Last year, the U.S. Army Yuma Proving Ground (YPG) faced a short suspense requirement to instrument an Apache's Ethernet bus. YPG was able to implement an effective method to satisfy this requirement; however, more capable and effective methodologies could not be developed and utilized due to time constraints. While continuing to support ongoing Apache testing, YPG is working to implement more efficient methods to capture and utilize the Ethernet data. This paper will discuss YPG’s initial implementation and the follow-on efforts being pursued.

Magíster en Ciencias, Mención Computación / Ingeniero Civil en Computación / La proliferación de sistemas con múltiples núcleos de procesamiento ha transformado la aplicación de técnicas de programación paralela en uno de los tópicos más estudiados en los últimos años, ello en pos de mejorar los rendimientos generales de cualquier operación. Una aplicación práctica de dicho enfoque es en el procesamiento de requerimientos DNS, los cuales han evidenciado un gran aumento de la mano del desarrollo de la Internet y la masificación de distintos tipos de dispositivos que demandan conectividad, y que por sus características son un buen candidato a un enfoque de procesamiento paralelo. Sin embargo, distintas investigaciones han revelado que la aplicación de técnicas multithreading per se no son una estrategia que garantice un escalamiento en los resultados. Distintas empresas de carácter global (como Google, Facebook y Toshiba) así como investigaciones locales (de la mano de NIC Chile) han reconocido la existencia de este problema, reiterando responsabilidades a los Internet Sockets provistos por el kernel de Linux, los cuales al ser expuestos a un consumo concurrente degradan su capacidad de consumo de datos y rendimiento general, aún cuando existe poder de cómputo excedente. Así estas empresas y otros trabajos de investigación han planteado varias hipótesis teóricamente razonables para explicar dicho comportamiento pero sin concretar las mismas en términos experimentales que permitan confirmarlas o desmentirlas. La presente investigación plantea un estudio experimental del caso de los Sockets UDP que combina técnicas de profiling y testing de distinto nivel, a fin de verificar las principales sospechas vigentes que den explicación al problema en cuestión, reunidas en 3 líneas de trabajo: Problemas de distribución de carga, degradación del rendimiento por mecanismos de bloqueo y problemas de manejo de caché y defectos de contención de recursos. En la misma línea, se ilustra el impacto de fenómeno de contención de recursos en un escenario concurrente y su repercusión en los canales de comunicación en el procesamiento de datos en arquitecturas modernas multiprocesador como la estudiada. Es fruto de este trabajo un veredicto por cada estudio que concluya explicando las características inherentes a los Internet Sockets que expliquen su mal desempeño, bajo los distintos análisis efectuados. Posteriormente, la investigación se traslada a estudiar la técnica denominada reuseport, un desarrollo de ingenieros de Google que plantea una solución al problema presentado y que promete mitigar el efecto negativo causado por el uso de multithreading en el contexto estudiado. Así también, se repasan aspectos como el rendimiento de este enfoque, y ciertas debilidades del mismo. Finalmente, es producto del presente trabajo el planteamiento e implementación de una solución propia al problema que, inspirado en el diseño de reuseport e implementado como un módulo del kernel, provee un mecanismo de distribución de paquetes que permite optar a mejoras de desempeño en el procesamiento de los mismos usando técnicas de procesamiento paralelo clásicas. Una solución que --en su configuración estándar-- provee un rendimiento competitivo a reuseport, pero que gracias a ser ampliamente configurable permite postular a mejores resultados que reuseport en contextos no uniformes de distribución de paquetes.

This thesis deals with the design of three labs in the simulation environment OPNET IT Guru. The first lab demonstrates the differences between the RM OSI transport layer protocols - TCP and UDP. The second lab discusses the role of ICMP protocol and its most famous feature - PING. The third lab is devoted to Application Characterization Environment (ACE) module, which is included in OPNET IT Guru. Theoretical background is provided for all of the mentioned topics. All designed labs can be used to teach at the Faculty of Electrical Engineering and Communication of BUT on subjects dealing with network technologies.

The semestral thesis describes ECG signal compression methods designed to modify the data for transmission via communication channels. The thesis contains an introduction to Ethernet and explanation of communication in the network. The transport protocols TCP and UDP are discussed in more detail. In the practical part of the thesis was created two separate applications. The first application in the sender's computer opens a text file with the ECG signal. Loaded ECG signal is filtered by cascade of filters to eliminate interference. The resulting signal is displayed. A part of the application is the R wave detection, calculating the length of RR interval and heart rate. The application also allows to compress an ECG signal. ECG signal is sent via Ethernet network via UDP protocol for individual samples. Applications in the recipient's computer receives signal samples from the network. Recieved compressed data is reconstructed. The resulting ECG signal is displayed and there are again detected R waves, the length of RR intervals and sampling frequency are calculated.

V této práci jsou zkoumaní základní principy odporů servisních útoků, nejběžnějších typů a účelu použití. Popsané dostupné techniky zmírnění různých typu útoků, nástrojů a přístupů v operačních systémech postavených na Linuxu. Nakonfigurován filtrcni server a pro účely testování simulovan SYN Flood, UDP Flood a ICMP Flood útoky. Bylo zjištěno, vhodne techniky vyrovnání tehto druhu útoku a realizováné příslušna konfigurace filtrování.

This thesis describes the project “A new Web Server for sensors”. The project has created a demonstration web service that can receive data from sensors ( both fixed sensors and movable sensors) and distribute the received information in the form of web pages. These web pages can provide forms that enable the user to enter commands which are to be given to sensors. The aim of this thesis project was to design and evaluate web-based application which could utilize sensor data. In this project, we focused on two aspects: (1) web access to sensors and (2) the potentialmobility of sensors. The web server provides web server mediated access to the sensors. Additionally, this project examined how to integrate a sensor with a mobile device, such as a personal data appliance. The web server provides an easy acces smechanism to users who want to use and control sensors. Those users can flexibly us etheir web browser to access to sensors through our web server. Moreover, a sensor could move, for example because it is integrated with a personal data appliance. The mobility of sensors increases the sensing scope of sensors because the sensors are notfixed in position. Such sensors can sense the environment along the path that they are moved. To achieve the goals of this thesis project, we analyzed what are the basic parts and functions that should exist for sensors in the web server. Furthermore, the thesis analyzed how a sensor can be integrated with a personal data appliance, for instance,how to supply the power to sensor; and how to synchronize data between the sensor and personal data appliance. As a result of this project, a web server with some of the necessary functions was developed. An approach of how to integrate a sensor with a personal data appliance is specified in this thesis. The thesis begins with an analysis of some existing solutions. Their advantages were used to specify the requirements for our own solution. The thesis describes the design and implementation of this proposed solution. Next the thesis describes the testing and evaluation of this solution in the context of this project. The thesis ends with some conclusions and suggests future work. / Denna avhandling beskriver projektet "En ny webbserver för sensorer". Projektet har skapat en tjänst demonstration nätet som kan ta emot data från sensorer (både fasta sensorer och rörliga sensorer) och distribuera fått information i form av webbsidor. Dessa webbsidor kan ge former som gör det möjligt för användaren attskriva in kommandon som ges till sensorer. Syftet med detta examensarbete var att designa och utvärdera webbaserad applikation som kan använda sensordata. I detta projekt har vi fokuserat på två aspekter: (1) webb tillgång till sensorer och (2) depotentiella rörlighet av sensorer. Webbservern ger Web Access Server förmedlas till sensorer. Dessutom undersökte detta projekt hur man kan integrera en sensor med en mobil enhet, t.ex. en personuppgifter apparat. Webbservern ger en enkel tillgång mekanism för användare som vill använda och styra sensorer. Dessa användare kanflexibelt använda sin webbläsare för att få tillgång till sensorer via vår webbserver. Dessutom kan en sensor röra sig, exempelvis genom att den är integrerad med en personuppgifter apparat. Rörligheten av sensorer ökar avkänning omfattningen av sensorer eftersom sensorerna inte är fasta på plats. Sådana sensorer kan känna miljön längs den väg som de flyttas. För att nå målen med denna avhandling projektet analyserade vi vad som är grundläggande delar och funktioner som bör finnas för sensorer i webbservern.Dessutom analyseras i avhandlingen hur en sensor kan integreras med en personuppgifterna apparat, till exempel, hur man levererar energi till sensorn, och hur man synkronisera data mellan sensorn och personuppgifter apparaten. Som ett resultatav detta projekt var en webbserver med några av de nödvändiga funktioner utvecklas.En strategi för hur man kan integrera en sensor med en personuppgifterna apparat som anges i denna avhandling. Avhandlingen inleds med en analys av några befintliga lösningar. Deras fördelar har använts för att specificera kraven för vår egen lösning. Avhandlingen beskriver utformningen och genomförandet av den föreslagna lösningen. Nästa avhandlingen beskriver testning och utvärdering av denna lösning i samband med detta projekt. Avhandlingen avslutas med några slutsatser och föreslår framtida arbete.

Multi-transport devices are becoming more common, but sophisticated software is needed to fully realize the advantages of these devices. In this paper, we examine the performance of dynamic transport switching, which selects the best available transport for communication between two devices. We simulate transport switching within the Quality of Transport (QoT) architecture and show that it can effectively mitigate the effects of congestion and interference for connections between two multi-transport devices. We then evaluate dynamic transport switching overhead to characterize its effect on application throughput. Based on these insights, we identify several limitations of the QoT architecture and present solutions to improve performance.

Analysis of SIP68: A UDP Glucosyltransferase for Its Role in Plant Growth and Immunity UDP-glucosyltransferases (GTs) are a group of enzymes that play a crucial role in plant metabolism by transferring glucosyl groups from UDP-glucose to various acceptor molecules. SIP68 is a UDP-glucosyltransferase enzyme that has been identified to interact with SABP2 in a yeast two-hybrid screen. Previous research conducted in our lab has demonstrated that SIP68 is involved in salicylic acid (SA)-mediated defense signaling in tobacco plants. In the current study, we aimed to investigate the potential role of SIP68 in plant development and immune response. Our analysis of SIP68 revealed that this UDP-glucosyltransferase has a gene family, and its gene and protein sequence, molecular attributes, gene structure, and localization in the chromosome, exon-intron distribution, cis-regulatory elements in the promoter region, homology modeling of protein, domain architecture, motif analysis, phylogenetic tree, and protein-protein interaction were analyzed to better understand its potential function in plant metabolism. Our in-silico analysis predicted that SIP68 may play a role in the cytokinin-mediated metabolic pathway, which could affect plant growth and cell proliferation. Specifically, our analysis suggested that SIP68 might transfer glucosyl groups to various acceptor molecules involved in the cytokinin-mediated metabolic pathway. This suggests that SIP68 may play a role in regulating plant growth and development by affecting the cytokinin pathway. To investigate the potential role of SIP68 in plant development, we generated SIP68-deficient transgenic tobacco plants by silencing the SIP68 protein. The observed phenotype of these plants was compared to that of wild-type plants. We found that root, shoot, leaf width, and overall biomass development were all affected in SIP68-deficient plants. This suggests that SIP68 plays a crucial role in regulating various aspects of plant growth and development. This agrees with our previous finding that SIP68 is involved in SA-mediated defense signaling in tobacco plants. Our analysis of protein-protein interactions revealed that SIP68 interacts with various classes of flavanols in-vitro. This interaction provides a starting point for investigating potential targets of SIP68 in tobacco plants. However, the specific in-planta substrate(s) of SIP68 has not yet been identified. Therefore, further investigation is needed to determine the intracellular targets of SIP68 and its specific role in plant metabolism. In conclusion, our study provides insights into the potential role of SIP68 in plant development and immune response. Our findings suggest that SIP68 plays a crucial role in regulating various aspects of plant growth and development. Furthermore, our in-silico analysis predicts that SIP68 may play a role in the cytokinin-mediated metabolic pathway, which could affect plant growth and cell proliferation. Future investigation is needed to determine the intracellular targets of SIP68 and its specific role in plant metabolism. Overall, this study highlights the importance of UDP-glucosyltransferase enzymes (SIP68) in plant development and immune response.

Flavonoids are polyphenolics compounds that constitute a major group of plant specialized metabolites, biosynthesized via the phenylpropanoid/polymalonate pathways. The resulting specialized metabolites can be due to decoration of flavonoid compounds with sugars, usually glucose, by the action of regiospecific UDP-glycosyltransferase (UGT) enzymes. In some cases, glycosylation can involve enzymatic attachment of other sugar moieties, such as glucuronic acid, galactose, rhamnose or arabinose. These modifications facilitate or impact the bioactivity, stability, solubility, bioavailability and taste of the resulting flavonoid metabolites. The present work shows the limitations of utilizing mammalian UDP-glucuronosyltransferases (UGATs) for flavonoid glucuronidation, and then proceeds to investigate plant UG(A)T candidates from the model legume Medicago truncatula for glucuronidating brain-targeted flavonoid metabolites that have shown potential in neurological protection. We identified and characterized several UG(A)T candidates from M. truncatula which efficiently glycosylate various flavonoids compounds with different/multiple regiospecificities. Biochemical characterization identified one enzyme, UGT84F9, that efficiently glucuronidates a range of flavonoid compounds in vitro. In addition, examination of the ugt84f9 gene knock-out mutation in M. truncatula indicates that UGT84F9 is the major UG(A)T enzyme that is necessary and sufficient for attaching glucuronic acid to flavonoid aglycones, particularly flavones, in this species. Finally, the identified UG(A)T candidates were analyzed via homology modeling and site-directed mutagenesis towards increasing the repertoire of UG(A)Ts applicable for synthesis of flavonoid glucuronides with potential human health benefits in neurological protection.

Hardware-acceleration techniques continue to be used to boost the performance of scientific codes. To do so, software developers identify portions of these codes that are amenable for offloading and map them to hardware accelerators. However, offloading such tasks to specialized hardware accelerators is non-trivial. Furthermore, these accelerators can add significant cost to a computing system. Consequently, this thesis proposes a framework called GePSeA (General Purpose Software Acceleration Framework), which uses a small fraction of the computational power on multi-core architectures to offload complex application-specific tasks. Specifically, GePSeA provides a lightweight process that acts as a helper agent to the application by executing application-specific tasks asynchronously and efficiently. GePSeA is not meant to replace hardware accelerators but to extend them. GePSeA provide several utilities called core components that offload tasks on to the core or to the special-purpose hardware when available in a way that is transparent to the application. Examples of such core components include reliable communication service, distributed lock management, global memory management, dynamic load distribution and network protocol processing. We then apply the GePSeA framework to two applications, namely mpiBLAST, an open-source computational biology application and Reliable Blast UDP (RBUDP) based file transfer application. We observe significant speed-up for both applications. / Master of Science