figure 46 : XYZ Stage developed as Access Grid physical tool possibility example Figure 47 : Chart of the trend estimate of employed persons in Australia Figure 48 : Chart of the trend unemployment rate in Australia

5 Acknowledgements My deep gratitude for the following people without whom this thesis would not have been possible: - Nicole Bordes for allowing me to work on the SensorNet project - Bernard Pailthorpe for his advice and orientation in the project - David Gwynne for his precious advice in programming - Chris Willing for his advice and his explanation of the project and its structure - Jean Baptiste Renard for his advice during my internship - Jean-Baptiste Bérard for the information provided on the Marine Biology of the coral. - Andreas Vaszolyi for his help in the grammar correction of this thesis 5

6 Résumé La conservation de la biodiversité marine est fondamentale pour maximiser les avantages sociaux et économiques à long terme de la planète. La Grande Barrière de Corail (GBC) est considéré un des environnements les plus riches au monde. Sa conservation est devenue une préoccupation mondiale. Pour mieux comprendre l'évolution de cet environnement unique, un projet à long terme de réseau de capteurs déployé sur la GBC a été élaboré par l'université du Queensland (UQ) de Brisbane, l'université James Cook (JCU) de Townsville et l'institut Australien de la Science Marine (AIMS) sous l union de la fondation du Queensland pour les sciences parallèles (QPSF). Dans ce projet, mon objectif était de fournir une approche et un développement de logiciel qui consistera à rendre disponible à des utilisateurs finals des données venant d un réseau de sondes qui pourront être visualisées et manipulées grâce à plusieurs outils se connectant à une base de données. Ce logiciel servira de structure de base pour développer l'application finale qui sera employée par les scientifiques pour extraire des connaissances à partir de ce réseau de capteur. Ce logiciel donne également une bonne idée des possibilités que peut fournir une telle structure générale pour n'importe quelles données spatiales temporelles rassemblées par l'intermédiaire d'un réseau de capteurs comme par exemple, astronomique ou archéologique. Le but final de ce projet est de développer une surveillance totale de la GBC par le biais d'un réseau de capteurs qui fournira tout type d'informations sur la qualité de l'eau, des températures aussi bien qu'une visualisation constante de la GBC par capteurs CCD. Les sondes seront essayées à l'avenir sur le récif Davies ; où une station météorologique est déjà installée. Le récif Davies est situé dans la GBC à latitude 18 50'S, longitude 'E à environ 70km de Townsville. Précédemment, la communication sans fil basé sur des micro-ondes de 10.5 GHz avait été testée avec succès sur ce même récif. Ce serra certainement cette technologie qui sera employée pour créer un réseau en Ad Hoc entre les bouées et les serveurs. Pour simuler les données récoltées par les bouées, j'ai utilisé une base de données de AIMS qui représente les températures de différentes Stations météorologiques situées sur la GBC et récoltées toutes les 30 minutes depuis 10 ans. Ces données ont été régulièrement récupérées par bateau ou par une liaison haute fréquence de 3.3MHz (qui n'a pas prouvé son efficacité) sur 149 bouées au total 6

7 répandues sur la GBC. Ainsi, dans ce projet, il a été décidé lorsque l implémentation viendra de recevoir les données directement par une liaison sans fil de 10.5 GHz de la bouée à la station terrestre, où les données peuvent circuler par toutes les bouées ou les serveurs (selon le meilleur chemin) pour être finalement stockées dans une base de données. Pour simuler les données en temps réel, une carte électronique, déjà disponible dans le laboratoire, fournira quatre mesures de thermocouples placés derrière différents ventilateurs dans la salle d ordinateurs de Vislab. Au final, l envoie des données a été mis en application avec succès d une bouée à la base de données par l'intermédiaire de logiciel serveur et client. Sur la base de données ont été développés trois utilitaires pour manipuler les données : Une interface graphique qui fournit une table des données choisie par une commande SQL avec un outil de sélection des données via la souris pour produire à souhait des graphiques. Un mode console a été développé pour accéder aux données sans avoir besoin d autre chose qu'un Shell. Finalement, un site Web a été développé pour que toute personne puisse s'informer sur les températures de la GBC durant les 10 dernières années. Ce site Web inclut une carte implémentée via Google Map, des graphiques et une table de Meta information concernant les bouées et leurs capteurs. La prochaine étape de ce projet consistera à employer plusieurs cartes électronique de capteurs afin de simuler plus d'une bouée et ainsi pouvoir simuler un réseau complet avec la gestion temps réel par multi tâche de plusieurs bouées et le routage dynamique des données par ring buffer. Figure 1 : Station météorologique ou bouée sur le récif Davis, AIMS 7

8 Abstract The conservation of marine biodiversity is fundamental to maximizing long-term social and economic prosperity and sustainability. The Great Barrier Reef (GBR) is considered one of the richest environments in the world and its preservation has become a global concern. To better understand the evolution of this unique environment, a long term project involving a sensor network installed on the GBR was conducted by the University of Queensland (UQ), Brisbane, James Cook University (JCU) from Townsville and the Australian Institute of Marine Science (AIMS) under the Queensland Parallel Science Foundation (QPSF). On this project, my objective was to provide an approach of a software implementation to stream the data from the sensors to the final users, who will be able to visualize and manipulate the data with several tools through a database. This software will serve as a basic structure in developing the final application that the scientists will use to extract data from the sensor network. It will also provide an idea of the possibilities of a general structure for any spatio-temporal data collected via a Sensor Network (like astronomical or archeological data). The final aim of this project is to develop a total monitoring of the GBR using a sensor network to provide information about water quality and temperature as well as a constant video visualization of the GBR. The sensors will be tested in the future at Davies Reef, where a weather station is already installed. Davies Reef is located on the GBR at latitude 18 50'S, longitude 'E, about 70km from Townsville. Previous tests of the reef with wireless connection based on microwaves have been successfully conducted and will certainly be the technology used to link the network. To test the computer program, I have used data from AIMS of the last 10 years from a previous project, which was to store the temperature from the buoys every 30 minutes. Those data were regularly collected by boat or by a low DataStream HF radio (that did not prove its efficiency) from 159 buoys spread on the GBR. Thus, in this project, it was decided (for the final implementation) to receive the data directly with a 10.5 GHz wireless network from the buoy on the earth station, where the data can be streamed from all the buoys or the servers to be stored on a database. To simulate live data, a sensor board from Weeder Technology, already available in the lab, will provide four temperature sensor measurements, placed behind 8

9 different fans of computers in the computer room of Vislab. As a result, the stream of data was successfully transferred from a buoy to a database via a software server. Three ways have been developed to manipulate the data. Firstly, a GUI that provides a grid of data selected by an SQL command and where the data displayed are ergonomically selectable to generate the desired graph. Secondly, a console mode has been developed to access data using only a shell. Finally, there is a website providing information about the temperature of the GBR over the past 10 years. This website includes a map navigation tool, Google Map, graphs and tables of meta-information about the buoys and the sensors. The next step in this project will be to use several boards to simulate more than one buoy and deal with them in multithread with different scenarios to obtain a dynamic routing of the data. Figure 2 : weather station or buoy on Davies reef, photo courtesy of AIMS 9

10 Chapter Outline Stage Environment: Here I will present the different organisations involved in this project and the links between them as well as the internal human architecture of the Vislab laboratory and its field of activity. State of the Project at the Start of the Training Course: I will present studies done before the start of the training course and the objectives from this project attributed to JCU and myself for UQ. State of Art: In this section I will approach the different aspects of the GBR and the SensorNet project. Firstly I will provide information about the GBR as such, before dealing with the coral and its environment. I will then describe the different organisations undertaking research on the GBR in Australia and around the World, before explaining the method of monitoring the coral with examples gathered through diving, boat and satellite observation of the coral. Specifically, I will describe the threat to the coral on the GBR. Next, I will turn to some examples of sensor network applications already in use, before explaining the constraints upon building sensors. The wireless propagation theory experimented last year on the GBR which will certainly be used to stream the data will be explained. Finally, I will finish this part with a brief presentation of the Google Map tool used for the website. Technical View of the Project: This is the technical part of the report where the application developed during this training course will be presented. An overview of the project will be followed by a description of the data used to validate the software and a description of the project architecture. I will then elaborate the various parts of the project by describing the protocol, the server, the database, the GUI, the console mode and the website. I will finish this part by giving a case study that will lead us to the main function of the applications and a conclusion for the technical part. 10

11 Human and Management Dimensions Internal to the Company: I will explain the environment in which I worked, and the relation I had with the staff of the laboratory and JCU the partner of the project. Discussion: Here I will explore possible improvements to the project, and a side project involving an XYZ stage. Then the different aspect concerning my ESIEA formation and the place of the communication in our societies will be discussed. I will finish by briefly describing my eighteen months in Australia. 11

12 Stage Environment The training course was conducted at the University of Queensland (UQ) in the Vislab Laboratory located in the Information Technology and Electrical Engineering (ITEE) building. This laboratory is part of the School of Physical Science (SPS) which is itself a part of the Faculty of Engineering, Physical Sciences and Architecture (EPSA). EPSA is one of seven faculties at UQ. UQ was founded in 1910 and is one of the top eight universities in Australia [22]. It is also well recognized at an international level for its strengths in teaching and research. The following tree shows the position of Vislab in the university s structure. Figure 3 : internal architecture of the University of Queensland Vislab is a University research and development laboratory created in 2003 by Bernard Pailthorpe, Nicole Bordes and Chris Willing. This research centre specialises in data analysis, computational and experimental science as well as grid and data computing. They constantly engage in projects at the cutting edge of technology like e-archaeology, Kepler workflows, molecular modelling or high resolution displays. These are just few examples of this laboratory s work. Some of these projects are done by the staff of the laboratory but most of them are the main projects of graduate or undergraduate students (in an internship position like me or as thesis student from the University). 12

13 Another Vislab Laboratory was created previously at the University of Sydney in 1992 by Bernard Pailthorpe. This laboratory is still active at the University of Sydney. See below the laboratory s hierarchy, with status are from lowest to highest. Professor Bernard Pailthorpe and Nicole Bordes established the laboratory, with Chris Willing, who manages the lab. Doug Kosovic manages the informatics maintenance service of the lab. David Gwynne is the data specialist of the team and it is with him that I began to conceive and develop the project. Terry Simmich arrived two months before the end of my training course, his main task is to coordinate and develop tools for archaeological research. Two new people are expected to manage their main project Access Grid, a multi application management tool for videoconferencing. The staff contracts are generally for one year renewable. My position is as an occupational trainee responsible for the SensorNet project. Several students who are doing occupational training or doing their thesis for UQ work on small research and development projects. Figure 4 : Internal Human Structure Of The Vislab Laboratory Hierarchy The SensorNet project was proposed by QPSF. QPSF is an incorporated body established in October 2000, consisting of seven Queensland public universities. The organisation was funded by the Department of State Development, Trade and Innovation of the Queensland Government. This foundation has several projects in which some or all the universities work together. To increase the possibilities of this foundation the universities have made a strong investment in High Performance Computing Infrastructure (HPCI) since its inception in

14 QPSF's major HPC facilities are housed at, and maintained by UQ however each university also houses HPC facilities. Those facilities allow the QPSF members to share resources for work on data projects such as the SensorNet project. They also use the Access Grid (multi application management tool for videoconferencing) to communicate and share applications in real time. See below the architecture of this foundation. Figure 5 : Architecture of QPSF 14

15 State of the Project at the Start of the Training Course The main project I worked on during this training course was SensorNet. The aim of this project was to develop, in collaboration with JCU, a sensor network system deployed in buoys around all the GBR to monitor different parameters like temperature, chemical properties of the water. In the future a camera will capture pictures of the ecosystem of the GBR. The project was created three years ago but the technical approach was developed only last year. When I am arrived, a thesis made the previous year by Jared Sanderson called Data Capture and the Management of Data Streaming from a Network of Sensors [17] helped me by providing a temperature database recording by AIMS. This project dealt with the sharing and the storage of a large archival collection of data across a connected grid of computers. This was achieved using the Storage Resources Broker (SBR) system to spread the data potentially to several databases on a networked grid of computers. The development of a new wireless communication using wave propagation through the upper layer of the sea level was successfully tested by Stuart Kininmonth, et al, in 2005 [1]. Some coding to experiment on the sensor boards was done in Python to capture data and display it in a graph on a web page. Those tests were done by Chris Willing and David Gwynne. During this training course, I was responsible for the aspects of the project involving the software development, under the guidance of David Gwynne. We used the videoconference system Access Grid (originally developed by Argonne National Laboratory [21]) to communicate with JCU which is currently working on their own hardware and software implementation. JCU was initially only in charge of the hardware implementation for the buoys and the different relays with an ad-hoc network which sends the data stream to the database (as will be described later in this thesis). Their aim is to find a hardware solution capable of resisting the extreme conditions to which the buoys and the relay are exposed on the GBR. For instance, the microprocessor and associated electronics must be resistant to temperatures greater than 50 C because they are fully exposed to the elements. The buoys must utilise solar and wind power to ensure extended autonomy, providing a use-time for the buoys. Other concerns about the sensors include diverse aggression (such as shark attack) and other factors which 15

16 can compromise the result or destroy the sensors; e.g. organic deposits like algae on the sensors. The communication system between the buoys and the final server involves ad-hoc wireless at a frequency of 10.5GHz that will use the surface layer of the sea to guide the signal to the relay server or the final server. This specific wireless communication was developed in 2005 (as mentioned before) and will be explained in the State of Art section. My laboratory directed the system s software implementation, from buoys to user. As the hardware was not already chosen, we developed a software solution as generic as possible to allow implementation in a wide range of embedded systems ranging from the simplest processor to the most sophisticated. In order to develop and test our solution we used an external electronic board sensor from Weeder Technology [2]. This board provides the values of four temperature probes to a computer by a serial connection. We will see further the criteria of this board in detail. The programs of the buoy, the server, the GUI and the console mode have been developed in Python to maintain compatibility with the rest of the system if necessary. Driver in C language, for the Weeder board, has been developed to provide the possibility to create a C program for the system in the buoys and in the relay or server. The software in C language for the buoy and server is currently being developed by David Gwynne and will be available in the future. This version will decrease the size of the code and the processing time to increase the routing time. These conditions are necessary in order to implement the program in a low consumption system in terms of memory, electricity and processing. We use a PostgreSQL database system to store the data where indexation and primary key have been used to increase its efficiency. The GUI interface and the console mode will be used by the final scientific user to manipulate the data in the Database. Finally, the website is tailored for a wide range of users, utilising PHP for the web server and JavaScript for the client using Google Map to provide interactive information. 16

17 State of Art The Great Barrier Reef: The GBR World Heritage Area is located three quarters of the way to the northern tip of Queensland on the East cost of Australia, ranging from the south of the Tropic of Capricorn to the coastal waters of Papua New Guinea. This area cover about 2300 km and lies between N S and E [3]. The GBR is the largest World Heritage area with its 33,126,500 ha of Marine Park and the most extensive coral reef in the world. It was declared World Heritage in The GBR comprises some 2,800 individual reefs including 750 fringing reefs, which range in size from under 1ha to over 1,000 ha [3]. The GBR is only two million years old and evolved during the quaternary period when ice formed and melted in higher latitudes causing major sea level fluctuations. The shape of each reef is quite different and is classified into three categories: the Barrier Reef (or Wall Reef), most northerly of the GBR; the Platform Reefs, which comprise the majority of the reefs (ovular shaped and found between seaward side of the continental shelf and the mainland); and the Fringing reefs, found growing out from the shores of continental islands and the mainland. At its conclusion, this project will provide precious information on the complexity of the water circulation and quality in those areas, which has created a complex ecosystem. The properties of the Coral Sea, land run-off, evaporation, southeast trade winds, forced upwellings due to strong tidal currents in narrow reef passages, and coastal water including mangroves, are all affecting the water circulation and thus the coral stability. The impact of people on water quality is also not well known. These complex parameters must be monitored and compared in order to understand their influence on such a fragile ecosystem. The map below presents the GBR Marine Park area described here. 17

18 Figure 6 : Presentation of the area (straight line) cover by the GBRMP [4] The Coral and its Environment: The Coral reefs flourish, apart from rare exceptions, mainly in the tropical latitudes 30 north or south of the equator. In the ecosystem of the GBR, there are approximately 356 reef building corals belonging to about 60 genera. They represent almost 75% of the known genera in the entire Indo-Pacific region [3]. Only the southernmost of reefs show a significant reduction in the number of species. Although many of the populations probably receive recruits only from neighbouring ones, they are part of a vast interconnected network in which larvae drifting from reef to reef and island to island ensure that populations are not isolated. Coral cover decreases and increases quite dramatically because of cyclones, Crown of Thorns Starfish (COTS), and coral bleaching, but there are no long-term declines in coral cover or diversity. Even on inshore Fringing reefs, where human impacts are highest, there are no indications of any general decline since the El Niño event in 1998 [5]. The GBR contains over 300 species of coral, creating an environment for more than 1,500 species of fish, 4,000 species of molluscs plus a great diversity of sponges, anemones, marine 18

19 worms, crustaceans, algae and finally a wide range of marine mammals [5]. Coral live in symbiosis with fish providing them a nutritious and protective environment. COTS is a parasite that feeds on the coral and can be damaging for the reef if in overpopulation. Coral also maintains a special symbiotic relationship with a microscopic organism (algae), especially zooxanthallae [6].These organisms provide their hosts with oxygen and a portion of the organic compounds they produce through photosynthesis. When stressed, many reef inhabitants have been observed expelling their zooxanthallae in large amounts. Coral is an important component of our ecosystem and must be preserved at all costs to keep the equilibrium the coral reef provides. In addition the ocean provides oxygen thanks to this ecosystem of coral and other different animals, and vegetal that affects life from the ocean to the earth. The Scientific Communities Around the GBR : Scientific research on the GBR started with the GBR Committee (now called the Australia Coral Reef Society) in 1922 and the British GBR Expedition in Nowadays, for local and visiting overseas scientists, field stations are operated by UQ at Heron Island, The University of Sydney at One Tree Island, the Australian Museum at Lizard Island, JCU at Orpheus Island and AIMS in Townsville [3]. The latter two have extensive coral reef research programs that cover the full ambit of science disciplines. Increasingly, these communities have lobbied the industries and the stakeholders around the Queensland coast to sponsor the monitoring and educational project on the GBR. The Australian Government has also developed Reef Check training to accredit volunteer teams on the preservation of the GBR [5]. Most of the financial support for this operation is provided from the dive tourism industry and other commercial businesses around the GBR. Globally, the International Coral Reef Initiative (ICRI) established in 1994 and the Global Coral Reef Monitoring Network (GCRMN, founded in 1996) plays an important role in the preservation of coral in the international domain. Their objectives are to link existing organisations and people to monitor ecological and social, cultural and economic aspects of coral reefs within interacting regional networks. A significant example of their action is the rezoning of the GBR World Heritage Area where 33% of the total area has since 2004 become protected from extractive industries such as fishing and collecting [5]. 19

20 Method of Monitoring the Coral: Monitoring the coral is a challenge that will lead us to a better understanding of the complexity of the ocean system by realising the importance of the coral in this area. This kind of study leads to more precise climatic model as well as a better evaluation of the human impact on the Earth and the natural evolution of the coral. The GBR is one of the most monitored coral sites in the world but nonetheless, information gathering covers only about 5% of it (some 2,800 reefs) [5]. I will now present various examples of monitoring systems in order to demonstrate the spectrum covered by this field of studies. The AIMS long-term monitoring program is designed to provide information about key groups of organisms on appropriate spatial scales. Broadscale Manta Tow surveys [19 and 23] have now been carried out through 11 latitudinal sectors over 21 years ( ) and played a significant role in the understanding of the interaction of the coral with its environment, especially for the COTS phenomenon [5] which is a good indicator of the state of a reef. Each year, the perimeters of 100 reefs are monitored. To make this survey, a diver is towed by a small boat around each reef where it stops every 2 minutes to allow the diver to count the number of COTS. The density of COTS at which coral damage is likely corresponds to 0.22 COTS per two-minute tow and if this rate is greater than 1, the reef is definitely damaged. An interesting result of this study shows that some reefs have been unaffected by COTS since the beginning of the monitoring program in 1985 which is the start of the study [5]. Figure 7 : Amount of COTS observed during the Broadscale Manta surveys [5] 20

21 You can observe in the preceding charts the mean coverage of hard coral by this study over the years. Each chart represents a part of the GBR coverage from a. to d. that splits the GBR in four parts respectively from north to south. The right vertical scale represents the average of COTS observed per tow. Below is an example of COTS feeding on a coral reef. The COTS can also feed on different encrusting organisms when coral is scarce, such as algae, gorgonians and even other COTS. Figure 8 : Example of COTS specimen feed on coral [7] AIMS also has two vessels which conducted 50 research trips between them in and operated for an average of 257 days. Their laboratories enable research such as DNA analysis, cell culture, microbiology, chemical isolation and fermentation etc... [8] The shortcomings of this kind of monitoring rest with the use of a boat to collect samples from the GBR and the evident problem of regularity when the sample is not taken for climatic or human reasons. Nevertheless, it is still useful to study the different organisms that populate the GBR. In the future, the SensorNet project will certainly turn to sensors incorporating a micro chemical lab that will regularly test certain properties of micro organisms. Coral reefs are predominantly monitored by satellite, which provides a precise picture of the extent of coral bleaching and can detect anomalies with special filters. It also monitors the temperature of the ocean with infrared radiometers installed on the satellite. One of those projects developed by NOAA Satellite and Information Service, called HotSpot provides twice weekly a map of the state of coral bleaching around the world [9]. 21

22 Figure 9 : Maximum temperature observed in the world after the El Nino phenomenon [9] Figure 10 : The Degree Heating per weeks observed for the last 90 days for the same period [9] Figure 11 : Maximum temperature observed nowadays [9] 22

23 Figure 12 : The Degree Heating per weeks observed for the last 90 days nowadays [9] NOAA operates two polar-orbiting satellites, each with an infrared sensor that detects the temperature of the ocean s surface. Because the satellites constantly orbit the earth, they measure the water temperature around the entire globe each day [9]. The maps displayed here present respectively for the period of El Niño in 1998 and nowadays in June 2006, the state of the seas temperatures around the world compared to their normal average and the accumulation of overheating during the last 12 weeks (The colour scales are explained in Annex 2). If the monthly average temperature is increase more than one degree and if the Degree Heating per Weeks (DHW) is greater than four, the coral starts to show stress due to the rise in temperature. During El Niño [24], high levels of stress everywhere in the world coincide with high temperatures, particularly in the GBR where temperature increased by an average of 2.5 degrees along the whole GBR for DHW indices of 16 at certain areas, which is the maximum on the scale. Currently, the state of the GBR and the coral around the world in general is not affected by this stress of temperature with no increase of temperature (less than four degrees on the scale of accumulation of over heating). Nevertheless it s periodically increase and the coral healthiness can become dramatic (at short term) in the next 50 years. The data of those studies and more have been stored in a database of AIMS. To develop interest in the GBR, the Conservation and Biodiversity Group launched (in ) a new research tool called Coral Id [10] to improve understanding of the migration of coral by the current or by fish population for professionals as well as for amateurs. The user can thus 23

24 interrogate a large database by describing the characteristics of the species and understand its evolution from data already captured over the years. What is Threatening the Great Barrier Reef? The major threat to coral is bleaching. This phenomenon can be described as a decline of the pigmentation of the polyps of the coral, which makes them appear nearly transparent, with its white skeleton. The presence of Zooxanthallae (explained above) is very important to its survival during and after a bleaching event. The major stresses that cause bleaching are natural; Cyclones and big storms cause major damage to the reefs with the increase of temperature involved in causing extensive bleaching of both hard and soft corals (as observed in 1998 with the El Niño phenomenon )[5]. The effect of the climate change also has a real impact on the coral even if we are not yet able to understand it well enough. The human pressures on this environment is not yet well know, but the change of the water quality of terrestrial run-off is one of the significant human impacts (sediment and nutrient input to the reef from terrestrial discharge has increased fourfold in the last 150 years) [5]. The other major issue identified is the effect of fishing in the Marine Park. This has caused the population of dugongs to decrease by 50% over the past eight years [5], for instance, while various turtle populations are still considered to be under threat. 24

25 Figure 13 : Effect of degree heating per month over the past and the future on the coral (a) [5] Figure 14 : Effect of natural catastrophe per decade over the past and the future on the coral (b) [5] According to the Status of Coral Reefs of the World [5] the state of the GBR was stable between 2001 and However there was a algal bloom (Chrysocystis fragilis) at many sites in the Cairns and Townsville regions in 2004 perhaps due to the over activity of tourism in those regions as agriculture. The first chart above shows the degree of heating per month observed since 1850 to its forecast in Mass bleaching events occur when the DHM is over one degree (at 4 degrees most of the coral will not recover from this bleaching). Forecasts including a global warming scenario due to the greenhouse effect predict that coral reefs will be at risk as shown in Figure 14. Extinction of the coral might happen around 2050 with more than 9 events per decade if those forecasts are correct. This does not leave much time to better understand how the coral evolves and its role in our environment. The Sensor Network and its Applications: A sensor network consists of a number of sensors spatially distributed across an area. Sensors can be used to monitor or detect events at a location, for instance, temperature changes or motion detection. Each sensor should be small and inexpensive using little energy to operate and transmit a stream of data over a wireless network. 25

26 Wireless sensor networks cause many dilemmas for practical implementation. In this project, the deployment of sensors in a marine environment caused additional problems: Saltwater is corrosive and tropical waters encourage the growth of biological life on the surfaces of sensors (P. Ridd and M. Heron [11] will develop experimental sensors for this project and will test it on the GBR to overcome those problems). The sensor net concept has expanded to find many different applications. For instance, several companies have been endeavouring to provide the industry with better monitoring of machines especially for temperature and material strain. Several applications are found across diverse fields: health care, manufacturing, environmental protection, transport, agriculture and every field of research science. Another important field involves security monitoring by spreading millions of micro-sensors on a special painting to fix it on the wall or spread from the sky to detect the chemical presence of dangerous products like explosives. A security sensor network is currently being tested in Tennessee (USA) as new protection against terrorism [12]. As with every source of information, there is the possibility of authorities monitoring people against their will with total discretion. Ultimately they will be able to monitor a whole country (as shown below). The new generation of tiny microchips are increasingly accessible along with nanotechnologies developed to give new perspectives in information acquisition. The network sensor provides such an important source of information that it must be used in a particularly ethical and reasonable way, like the GBR observation project. Figure 15 : Poster representing the different technologies involve in the Security network sensor project of US [12] 26

27 Many businesses are developed around monitoring technology, like the company FollowUs, which provides tracking of a family member or employee from its mobile phone [13]. So sensor networks must be used as all science with many precautions to avoid restrictions of liberty. Another example of the project is the lake tunnel built in China, where a sensor network was installed in 2005 to monitor temperature by linking all the sensors with optic fibre along the tunnel [14]. Figure 16 : Cut of the tunnel view where a sensornet cable in optic fibber is installed [14] Figure 17 : graph of the sensor cable monitoring [14] In the United States at least, the export of underlying technology (Sensor Network) is controlled and has to be declared to the Department of Commerce or the Department of State [12]. Currently, there is no norm in the sensor network because of compromises, but with more development will emerge new standards. As described above, the sensor network technology is already developing new markets with huge applications. According to Commsdesign [15]: The total market will rise to at least 50 million units, or $1 billion, per year by These examples are just a little sample of the numerous projects already running or in preparation in the world. The Sensors Constructing these micro sensors for a governmental security project has required 200 scientists from various fields: Electrical, mechanical, chemical engineers; physicists, material scientists; chemists; photonics designers; and meteorologists. They construct measurement systems using ultrasonic, no contact temperature, optics, electro-optics, radiofrequency, microwaves, microelectromachanical systems (MEMS), nanoelectromechanical, microfluidics (lab on a chip) and wireless technologies [12]. 27

28 In our application, AIMS are devising and implementing the type of sensor for the GBR [11]. Those sensors will integrate the wireless communication system as well as capture and store the data. Figure 18 shows a schematic of the sensor. The sensor will hold several temperature probes at different depths which will capture the data and send them to an A/D converter before being processed by the system, which will store them in a buffer and a text file. The data will be sent by an b wireless to the nearest server or sensor by an aerial antenna. For this purpose, a modem is also installed to communicate with the other sensors or the server. They will also include a compact Flash GPS to give their position and a serial or USB connection to download and upload data onsite. The power supply under consideration is a coupling of sun and wind power to stay operational without a heavy battering of the sensor by day or night. A pure copper housing prevents the sensors from degradation in this environment hostile to electronics, especially due to salty water. The sensors could be cleaned every six months to avoid the deposit of organic systems like algae, which will falsify the measurements. Despite this, the individual sensors are not expensive, the real efficiency of a such sensor network can only be reached by spreading a large amount of them along the GBR, considerably increasing the cost. The cost may be reduced, however, by mass producing sensors. Those sensors will not need miniaturisation as in the American project, despite that they have to fit on the existing weather stations. 28

29 Figure 18 : Thermocouple with its storage and communication system desired for the SensorNet project [11] AIMS wants to develop sensors for monitoring all the aspects of the environment including chemicals, water current pressure, fauna and flora, as well as spread of the coral. Ultimately, AIMS plans to use video cameras, in addition to sensors, that can scan the evolution of an environment of two cubic meters per camera. 29

30 Wireless Propagation Theory: Initially, AIMS communicated with their weather stations using a 3.3 MHz HF Radio spread along the GBR for the nearest reefs and a mobile phone network for distant stations [1]. The HF propagation relied on ground wave diffractions and was thus unreliable for horizontal propagation in the ocean. The previous system stored data up to 21 days in text files until the communication was established or downloaded on site. However, low maximum data as well as a non stable connection can lead to lost data during long term weather perturbations. A new approach based on microwave propagation has lead to interesting results. The principle applied here is to use the evaporation duct just above the ocean to provide a suitable means to guide signals well beyond the optical horizon [1]. The frequency providing the best effectiveness in term of distance of transmitting, path loss and size of antenna is 10.5 GHz. This band of frequency is licensed free in Australia. The noise ratio with conventional radio equipment is estimated 40db and the height of antennas should be between 3 to 4 meters to minimize the path loss [1]. However if the path loss is increased by an additional 20dB the communication will fail. The system shows that communication will work most of the time but cannot be expected to be 100% reliable. Figure 19 shows how the electromagnetic waves are propagated by refraction depending on their frequency. With the microwave concept, the wave is trapped in this evaporation duct layer at the surface of the ocean and thus bonds to the ocean surface following the curve of the earth as, for instance, the Ionosphere is used as a reflector channel for electromagnetic waves. Figure 19 : Representation of the method of faking electromagnetic waves for different frequencies from subrefraction (low frequencies) to trapping (high frequencies) [1] 30

31 Ultimately, the aim is to create an ad hoc network where the sensors will be able to transmit data directly to the main server, or if communication is impossible, on behalf other sensors. This wireless system was tested at Davies Reef in December 2004 by S. Kinninmonth and I. Atkinson [1]. For a traveling distance of approximately 70 Km, the signal to noise ratio was >20dB most of the time and up to 25 db. 34 Mbps transmissions were achieved with Code Division Multiple Access (CDMA). This wireless system will be, in the future, used with the software applications presented in this report. A ring buffer [25] will probably be added to the system, as well as an SRB sharing system data to make a database transparent to the user whatever where the data have been stored by finding the best path to reach the database and prevent loss of data. Google map API The Google Maps API was created by Google to facilitate developers integrating Google Maps into their web sites, with their own data points. It is a free service that currently does not contain ads, but Google states in their terms of use [16] that they reserve the right to display ads in the future. By using the Google Maps API you can embed the full Google Maps on an external web site. The identification to access to the client Google Map is an API Key that is bound to the web site and directory you enter when creating the key. Creating your own map interface involves adding the Google JavaScript code to your page, and then using JavaScript functions to add points to the map. Some plug-in libraries are also available to display labels, for instance the Tlabel plug-in, which is used in the project. We will use Google Maps as an interactive map to enable the use of satellites, road or hybrid maps to locate precisely a particular place in the world. You can add to this tool an icon and label interactive click to make a website visually interesting. For a project like the GBR it was particularly helpful to be able to locate the buoys with the precision of a satellite photo providing visual information on the shape of the reef and, of course, its location. This map is particularly important because SensorNet is a map that itself evaluates in real time by following changes in measurements of the environment to provide an accurate and up-to-date map revealing the evolution of this natural and complex system. 31

32 Figure 20 : Example of use of Google Map in the website developed during the project. 32

33 Technical Dimension of the Project Overview As described above, SensorNet is a project that aims to provide the infrastructure for monitoring the GBR. It will be used to capture environmental data at numerous locations and to create a map in real time of the parameters which can affect the fragile environment of the coral reef. Buoys that will ultimately contain a variety of sensors and a GPS will be spread along the GBR. Possible uses for the sensors include monitoring changes in temperature, salinity, carbon dioxide and calcium levels, light intensity, and the presence of pollutants. Cameras may also be deployed to allow real time observations of the reef environment by researchers. Due to the distances involved and constraints on the equipment used in the sensors it will be necessary to route by wireless the information produced by the sensors, which is destined for storage, via intermediate servers. The device ultimately storing the sensors data will store it directly in a database for use by researchers. The user will then access the data via another server which will manage the access right to the database from a GUI, a console mode and a website. Below is a schematic description of what the whole system is supposed to be. Figure 21 : Overview of the data streaming from buoys to final users 33

34 Data Used in the Project The usefulness of the data depends on the accuracy and precision of the collection process in the field as well as effective archiving and reporting. Archived Data In 2005 Jared Sanderson [17] collected data from AIMS. Those data cover the past ten years of temperature data recorded by 149 buoys spread along the GBR by AIMS. Originally, those data were stored in a Microsoft Access database with more than 1.5 million entries. Stuart Kininmonth from AIMS provided the data for Jared Sanderson s project. He transferred them to a PostgreSQL database in order to remove the limitations that Microsoft Access database has with concurrency issues and its inability to operate within a Linux environment. I have transferred those data from his PostgreSQL Scheme to my PostgreSQL scheme (available in the Database section). The next map shows the current monitoring site on the GBR. There are in total 149 weather stations spread over various important reefs. Figure 22 : Map of the existing monitoring site on the GBR, PNG and West Australia 34

35 Live Data Capture Several thermocouples were wired to a Thermocouple Input Module created and manufactured by Weeder Technologies [18]. The thermocouples were placed behind the fans of several computers to measure fluctuations in temperature, and connected to the Weeder module. This input module was connected to a Linux machine (known as the client or buoy) via an RS-232 serial port. The module converts the data from analogue to digital. Software running on the server machine applied trivial manipulation by averaging the sampled data for each thermocouple and logging the results for the set period. Figure 23 and 24 present respectively the Weeder board and how temperature data are collected as described above. Figure 23 : Weeder electronic board that capture data from thermocouple [17] Figure 24 : Scheme of the stream of the data from the thermocouple to the computer that simulate the buoy Project Architecture The architecture of the project describes how the data are streamed and integrated from the buoy and integrated into the database. This description will be aided by the schematics on the next page. We will consider one element of the whole network from the sensor to the database as an example, but the principle is applicable for the whole system. On the Node (buoy), the data from four sensors (in our experimental case) are collected periodically at certain intervals of time. Each measurement is stored with the ID of the relevant probe, the state of the probe (to give a degree of reliability of the measurement), the time when the measurement was taken, and finally its value. Every data also has the ID of the sensor to which it belongs. All the sensors are identified by their ID, type, name, location in 35

36 three dimensions, and serial number. On the upper layer of the node is the embedded PC which interrogates the sensors and stores the measurements it receives in return with all the labels described above. The embedded PC is identified by an ID that refers to a particular node, an English name, an IP address, a location and a session ID which will serve to keep track of the stream of data. Following identification to the server relay (see the protocol following), the node sends (at each nominated discretion of time) the data stored and erases the data sent once it has acknowledgement of reception from the server relay. The data are stored in the server relay and sent to the main server on the earth s surface. This server treats the raw data to make it understandable to humans, stores and sends them to the database. Once the data are stored in the database the server erases them. The Database is accessible from the web, a specific GUI interface or a command line console. 36

37 !! Figure 25 : Technical architecture of the SensorNet software project. 37

38 The Protocol The protocol has two parts: the Node (the device with sensors on the reef) and the Server (the software that turns sensor data into something that can be stored in the DataBase). The protocol uses TCP/IP, and can use a standard IP network to communicate. The Server can be considered a normal network daemon since it will sit listening sockets waiting for connections from the Nodes. The Node opens a session with the server by connecting and immediately sending a hello message. The only content of the hello packet is a session ID. The node s IP address and its session ID uniquely identify the set of readings that it will be sending to the Server. Upon receiving the session ID the server will check if there is a session number already registered for the IP address of the client. If so, the server sends a Resume message that identifies the last reading successfully received by the server. If the session ID is unknown to the server it will send a Start message to the Node. When a Node receives a Start message from the Server it is required to send information about its configuration to the Server. This information is described by the Host and Sensor packets. The Host packet contains the Host s name and the number of sensors the node has. For each sensor a sensor message is sent describing its ID, type, description (what they are measuring) and serial number (to find, if necessary, information on the product). After a Resume, or after the required Host and Sensor messages are sent, the Node may send all the readings it has collected that the Server has not yet received. The readings message contains the sensor ID from which this measurement was taken, an ID for this reading, a status for the reading, the time the measurement was taken, the location at which it was taken, and the value of the reading itself. 38

39 " # $ # % #! # & ' & ((( Figure 26 : Protocol of the network dialogue between the buoy and the server At any point after the Resume or Host/Sensor messages the Server may send messages that update the operation of the Node. For example, the Server may require more frequent measurements. To achieve this it would send an update message with the necessary information. If the TCP connection is interrupted, the Node will continue to take measurements and cache them in memory as long as possible. Upon reconnection it will relay these readings to the Server from the last reading that the server received. 39

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