Generación automática de ficheros de configuración para encaminadores

Este Proyecto Fin de Grado (PFG) tiene como objetivo diseñar e implementar un sistema que genere un fichero de texto que contenga la configuración básica de un encaminador. De esta manera se desea mejorar la eficiencia del personal del departamento donde se va a implantar dicho sistema, liberando a los miembros del mismo de un trabajo repetitivo que se hace varias veces al día. Hasta ahora, esta configuración la realiza cada instalador. Para ello, una vez que se ha cargado y probado la configuración en distintos equipos de manera satisfactoria, se generan un conjunto de plantillas que sirven de modelo para las siguientes configuraciones. Aunque el instalador toma estas plantillas como punto de partida, tiene que modificar manualmente todas las variables que dependen de cada configuración particular. Por tanto, aunque no ha de ejecutar todos los comandos paso a paso, sí debe hacer una revisión total de cada plantilla para generar la configuración adecuada y después cargarla en el encaminador. Para cada configuración se consultan un total de entre tres y siete plantillas. Si a esto se añade que en el departamento se configuran encaminadores de la marca Cisco y Teldat, que de cada marca se utilizan distintos modelos y que la empresa ofrece cuatro tipos de servicio, cada uno con sus particularidades, la tarea de configurar un equipo es costosa. El sistema estará constituido por un servidor web que alojará una base de datos y un programa que permite realizar operaciones de consulta sobre la misma, un sitio web sencillo que hará las funciones de interfaz de usuario y una aplicación que permite generar el fichero de texto que contiene la configuración del encaminador en base a una serie de condicionantes. La base de datos desarrollada es una representación de la utilizada en el entorno real que tiene como objetivo realizar simulaciones del funcionamiento que tendrá el sistema. Por su parte, la funcionalidad del sitio web debe ser la de ofrecer al usuario una interfaz sencilla de utilizar y de interpretar, a través de la cual se puedan realizar consultas a la base de datos así como presentar los resultados de dichas consultas de forma ordenada. La aplicación se encargará de validar los datos a partir de los que se va a generar la configuración, determinar qué plantillas se deben consultar en función a aspectos como el servicio a configurar o la marca del encaminador y finalmente generar el fichero de texto resultado. De este modo, el instalador simplemente tendrá que volcar la información de dicho fichero sobre el encaminador. El sistema se ha diseñado de manera que sea lo más flexible a cambios, puesto que la idea de los miembros del departamento es ampliar la funcionalidad de esta herramienta. ABSTRACT. This Final Degree Project is focused on the design and implementation of a system which is able to generate a text file that contains the basic configuration of a router. With this system we want to improve the efficiency of the department members where this system is going to be introduced, releasing them from repetitive work which is done several times per day. Up to now, each installer has to configure the router manually. After checking the configuration of several devices successfully, they create a set of templates which work as models. Although the installers use those templates, they have to modify the variables that depend on the specific features of each kind of configuration. Thus, even though they don´t have to execute the commands step by step, they have to do a review of each used template in order to generate the right configuration. For each configuration, three to seven templates have to be checked. In addition, if the configured routers are both Cisco and Teldat, there are several models per brand and the company offers four types of services to be installed, so the configuration becomes a hard task to do. The system is comprised of a web server in which both the database and the program responsible for doing queries are hosted, a simple web site that will be the graphic user interface, and an application focused on generating the text file which contains the router configuration based on a set of conditions. The developed database is the representation of the real one and its aim is to simulate the way the system will work. The function of the web site is to offer an easy interface whereby you can submit a query or you can see the obtained results as a data table. Furthermore, the application has to validate the data in which the text file with the router configuration is based on. Then, it has to decide which templates it is going to use according to different aspects, such as the brand of the router or the type of service we want to configure. Finally, the application generates a text file with the necessary commands. As a result of this, the user of the system only has to copy the contents of this file to the router. The system has been designed to be flexible to changes because the members of the department want to increase the utility of this tool in the future.

Plataformas de ejercicios de ciberseguridad

El objetivo principal de este proyecto es estudiar, desde un punto de vista práctico, las posibilidades que ofrece la plataforma de ejercicios de ciberseguridad propuesta por la Universidad de Rhode Island en Estado Unidos, denominada Open Cyber Challenge Platform (OCCP); para ello primero nos ubicaremos dentro del campo de la ciberseguridad, estudiando porqué este área está tomando tanta relevancia, observando datos de estudios reales realizados por instituciones de prestigio, al mismo tiempo estudiaremos la tendencia actual y futura de los ciberataques. Seguidamente, analizaremos el estado del arte de la enseñanza en ciberseguridad y como se está enfocando por parte de las universidades y empresas más importantes en el sector. En esta parte del sector se está imponiendo una novedosa forma para desarrollar el aprendizaje tanto práctico como teórico basada en simular situaciones reales mediante escenarios virtuales. Una vez vistas otras opciones, nos centraremos en OCCP, podremos estudiar el estado de desarrollo de esta plataforma, la situación actual y las principales características. Además detallaremos el primer escenario propuesto por ellos mismos, estudiando los principales componentes, la topología de la red virtual de la empresa virtualizada, los principales ficheros de configuración, e incluso la montaremos y ejecutaremos y podremos observar como el equipo rojo ataca el servidor web de la empresa que lo tiene que proteger el equipo azul y consigue que la web deje de funcionar. También incluiremos una guía de instalación del escenario para que el lector pueda probar con su propio ordenador las posibilidades de esta plataforma. VirtualBox es un programa gratuito de virtualización perteneciente a la empresa Oracle. Más adelante estudiaremos este programa centrándonos en el servicio web ofrecido por VirtualBox ya que es utilizado por la plataforma Open Cyber Challenge Platform como virtualizador o hipervisor. Podremos ver como suelen funcionar los servicios web de este tipo en general y después nos centraremos principalmente en el archivo descriptivo de las interfaces que ofrece esta plataforma. Finalmente, resumiremos los resultados y conclusiones proponiendo un trabajo futuro ya que como hemos dicho esta plataforma está en estado de desarrollo y seguramente al final de la lectura del proyecto incluso el lector se haya podido percatar del potencial tan elevado que tiene una plataforma de este estilo. ABSTRACT. The main objective of this project is to study, from a practical standpoint the possibilities offered by the cybersecurity exercises platform proposed by the University of Rhode Island in United States, called Cyber Challenge Open Platform (OCCP); therefore we will place first in the field of cybersecurity, studying why this area is taking so much relevance, watching real data studies by prestigious institutions and the current and future trend of cyber-attacks. Then, we will discuss the state of the art of teaching cybersecurity and how universities and major companies in the sector are focusing to reach the aims among students or workers. In this part of the sector it is increasing the popularity of a new way to develop both practical and theoretical learning based on simulating real situations through virtual scenarios. Once seen other options, we will focus on OCCP, we can study the state of development of this platform, the current situation and main characteristics. In addition we will detail the first proposed scenario by the very own university, studying the main components, the topology of the virtual network virtualized enterprise, the main configuration files, and even we would mount and execute it. We will see how the red team attacks the web server of the company and get it thrown out. At the same time the blue team will have to protect it. We will also include an installation guide of the scenario so that the reader can test in their own computer the possibilities of this tool. VirtualBox is a free virtualization program belonging to the Oracle enterprise. Later on we will study this program focusing on the web service provided by VirtualBox because it is used by the Open Cyber Challenge Platform like hypervisor. We will see how this kind of web services work and then we will focus mainly on the descriptive file of the interfaces provided by this tool. Finally we summarize the results and conclusions proposing a future work since as we have said this platform is in the development stage and certainly at the end of reading the project even the reader may have realized of such high potential as would have a tool of this kind.

SpliceDB: database of canonical and non-canonical mammalian splice sites

A database (SpliceDB) of known mammalian splice site sequences has been developed. We extracted 43 337 splice pairs from mammalian divisions of the gene-centered Infogene database, including sites from incomplete or alternatively spliced genes. Known EST sequences supported 22 815 of them. After discarding sequences with putative errors and ambiguous location of splice junctions the verified dataset includes 22 489 entries. Of these, 98.71% contain canonical GT–AG junctions (22 199 entries) and 0.56% have non-canonical GC–AG splice site pairs. The remainder (0.73%) occurs in a lot of small groups (with a maximum size of 0.05%). We especially studied non-canonical splice sites, which comprise 3.73% of GenBank annotated splice pairs. EST alignments allowed us to verify only the exonic part of splice sites. To check the conservative dinucleotides we compared sequences of human non-canonical splice sites with sequences from the high throughput genome sequencing project (HTG). Out of 171 human non-canonical and EST-supported splice pairs, 156 (91.23%) had a clear match in the human HTG. They can be classified after sequence analysis as: 79 GC–AG pairs (of which one was an error that corrected to GC–AG), 61 errors corrected to GT–AG canonical pairs, six AT–AC pairs (of which two were errors corrected to AT–AC), one case was produced from a non-existent intron, seven cases were found in HTG that were deposited to GenBank and finally there were only two other cases left of supported non-canonical splice pairs. The information about verified splice site sequences for canonical and non-canonical sites is presented in SpliceDB with the supporting evidence. We also built weight matrices for the major splice groups, which can be incorporated into gene prediction programs. SpliceDB is available at the computational genomic Web server of the Sanger Centre: http://genomic.sanger.ac.uk/spldb/SpliceDB.html and at http://www.softberry.com/spldb/SpliceDB.html.

Multi-objective adaptive evolutionary strategy for tuning compilations

Tuning compilations is the process of adjusting the values of a compiler options to improve some features of the final application. In this paper, a strategy based on the use of a genetic algorithm and a multi-objective scheme is proposed to deal with this task. Unlike previous works, we try to take advantage of the knowledge of this domain to provide a problem-specific genetic operation that improves both the speed of convergence and the quality of the results. The evaluation of the strategy is carried out by means of a case of study aimed to improve the performance of the well-known web server Apache. Experimental results show that a 7.5% of overall improvement can be achieved. Furthermore, the adaptive approach has shown an ability to markedly speed-up the convergence of the original strategy.

Reducing task’s redundancy – the strategy of Faculty of Pharmacy Library to centralize all scientific research

Introduction – Based on a previous project of University of Lisbon (UL) – a Bibliometric Benchmarking Analysis of University of Lisbon, for the period of 2000-2009 – a database was created to support research information (ULSR). However this system was not integrated with other existing systems at University, as the UL Libraries Integrated System (SIBUL) and the Repository of University of Lisbon (Repositório.UL). Since libraries were called to be part of the process, the Faculty of Pharmacy Library’ team felt that it was very important to get all systems connected or, at least, to use that data in the library systems. Objectives – The main goals were to centralize all the scientific research produced at Faculty of Pharmacy, made it available to the entire Faculty, involve researchers and library team, capitalize and reinforce team work with the integration of several distinct projects and reducing tasks’ redundancy. Methods – Our basis was the imported data collection from the ISI Web of Science (WoS), for the period of 2000-2009, into ULSR. All the researchers and indexed publications at WoS, were identified. A first validation to identify all the researchers and their affiliation (university, faculty, department and unit) was done. The final validation was done by each researcher. In a second round, concerning the same period, all Pharmacy Faculty researchers identified their published scientific work in other databases/resources (NOT WoS). To our strategy, it was important to get all the references and essential/critical to relate them with the correspondent digital objects. To each researcher previously identified, was requested to register all their references of the ‘NOT WoS’ published works, at ULSR. At the same time, they should submit all PDF files (for both WoS and NOT WoS works) in a personal area of the Web server. This effort enabled us to do a more reliable validation and prepare the data and metadata to be imported to Repository and to Library Catalogue. Results – 558 documents related with 122 researchers, were added into ULSR. 1378 bibliographic records (WoS + NOT WoS) were converted into UNIMARC and Dublin Core formats. All records were integrated in the catalogue and repository. Conclusions – Although different strategies could be adopted, according to each library team, we intend to share this experience and give some tips of what could be done and how Faculty of Pharmacy created and implemented her strategy.

Discovering user access pattern based on probabilistic latent factor model

There has been an increased demand for characterizing user access patterns using web mining techniques since the informative knowledge extracted from web server log files can not only offer benefits for web site structure improvement but also for better understanding of user navigational behavior. In this paper, we present a web usage mining method, which utilize web user usage and page linkage information to capture user access pattern based on Probabilistic Latent Semantic Analysis (PLSA) model. A specific probabilistic model analysis algorithm, EM algorithm, is applied to the integrated usage data to infer the latent semantic factors as well as generate user session clusters for revealing user access patterns. Experiments have been conducted on real world data set to validate the effectiveness of the proposed approach. The results have shown that the presented method is capable of characterizing the latent semantic factors and generating user profile in terms of weighted page vectors, which may reflect the common access interest exhibited by users among same session cluster.

Quantitative online prediction of peptide binding to the major histocompatibility complex

With its implications for vaccine discovery, the accurate prediction of T cell epitopes is one of the key aspirations of computational vaccinology. We have developed a robust multivariate statistical method, based on partial least squares, for the quantitative prediction of peptide binding to major histocompatibility complexes (MHC), the principal checkpoint on the antigen presentation pathway. As a service to the immunobiology community, we have made a Perl implementation of the method available via a World Wide Web server. We call this server MHCPred. Access to the server is freely available from the URL: http://www.jenner.ac.uk/MHCPred. We have exemplified our method with a model for peptides binding to the common human MHC molecule HLA-B*3501.

webComputing Service Framework

Presented is webComputing – a general framework of mathematically oriented services including remote access to hardware and software resources for mathematical computations, and web interface to dynamic interactive computations and visualization in a diversity of contexts: mathematical research and engineering, computer-aided mathematical/technical education and distance learning. webComputing builds on the innovative webMathematica technology connecting technical computing system Mathematica to a web server and providing tools for building dynamic and interactive web-interface to Mathematica-based functionality. Discussed are the conception and some of the major components of webComputing service: Scientific Visualization, Domain- Specific Computations, Interactive Education, and Authoring of Interactive Pages.

EnDNA-Prot:identification of DNA-binding proteins by applying ensemble learning

DNA-binding proteins are crucial for various cellular processes, such as recognition of specific nucleotide, regulation of transcription, and regulation of gene expression. Developing an effective model for identifying DNA-binding proteins is an urgent research problem. Up to now, many methods have been proposed, but most of them focus on only one classifier and cannot make full use of the large number of negative samples to improve predicting performance. This study proposed a predictor called enDNA-Prot for DNA-binding protein identification by employing the ensemble learning technique. Experiential results showed that enDNA-Prot was comparable with DNA-Prot and outperformed DNAbinder and iDNA-Prot with performance improvement in the range of 3.97-9.52% in ACC and 0.08-0.19 in MCC. Furthermore, when the benchmark dataset was expanded with negative samples, the performance of enDNA-Prot outperformed the three existing methods by 2.83-16.63% in terms of ACC and 0.02-0.16 in terms of MCC. It indicated that enDNA-Prot is an effective method for DNA-binding protein identification and expanding training dataset with negative samples can improve its performance. For the convenience of the vast majority of experimental scientists, we developed a user-friendly web-server for enDNA-Prot which is freely accessible to the public. © 2014 Ruifeng Xu et al.

Selection of conserved epitopes from hepatitis C virus for pan-populational stimulation of T-cell responses

The hepatitis C virus (HCV) is able to persist as a chronic infection, which can lead to cirrhosis and liver cancer. There is evidence that clearance of HCV is linked to strong responses by CD8 cytotoxic T lymphocytes (CTLs), suggesting that eliciting CTL responses against HCV through an epitope-based vaccine could prove an effective means of immunization. However, HCV genomic plasticity as well as the polymorphisms of HLA I molecules restricting CD8 T-cell responses challenges the selection of epitopes for a widely protective vaccine. Here, we devised an approach to overcome these limitations. From available databases, we first collected a set of 245 HCV-specific CD8 T-cell epitopes, all known to be targeted in the course of a natural infection in humans. After a sequence variability analysis, we next identified 17 highly invariant epitopes. Subsequently, we predicted the epitope HLA I binding profiles that determine their potential presentation and recognition. Finally, using the relevant HLA I-genetic frequencies, we identified various epitope subsets encompassing 6 conserved HCV-specific CTL epitopes each predicted to elicit an effective T-cell response in any individual regardless of their HLA I background. We implemented this epitope selection approach for free public use at the EPISOPT web server. © 2013 Magdalena Molero-Abraham et al.

Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation

Background: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome annotation. There have been several computational methods proposed in the literature to deal with the DNA-binding protein identification. However, most of them can't provide an invaluable knowledge base for our understanding of DNA-protein interactions. Results: We firstly presented a new protein sequence encoding method called PSSM Distance Transformation, and then constructed a DNA-binding protein identification method (SVM-PSSM-DT) by combining PSSM Distance Transformation with support vector machine (SVM). First, the PSSM profiles are generated by using the PSI-BLAST program to search the non-redundant (NR) database. Next, the PSSM profiles are transformed into uniform numeric representations appropriately by distance transformation scheme. Lastly, the resulting uniform numeric representations are inputted into a SVM classifier for prediction. Thus whether a sequence can bind to DNA or not can be determined. In benchmark test on 525 DNA-binding and 550 non DNA-binding proteins using jackknife validation, the present model achieved an ACC of 79.96%, MCC of 0.622 and AUC of 86.50%. This performance is considerably better than most of the existing state-of-the-art predictive methods. When tested on a recently constructed independent dataset PDB186, SVM-PSSM-DT also achieved the best performance with ACC of 80.00%, MCC of 0.647 and AUC of 87.40%, and outperformed some existing state-of-the-art methods. Conclusions: The experiment results demonstrate that PSSM Distance Transformation is an available protein sequence encoding method and SVM-PSSM-DT is a useful tool for identifying the DNA-binding proteins. A user-friendly web-server of SVM-PSSM-DT was constructed, which is freely accessible to the public at the web-site on http://bioinformatics.hitsz.edu.cn/PSSM-DT/.

PDNAsite:identification of DNA-binding site from protein sequence by incorporating spatial and sequence context

Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. Subsequently, Latent Semantic Analysis (LSA) was applied to remove the redundancies in the feature space. Finally, a predictor (PDNAsite) was developed through the integration of the support vector machines (SVM) classifier and ensemble learning. Results on the PDNA-62 and the PDNA-224 datasets demonstrate that features extracted from spatial context provide more information than those from sequence context and the combination of them gives more performance gain. An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. The comparison between our proposed PDNAsite method and the existing methods indicate that PDNAsite outperforms most of the existing methods and is a useful tool for DNA-binding site identification. A web-server of our predictor (http://hlt.hitsz.edu.cn:8080/PDNAsite/) is made available for free public accessible to the biological research community.

Internet Protocol Television (IPTV) controller realization with Very Large Scale Integration (VLSI) modules

Internet Protocol Television (IPTV) is a system where a digital television service is delivered by using Internet Protocol over a network infrastructure. There is considerable confusion and concern about the IPTV, since two different technologies have to be mended together to provide the end customers with some thing better than the conventional television. In this research, functional architecture of the IPTV system was investigated. Very Large Scale Integration based system for streaming server controller were designed and different ways of hosting a web server which can be used to send the control signals to the streaming server controller were studied. The web server accepts inputs from the keyboard and FPGA board switches and depending on the preset configuration the server will open a selected web page and also sends the control signals to the streaming server controller. It was observed that the applications run faster on PowerPC since it is embedded into the FPGA. Commercial market and Global deployment of IPTV were discussed.

Analytical approximations to predict performance measures of manufacturing systems with job failures and parallel processing

Parallel processing is prevalent in many manufacturing and service systems. Many manufactured products are built and assembled from several components fabricated in parallel lines. An example of this manufacturing system configuration is observed at a manufacturing facility equipped to assemble and test web servers. Characteristics of a typical web server assembly line are: multiple products, job circulation, and paralleling processing. The primary objective of this research was to develop analytical approximations to predict performance measures of manufacturing systems with job failures and parallel processing. The analytical formulations extend previous queueing models used in assembly manufacturing systems in that they can handle serial and different configurations of paralleling processing with multiple product classes, and job circulation due to random part failures. In addition, appropriate correction terms via regression analysis were added to the approximations in order to minimize the gap in the error between the analytical approximation and the simulation models. Markovian and general type manufacturing systems, with multiple product classes, job circulation due to failures, and fork and join systems to model parallel processing were studied. In the Markovian and general case, the approximations without correction terms performed quite well for one and two product problem instances. However, it was observed that the flow time error increased as the number of products and net traffic intensity increased. Therefore, correction terms for single and fork-join stations were developed via regression analysis to deal with more than two products. The numerical comparisons showed that the approximations perform remarkably well when the corrections factors were used in the approximations. In general, the average flow time error was reduced from 38.19% to 5.59% in the Markovian case, and from 26.39% to 7.23% in the general case. All the equations stated in the analytical formulations were implemented as a set of Matlab scripts. By using this set, operations managers of web server assembly lines, manufacturing or other service systems with similar characteristics can estimate different system performance measures, and make judicious decisions - especially setting delivery due dates, capacity planning, and bottleneck mitigation, among others.

Design of a dynamic e-commerce system with engineering applications

The primary purpose of this thesis was to design and develop a prototype e-commerce system where dynamic parameters are included in the decision-making process and execution of an online transaction. The system developed and implemented takes into account previous usage history, priority and associated engineering capabilities. The system was developed using three-tiered client server architecture. The interface was the Internet browser. The middle tiered web server was implemented using Active Server Pages, which form a link between the client system and other servers. A relational database management system formed the data component of the three-tiered architecture. It includes a capability for data warehousing which extracts needed information from the stored data of the customers as well as their orders. The system organizes and analyzes the data that is generated during a transaction to formulate a client's behavior model during and after a transaction. This is used for making decisions like pricing, order rescheduling during a client's forthcoming transaction. The system helps among other things to bring about predictability to a transaction execution process, which could be highly desirable in the current competitive scenario.