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The engineering of biological systems with predictable behavior is a challenging problem. One reason for this difficulty is that engineered biological systems are embedded within complex and variable host cells. To help enable the future engineering of biological systems, we are studying and optimizing the interface between an engineered biological system and its host cell or ``chassis''. Other engineering disciplines use modularity to make interacting systems interchangeable and to insulate one system from another. Engineered biological systems are more likely to work as predicted if system function is decoupled from the state of the host cell. Also, specifying and standardizing the interfaces between a system and the chassis will allow systems to be engineered independent of chassis and allow systems to be interchanged between different chassis. To this end, we have assembled orthogonal transcription and translation systems employing dedicated machinery, independent from the equivalent host cell machinery. In parallel, we are developing test systems and metrics to measure the interactions between an engineered system and its chassis. Lastly, we are exploring methods to``port'' a simple engineered system from a prokaryotic to a eukaryotic organism so that the system can function in both organisms. / Poster presented at the 2005 ICSB meeting, held at Harvard Medical School in Boston, MA.

As databases grow in size, the need for optimizing databases is becoming a necessity. Choosing the right operating system to support your database becomes paramount to ensure that the database is fully utilized. Furthermore with the virtualization of operating systems becoming more commonplace, we find ourselves with more choices than we ever faced before. This paper demonstrates why the choice of operating system plays an integral part in deciding the right database for your system in a virtual environment. This paper contains an experiment which measured benchmark performance of a Database management system on various virtual operating systems. This experiment shows the effect a virtual operating system has on the database management system that runs upon it. These findings will help to promote future research into this area as well as provide a foundation on which future research can be based upon.

The purpose of master’s thesis is to project virtualization solution together with replication of the servers. Thesis is divided into the three parts and that it theoretical, analytical and projection part. In analytical part there are basic information about virtualization technologies, in analytical part there is analysis of the present status of the company and mainly about status of the IT infrastructure and in the end projection part there is realization of the virtualization solution from choosing the right type of cluster to choosing hardware solution.

Due to the growth of cloud computing in recent years, the use of virtualization has exploded. Virtual machines (VMs) and containers are both virtualization technologies used to create isolated computing environments. While VMs are created and managed by hypervisors and need their own full guest operating system, containers share the kernel of the host computers and do not need a full guest operating system. Because of this, containers are rumored to have less overhead involved, yielding higher performance and less resource usage compared to VMs.  In this paper we perform a literature study along with an empirical study to examine the differences between containers and virtual machines when it comes to cpu, memory and disk performance, cpu and memory resource utilization, and power consumption. To answer the question regarding performance, a series of benchmarks were run inside both a container and a VM. During these benchmarks the resource utilization of the host machine was also measured to answer the second question and to answer the third and final question the power draw was measured while some of the benchmarks were running. The results showed that the cpu performance was extremely similar between the two and memory performance seemed to be similar for the most part but fairly big differences were seen in favor of both depending on the benchmark in some cases. With disk performance the container was between 15-50% faster depending on the benchmark. As for resource usage, the cpu usage was the same for both technologies but memory usage differed greatly in favor of the container. The VM used between 3-4 GiB and the container between 70 MiB - 2.5 GiB depending on the benchmark. The power draw was the same for both technologies when under cpu and memory load but when idle the VM proved to draw around 40% more power.

Cuando una startup sale al mercado, se enfoca en crecer exponencialmente, utilizando una idea innovadora y un presupuesto relativamente bajo. Este crecimiento exponencial se apoya en la tecnología, la cual debe manejar un rendimiento adecuado en los recursos de hardware para los servicios, acorde con el giro del negocio. El objetivo principal de este trabajo es realizar un análisis de una plataforma para aplicaciones web con una arquitectura basada en contenedores, que sea capaz de soportar el crecimiento exponencial de usuarios de sus servicios Web. Las arquitecturas tradicionales basadas en servidores físicos implican tiempos y costos de configuración, despliegue y mantenimiento que son altos. Cuando se hace necesario escalar, se requiere, normalmente, de más recursos de hardware y de tiempo para realizar las configuraciones necesarias. La flexibilidad que provee la virtualización de servidores agiliza los procedimientos de escalamiento y reduce considerablemente el tiempo y los costos, comparados con las soluciones basadas solamente en hardware. Sin embargo, para atender requerimientos más exigentes, la virtualización tiene una huella muy pesada y tiempos de despliegue todavía elevados. La tecnología de contenedores nos ofrece una plataforma liviana y eficiente. Un contenedor es un paquete ejecutable muy liviano que aísla una pieza de software, incluyendo todo lo necesario para ser ejecutado. Está claro que la velocidad y la eficiencia son las mayores necesidades para las startups, y Docker, uno de los líderes en el mercado de contenedores de software, es capaz de proporcionarlas de manera efectiva. Si bien es cierto no ha reemplazado a las máquinas virtuales, se está notando el potencial de Docker. Eso no quiere decir que las máquinas virtuales quedaran obsoletas, por el contrario, Docker y las máquinas virtuales coexistirán uno al lado del otro, dando a los startups más opciones para ejecutar sus aplicaciones en la nube. / When a startup goes to market, it focuses on growing exponentially, using an innovative idea and a relatively low budget. This exponential growth is supported by technology, which must handle adequate performance in the hardware resources for services, in accordance with the line of business. The main objective of this work is to carry out an analysis of a platform for web applications with a container-based architecture, which is capable of supporting the exponential growth of users of its Web services. Traditional physical server-based architectures involve high configuration, deployment, and maintenance times and costs. When scaling becomes necessary, it usually takes more hardware and time to complete the necessary configurations. The flexibility that server virtualization provides streamlines escalation procedures and greatly reduces time and cost, compared to hardware-only solutions. However, to meet more demanding requirements, virtualization has a very heavy footprint and still high deployment times. Container technology offers us a lightweight and efficient platform. A container is a very lightweight executable package that isolates a piece of software, including everything needed to be run. It is clear that speed and efficiency are the greatest needs for startups, and Docker, one of the leaders in the software container market, is capable of providing them effectively. While it's true it hasn't replaced virtual machines, Docker's potential is being noticed. That doesn't mean that virtual machines will become obsolete, on the contrary, Docker and virtual machines will coexist side by side, giving startups more options to run their applications in the cloud. / Tesis

Because software systems are imperfect, developers are forced to fix bugs and add new features. The common way of applying changes to a running system is to stop the application or machine and restart with the new version. Stopping and restarting causes a disruption in service that is at best inconvenient and at worst causes revenue loss and compromises safety. Dynamic software updating (DSU) addresses these problems by updating programs while they execute. Prior DSU systems for managed languages like Java and C# lack necessary functionality: they are inefficient and do not support updates that occur commonly in practice. This dissertation presents the design and implementation of Jvolve, a DSU system for Java. Jvolve's combination of flexibility, safety, and efficiency is a significant advance over prior approaches. Our key contribution is the extension and integration of existing Virtual Machine services with safe, flexible, and efficient dynamic updating functionality. Our approach is flexible enough to support a large class of updates, guarantees type-safety, and imposes no space or time overheads on steady-state execution. Jvolve supports many common updates. Users can add, delete, and change existing classes. Changes may add or remove fields and methods, replace existing ones, and change type signatures. Changes may occur at any level of the class hierarchy. To initialize new fields and update existing ones, Jvolve applies class and object transformer functions, the former for static fields and the latter for object instance fields. These features cover many updates seen in practice. Jvolve supports 20 of 22 updates to three open-source programs---Jetty web server, JavaEmailServer, and CrossFTP server---based on actual releases occurring over a one to two year period. This support is substantially more flexible than prior systems. Jvolve is safe. It relies on bytecode verification to statically type-check updated classes. To avoid dynamic type errors due to the timing of an update, Jvolve stops the executing threads at a DSU safe point and then applies the update. DSU safe points are a subset of VM safe points, where it is safe to perform garbage collection and thread scheduling. DSU safe points further restrict the methods that may be on each thread's stack, depending on the update. Restricted methods include updated methods for code consistency and safety, and user-specified methods for semantic safety. Jvolve installs return barriers and uses on-stack replacement to speed up reaching a safe point when necessary. While Jvolve does not guarantee that it will reach a DSU safe point, in our multithreaded benchmarks it almost always does. Jvolve includes a tool that automatically generates default object transformers which initialize new and changed fields to default values and retain values of unchanged fields in heap objects. If needed, programmers may customize the default transformers. Jvolve is the first dynamic updating system to extend the garbage collector to identify and transform all object instances of updated types. This dissertation introduces the concept of object-specific state transformers to repair application heap state for certain classes of bugs that corrupt part of the heap, and a novel methodology that employes dynamic analysis to automatically generate these transformers. Jvolve's eager object transformation design and implementation supports the widest class of updates to date. Finally, Jvolve is efficient. It imposes no overhead during steady-state execution. During an update, it imposes overheads to classloading and garbage collection. After an update, the adaptive compilation system will incrementally optimize the updated code in its usual fashion. Jvolve is the first full-featured dynamic updating system that imposes no steady-state overhead. In summary, Jvolve is the most-featured, most flexible, safest, and best-performing dynamic updating system for Java and marks a significant step towards practical support for dynamic updates in managed language virtual machines. / text

Saugos problemos virtualizuotose aplinkose tampa vis aktualesnės, todėl darbe nagrinėjama piktavališkos programinės įrangos virtualių mašinų aplinkoje aptikimo problematika. Darbe pateikiama: 1)piktavališkos programinės įrangos veikiančios virtualizuotose aplinkose analizė 2)metodikos, piktavališkos programinės įrangos virtualių mašinų aplinkoje aptikimui, sudarymas 3)piktavališkos programinės įrangos virtualioje mašinoje aptikimo, panaudojant sudaryta metodiką, eksperimento rezultatai ir jų priklausomybė nuo virtualios mašinos darbinės atminties dydžio. / In the context of virtual environment, The Security problems are highly important. The work presents analysis of malware types and it‘s presence in virtualized environments. Work also presents some results of experiments that have been carried out within the real virtual machine environment through modeling aiming to identify dependencies between the malware type, called Rootkits, detection time and the virtual machine memory size. Rootkits exploit kernel vulnerabilities and gain privileges (popularity) within any system, virtual or not. The basic result of the work is as follows: 1) the malware detection methodology for the virtual environment when the memory size of a virtual machine is changing; 2) dependences between the virtual machine memory size and Rootkit detection time.

The convergence of mobile computing and cloud computing enables new mobile applications that are both resource-intensive and interactive. For these applications, end-to-end network bandwidth and latency matter greatly when cloud resources are used to augment the computational power and battery life of a mobile device. This dissertation designs and implements a new architectural element called a cloudlet, that arises from the convergence of mobile computing and cloud computing. Cloudlets represent the middle tier of a 3-tier hierarchy, mobile device — cloudlet—cloud, to achieve the right balance between cloud consolidation and network responsiveness. We first present quantitative evidence that shows cloud location can affect the performance of mobile applications and cloud consolidation. We then describe an architectural solution using cloudlets that are a seamless extension of todays cloud computing infrastructure. Finally, we define minimal functionalities that cloudlets must offer above/beyond standard cloud computing, and address corresponding technical challenges.

Today's cloud landscape has evolved computing infrastructure into a dynamic, high utilization, service-oriented paradigm. This shift has enabled the commoditization of large-scale storage and distributed computation, allowing engineers to tackle previously untenable problems without large upfront investment. A key enabler of flexibility in the cloud is the ability to transfer running virtual machines across subnets or even datacenters using live migration. However, live migration can be a costly process, one that has the potential to interfere with other applications not involved with the migration. This work investigates storage interference through experimentation with real-world systems and well-established benchmarks. In order to address migration interference in general, a buffering technique is presented that offloads the migration's read, eliminating interference in the majority of scenarios.