Rapid and Proactive Approach on Exploration of Database Vulnerabilities

In today's complicated computing environment, managing data has become the primary concern of all industries. Information security is the greatest challenge and it has become essential to secure the enterprise system resources like the databases and the operating systems from the attacks of the unknown outsiders. Our approach plays a major role in detecting and managing vulnerabilities in complex computing systems. It allows enterprises to assess two primary tiers through a single interface as a vulnerability scanner tool which provides a secure system which is also compatible with the security compliance of the industry. It provides an overall view of the vulnerabilities in the database, by automatically scanning them with minimum overhead. It gives a detailed view of the risks involved and their corresponding ratings. Based on these priorities, an appropriate mitigation process can be implemented to ensure a secured system. The results show that our approach could effectively optimize the time and cost involved when compared to the existing systems

Computing median and antimedian sets in median graphs

The median (antimedian) set of a profile π = (u1, . . . , uk) of vertices of a graphG is the set of vertices x that minimize (maximize) the remoteness i d(x,ui ). Two algorithms for median graphs G of complexity O(nidim(G)) are designed, where n is the order and idim(G) the isometric dimension of G. The first algorithm computes median sets of profiles and will be in practice often faster than the other algorithm which in addition computes antimedian sets and remoteness functions and works in all partial cubes

Soft Computing Approach for Optimization of siRNA Efficiency Prediction for Post-transcriptional Gene Silencing

Post-transcriptional gene silencing by RNA interference is mediated by small interfering RNA called siRNA. This gene silencing mechanism can be exploited therapeutically to a wide variety of disease-associated targets, especially in AIDS, neurodegenerative diseases, cholesterol and cancer on mice with the hope of extending these approaches to treat humans. Over the recent past, a significant amount of work has been undertaken to understand the gene silencing mediated by exogenous siRNA. The design of efficient exogenous siRNA sequences is challenging because of many issues related to siRNA. While designing efficient siRNA, target mRNAs must be selected such that their corresponding siRNAs are likely to be efficient against that target and unlikely to accidentally silence other transcripts due to sequence similarity. So before doing gene silencing by siRNAs, it is essential to analyze their off-target effects in addition to their inhibition efficiency against a particular target. Hence designing exogenous siRNA with good knock-down efficiency and target specificity is an area of concern to be addressed. Some methods have been developed already by considering both inhibition efficiency and off-target possibility of siRNA against agene. Out of these methods, only a few have achieved good inhibition efficiency, specificity and sensitivity. The main focus of this thesis is to develop computational methods to optimize the efficiency of siRNA in terms of “inhibition capacity and off-target possibility” against target mRNAs with improved efficacy, which may be useful in the area of gene silencing and drug design for tumor development. This study aims to investigate the currently available siRNA prediction approaches and to devise a better computational approach to tackle the problem of siRNA efficacy by inhibition capacity and off-target possibility. The strength and limitations of the available approaches are investigated and taken into consideration for making improved solution. Thus the approaches proposed in this study extend some of the good scoring previous state of the art techniques by incorporating machine learning and statistical approaches and thermodynamic features like whole stacking energy to improve the prediction accuracy, inhibition efficiency, sensitivity and specificity. Here, we propose one Support Vector Machine (SVM) model, and two Artificial Neural Network (ANN) models for siRNA efficiency prediction. In SVM model, the classification property is used to classify whether the siRNA is efficient or inefficient in silencing a target gene. The first ANNmodel, named siRNA Designer, is used for optimizing the inhibition efficiency of siRNA against target genes. The second ANN model, named Optimized siRNA Designer, OpsiD, produces efficient siRNAs with high inhibition efficiency to degrade target genes with improved sensitivity-specificity, and identifies the off-target knockdown possibility of siRNA against non-target genes. The models are trained and tested against a large data set of siRNA sequences. The validations are conducted using Pearson Correlation Coefficient, Mathews Correlation Coefficient, Receiver Operating Characteristic analysis, Accuracy of prediction, Sensitivity and Specificity. It is found that the approach, OpsiD, is capable of predicting the inhibition capacity of siRNA against a target mRNA with improved results over the state of the art techniques. Also we are able to understand the influence of whole stacking energy on efficiency of siRNA. The model is further improved by including the ability to identify the “off-target possibility” of predicted siRNA on non-target genes. Thus the proposed model, OpsiD, can predict optimized siRNA by considering both “inhibition efficiency on target genes and off-target possibility on non-target genes”, with improved inhibition efficiency, specificity and sensitivity. Since we have taken efforts to optimize the siRNA efficacy in terms of “inhibition efficiency and offtarget possibility”, we hope that the risk of “off-target effect” while doing gene silencing in various bioinformatics fields can be overcome to a great extent. These findings may provide new insights into cancer diagnosis, prognosis and therapy by gene silencing. The approach may be found useful for designing exogenous siRNA for therapeutic applications and gene silencing techniques in different areas of bioinformatics.

Rezentralisierung: Server-Based Computing in der Praxis einer Universitätsbibliothek

Der Beitrag beschreibt die Ein- und Durchführung einer Server-basierten Computerinfrastruktur in einer Universitätsbibliothek. Beschrieben wird das so genannte MetaFrame-DV-Konzept der Universitätsbibliothek Kassel, das das dortige Informationsmanagement in den letzten vier Jahren initiiert, konzipiert und umgesetzt hat. Hierbei werden nunmehr nicht mehr nur Applikationsserver z.B. für das CD-Angebot eingesetzt, sondern sämtliche ca. 200 Mitarbeiter- und Funktionsarbeitsplätze über eine Citrix MetaFrame-Installation serverseitig betreut. Besonderes Augenmerk gilt in diesem Beitrag der Konfiguration, der praktischen Administration und den täglichen Arbeitsbedingungen an den Bibliotheksmitarbeiterarbeitsplätzen.

Micro-electromechanical structural design and optimization of vertical cavity photonic devices with wide continuous tuning

Diese Arbeit umfaßt das elektromechanische Design und die Designoptimierung von weit durchstimmbaren optischen multimembranbasierten Bauelementen, mit vertikal orientierten Kavitäten, basierend auf der Finiten Element Methode (FEM). Ein multimembran InP/Luft Fabry-Pérot optischer Filter wird dargestellt und umfassend analysiert. In dieser Arbeit wird ein systematisches strukturelles Designverfahren dargestellt. Genaue analytische elektromechanischer Modelle für die Bauelemente sind abgeleitet worden. Diese können unschätzbare Werkzeuge sein, um am Anfang der Designphase schnell einen klaren Einblick zur Verfügung zu stellen. Mittels des FEM Programms ist der durch die nicht-lineare Verspannung hervorgerufene versteifende Effekt nachgeforscht und sein Effekt auf die Verlängerung der mechanischen Durchstimmungsstrecke der Bauelemente demonstriert worden. Interessant war auch die Beobachtung, dass die normierte Relation zwischen Ablenkung und Spannung ein unveränderliches Profil hat. Die Deformation der Membranflächen der in dieser Arbeit dargestellten Bauelementformen erwies sich als ein unerwünschter, jedoch manchmal unvermeidbarer Effekt. Es zeigt sich aber, dass die Wahl der Größe der strukturellen Dimensionen den Grad der Membrandeformation im Falle der Aktuation beeinflusst. Diese Arbeit stellt ein elektromechanisches in FEMLAB implementierte quasi-3D Modell, das allgemein für die Modellierung dünner Strukturen angewendet werden kann, dar; und zwar indem man diese als 2D-Objekte betrachtet und die dritte Dimension als eine konstante Größe (z.B. die Schichtdicke) oder eine Größe, welche eine mathematische Funktion ist, annimmt. Diese Annahme verringert drastisch die Berechnungszeit sowie den erforderlichen Arbeitsspeicherbedarf. Weiter ist es für die Nachforschung des Effekts der Skalierung der durchstimmbaren Bauelemente verwendet worden. Eine neuartige Skalierungstechnik wurde abgeleitet und verwendet. Die Ergebnisse belegen, dass das daraus resultierende, skalierte Bauelement fast genau die gleiche mechanische Durchstimmung wie das unskalierte zeigt. Die Einbeziehung des Einflusses von axialen Verspannungen und Gradientenverspannungen in die Berechnungen erforderte die Änderung der Standardimplementierung des 3D Mechanikberechnungsmodus, der mit der benutzten FEM Software geliefert wurde. Die Ergebnisse dieser Studie zeigen einen großen Einfluss der Verspannung auf die Durchstimmungseigenschaften der untersuchten Bauelemente. Ferner stimmten die Ergebnisse der theoretischen Modellrechnung mit den experimentellen Resultaten sehr gut überein.

Design, implementation and application of a generic framework for integrated regional land-use modeling

Land use is a crucial link between human activities and the natural environment and one of the main driving forces of global environmental change. Large parts of the terrestrial land surface are used for agriculture, forestry, settlements and infrastructure. Given the importance of land use, it is essential to understand the multitude of influential factors and resulting land use patterns. An essential methodology to study and quantify such interactions is provided by the adoption of land-use models. By the application of land-use models, it is possible to analyze the complex structure of linkages and feedbacks and to also determine the relevance of driving forces. Modeling land use and land use changes has a long-term tradition. In particular on the regional scale, a variety of models for different regions and research questions has been created. Modeling capabilities grow with steady advances in computer technology, which on the one hand are driven by increasing computing power on the other hand by new methods in software development, e.g. object- and component-oriented architectures. In this thesis, SITE (Simulation of Terrestrial Environments), a novel framework for integrated regional sland-use modeling, will be introduced and discussed. Particular features of SITE are the notably extended capability to integrate models and the strict separation of application and implementation. These features enable efficient development, test and usage of integrated land-use models. On its system side, SITE provides generic data structures (grid, grid cells, attributes etc.) and takes over the responsibility for their administration. By means of a scripting language (Python) that has been extended by language features specific for land-use modeling, these data structures can be utilized and manipulated by modeling applications. The scripting language interpreter is embedded in SITE. The integration of sub models can be achieved via the scripting language or by usage of a generic interface provided by SITE. Furthermore, functionalities important for land-use modeling like model calibration, model tests and analysis support of simulation results have been integrated into the generic framework. During the implementation of SITE, specific emphasis was laid on expandability, maintainability and usability. Along with the modeling framework a land use model for the analysis of the stability of tropical rainforest margins was developed in the context of the collaborative research project STORMA (SFB 552). In a research area in Central Sulawesi, Indonesia, socio-environmental impacts of land-use changes were examined. SITE was used to simulate land-use dynamics in the historical period of 1981 to 2002. Analogous to that, a scenario that did not consider migration in the population dynamics, was analyzed. For the calculation of crop yields and trace gas emissions, the DAYCENT agro-ecosystem model was integrated. In this case study, it could be shown that land-use changes in the Indonesian research area could mainly be characterized by the expansion of agricultural areas at the expense of natural forest. For this reason, the situation had to be interpreted as unsustainable even though increased agricultural use implied economic improvements and higher farmers' incomes. Due to the importance of model calibration, it was explicitly addressed in the SITE architecture through the introduction of a specific component. The calibration functionality can be used by all SITE applications and enables largely automated model calibration. Calibration in SITE is understood as a process that finds an optimal or at least adequate solution for a set of arbitrarily selectable model parameters with respect to an objective function. In SITE, an objective function typically is a map comparison algorithm capable of comparing a simulation result to a reference map. Several map optimization and map comparison methodologies are available and can be combined. The STORMA land-use model was calibrated using a genetic algorithm for optimization and the figure of merit map comparison measure as objective function. The time period for the calibration ranged from 1981 to 2002. For this period, respective reference land-use maps were compiled. It could be shown, that an efficient automated model calibration with SITE is possible. Nevertheless, the selection of the calibration parameters required detailed knowledge about the underlying land-use model and cannot be automated. In another case study decreases in crop yields and resulting losses in income from coffee cultivation were analyzed and quantified under the assumption of four different deforestation scenarios. For this task, an empirical model, describing the dependence of bee pollination and resulting coffee fruit set from the distance to the closest natural forest, was integrated. Land-use simulations showed, that depending on the magnitude and location of ongoing forest conversion, pollination services are expected to decline continuously. This results in a reduction of coffee yields of up to 18% and a loss of net revenues per hectare of up to 14%. However, the study also showed that ecological and economic values can be preserved if patches of natural vegetation are conservated in the agricultural landscape. -----------------------------------------------------------------------

Computing Generators of Free Modules over Orders in Group Algebras

Let E be a number field and G be a finite group. Let A be any O_E-order of full rank in the group algebra E[G] and X be a (left) A-lattice. We give a necessary and sufficient condition for X to be free of given rank d over A. In the case that the Wedderburn decomposition E[G] \cong \oplus_xM_x is explicitly computable and each M_x is in fact a matrix ring over a field, this leads to an algorithm that either gives elements \alpha_1,...,\alpha_d \in X such that X = A\alpha_1 \oplus ... \oplusA\alpha_d or determines that no such elements exist. Let L/K be a finite Galois extension of number fields with Galois group G such that E is a subfield of K and put d = [K : E]. The algorithm can be applied to certain Galois modules that arise naturally in this situation. For example, one can take X to be O_L, the ring of algebraic integers of L, and A to be the associated order A(E[G];O_L) \subseteq E[G]. The application of the algorithm to this special situation is implemented in Magma under certain extra hypotheses when K = E = \IQ.

Asymptotically Zero Energy Computing Using Split-Level Charge Recovery Logic

The dynamic power requirement of CMOS circuits is rapidly becoming a major concern in the design of personal information systems and large computers. In this work we present a number of new CMOS logic families, Charge Recovery Logic (CRL) as well as the much improved Split-Level Charge Recovery Logic (SCRL), within which the transfer of charge between the nodes occurs quasistatically. Operating quasistatically, these logic families have an energy dissipation that drops linearly with operating frequency, i.e., their power consumption drops quadratically with operating frequency as opposed to the linear drop of conventional CMOS. The circuit techniques in these new families rely on constructing an explicitly reversible pipelined logic gate, where the information necessary to recover the energy used to compute a value is provided by computing its logical inverse. Information necessary to uncompute the inverse is available from the subsequent inverse logic stage. We demonstrate the low energy operation of SCRL by presenting the results from the testing of the first fully quasistatic 8 x 8 multiplier chip (SCRL-1) employing SCRL circuit techniques.

Reconfigurable Architectures for General-Purpose Computing

General-purpose computing devices allow us to (1) customize computation after fabrication and (2) conserve area by reusing expensive active circuitry for different functions in time. We define RP-space, a restricted domain of the general-purpose architectural space focussed on reconfigurable computing architectures. Two dominant features differentiate reconfigurable from special-purpose architectures and account for most of the area overhead associated with RP devices: (1) instructions which tell the device how to behave, and (2) flexible interconnect which supports task dependent dataflow between operations. We can characterize RP-space by the allocation and structure of these resources and compare the efficiencies of architectural points across broad application characteristics. Conventional FPGAs fall at one extreme end of this space and their efficiency ranges over two orders of magnitude across the space of application characteristics. Understanding RP-space and its consequences allows us to pick the best architecture for a task and to search for more robust design points in the space. Our DPGA, a fine- grained computing device which adds small, on-chip instruction memories to FPGAs is one such design point. For typical logic applications and finite- state machines, a DPGA can implement tasks in one-third the area of a traditional FPGA. TSFPGA, a variant of the DPGA which focuses on heavily time-switched interconnect, achieves circuit densities close to the DPGA, while reducing typical physical mapping times from hours to seconds. Rigid, fabrication-time organization of instruction resources significantly narrows the range of efficiency for conventional architectures. To avoid this performance brittleness, we developed MATRIX, the first architecture to defer the binding of instruction resources until run-time, allowing the application to organize resources according to its needs. Our focus MATRIX design point is based on an array of 8-bit ALU and register-file building blocks interconnected via a byte-wide network. With today's silicon, a single chip MATRIX array can deliver over 10 Gop/s (8-bit ops). On sample image processing tasks, we show that MATRIX yields 10-20x the computational density of conventional processors. Understanding the cost structure of RP-space helps us identify these intermediate architectural points and may provide useful insight more broadly in guiding our continual search for robust and efficient general-purpose computing structures.

A Privacy Conscious Bluetooth Infrastructure for Location Aware Computing

We present a low cost and easily deployed infrastructure for location aware computing that is built using standard Bluetooth® technologies and personal computers. Mobile devices are able to determine their location to room-level granularity with existing bluetooth technology, and to even greater resolution with the use of the recently adopted bluetooth 1.2 specification, all while maintaining complete anonymity. Various techniques for improving the speed and resolution of the system are described, along with their tradeoffs in privacy. The system is trivial to implement on a large scale – our network covering 5,000 square meters was deployed by a single student over the course of a few days at a cost of less than US$1,000.

Towards Grid-Wide Modeling and Simulation

Modeling and simulation permeate all areas of business, science and engineering. With the increase in the scale and complexity of simulations, large amounts of computational resources are required, and collaborative model development is needed, as multiple parties could be involved in the development process. The Grid provides a platform for coordinated resource sharing and application development and execution. In this paper, we survey existing technologies in modeling and simulation, and we focus on interoperability and composability of simulation components for both simulation development and execution. We also present our recent work on an HLA-based simulation framework on the Grid, and discuss the issues to achieve composability.

Failure-Oblivious Computing and Boundless Memory Blocks

Memory errors are a common cause of incorrect software execution and security vulnerabilities. We have developed two new techniques that help software continue to execute successfully through memory errors: failure-oblivious computing and boundless memory blocks. The foundation of both techniques is a compiler that generates code that checks accesses via pointers to detect out of bounds accesses. Instead of terminating or throwing an exception, the generated code takes another action that keeps the program executing without memory corruption. Failure-oblivious code simply discards invalid writes and manufactures values to return for invalid reads, enabling the program to continue its normal execution path. Code that implements boundless memory blocks stores invalid writes away in a hash table to return as the values for corresponding out of bounds reads. he net effect is to (conceptually) give each allocated memory block unbounded size and to eliminate out of bounds accesses as a programming error. We have implemented both techniques and acquired several widely used open source servers (Apache, Sendmail, Pine, Mutt, and Midnight Commander).With standard compilers, all of these servers are vulnerable to buffer overflow attacks as documented at security tracking web sites. Both failure-oblivious computing and boundless memory blocks eliminate these security vulnerabilities (as well as other memory errors). Our results show that our compiler enables the servers to execute successfully through buffer overflow attacks to continue to correctly service user requests without security vulnerabilities.

Propuesta de computación en la nube para los libreros del sector de San Victorino en Bogotá para el año 2012 estudio de caso

El trabajo de grado titulado “Propuesta de Computación en la Nube para los Libreros del Sector de San Victorino en Bogotá para el Año 2012. Estudio de Caso”, tiene como objetivo elaborar una propuesta de computación en la nube que sea aplicable a uno de los sectores más dinámicos del centro de Bogotá como es el de los libreros de San Victorino; Este trabajo busca la apropiación de las herramientas que proporcionan las nuevas tecnologías de la información y las comunicaciones en la disciplina de la administración de empresas, como un nuevo escenario de competitividad ajustado a las nuevas condiciones de las organizaciones. La computación en la nube como nueva herramienta tecnológica, permite que diversos usuarios - empresas accedan a la información consolidada, la cual puede ser aportada por ellos mismos, para brindar a los clientes un servicio más eficiente y eficaz, con bajos costos y generando innumerables ventajas que aportan a la competitividad de cada una de las unidades de negocio, las cuales se consolidan como una única organización o clúster. En este sentido se determinó, cómo el sector de San Victorino, en particular el de los libreros, comparten una serie de características y metas similares, que permiten su implantación con los beneficios que se señalan en este trabajo de grado, permitiendo el acceso a información general de productos editoriales e inventarios y la ubicación exacta del librero que lo posee.

School of Mathematics Computing Guide

Guide for computing in the School of Mathematics. Intended for new staff and PG students. Originally written by Anton Prowse from a number of earlier documents.