The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692-1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.

Trust region versus line search for computing the optical flow

We consider the numerical treatment of the optical flow problem by evaluating the performance of the trust region method versus the line search method. To the best of our knowledge, the trust region method is studied here for the first time for variational optical flow computation. Four different optical flow models are used to test the performance of the proposed algorithm combining linear and nonlinear data terms with quadratic and TV regularization. We show that trust region often performs better than line search; especially in the presence of non-linearity and non-convexity in the model.

Effects of computing parameters and measurement locations on the estimation of 3D NPS in non-stationary MDCT images.

The goal of this study was to investigate the impact of computing parameters and the location of volumes of interest (VOI) on the calculation of 3D noise power spectrum (NPS) in order to determine an optimal set of computing parameters and propose a robust method for evaluating the noise properties of imaging systems. Noise stationarity in noise volumes acquired with a water phantom on a 128-MDCT and a 320-MDCT scanner were analyzed in the spatial domain in order to define locally stationary VOIs. The influence of the computing parameters in the 3D NPS measurement: the sampling distances bx,y,z and the VOI lengths Lx,y,z, the number of VOIs NVOI and the structured noise were investigated to minimize measurement errors. The effect of the VOI locations on the NPS was also investigated. Results showed that the noise (standard deviation) varies more in the r-direction (phantom radius) than z-direction plane. A 25 × 25 × 40 mm(3) VOI associated with DFOV = 200 mm (Lx,y,z = 64, bx,y = 0.391 mm with 512 × 512 matrix) and a first-order detrending method to reduce structured noise led to an accurate NPS estimation. NPS estimated from off centered small VOIs had a directional dependency contrary to NPS obtained from large VOIs located in the center of the volume or from small VOIs located on a concentric circle. This showed that the VOI size and location play a major role in the determination of NPS when images are not stationary. This study emphasizes the need for consistent measurement methods to assess and compare image quality in CT.

Computational and Energy Costs of Cryptographic Algorithms on Handheld Devices

Networks are evolving toward a ubiquitous model in which heterogeneousdevices are interconnected. Cryptographic algorithms are required for developing securitysolutions that protect network activity. However, the computational and energy limitationsof network devices jeopardize the actual implementation of such mechanisms. In thispaper, we perform a wide analysis on the expenses of launching symmetric and asymmetriccryptographic algorithms, hash chain functions, elliptic curves cryptography and pairingbased cryptography on personal agendas, and compare them with the costs of basic operatingsystem functions. Results show that although cryptographic power costs are high and suchoperations shall be restricted in time, they are not the main limiting factor of the autonomyof a device.

ZigBee/ZigBee PRO security assessment based on compromised cryptographic keys

Sensor networks have many applications in monitoring and controlling of environmental properties such as sound, acceleration, vibration and temperature. Due to limitedresources in computation capability, memory and energy, they are vulnerable to many kinds of attacks. The ZigBee specification based on the 802.15.4 standard, defines a set of layers specifically suited to sensor networks. These layers support secure messaging using symmetric cryptographic. This paper presents two different ways for grabbing the cryptographic key in ZigBee: remote attack and physical attack. It also surveys and categorizes some additional attacks which can be performed on ZigBee networks: eavesdropping, spoofing, replay and DoS attacks at different layers. From this analysis, it is shown that some vulnerabilities still in the existing security schema in ZigBee technology.

Evaluation of performance analysis software for Linux computing cluster

Tietokonejärjestelmän osien ja ohjelmistojen suorituskykymittauksista saadaan tietoa,jota voidaan käyttää suorituskyvyn parantamiseen ja laitteistohankintojen päätöksen tukena. Tässä työssä tutustutaan suorituskyvyn mittaamiseen ja mittausohjelmiin eli ns. benchmark-ohjelmistoihin. Työssä etsittiin ja arvioitiin eri tyyppisiä vapaasti saatavilla olevia benchmark-ohjelmia, jotka soveltuvat Linux-laskentaklusterin suorituskyvynanalysointiin. Benchmarkit ryhmiteltiin ja arvioitiin testaamalla niiden ominaisuuksia Linux-klusterissa. Työssä käsitellään myös mittausten tekemisen ja rinnakkaislaskennan haasteita. Benchmarkkeja löytyi moneen tarkoitukseen ja ne osoittautuivat laadultaan ja laajuudeltaan vaihteleviksi. Niitä on myös koottu ohjelmistopaketeiksi, jotta laitteiston suorituskyvystä saisi laajemman kuvan kuin mitä yhdellä ohjelmalla on mahdollista saada. Olennaista on ymmärtää nopeus, jolla dataa saadaan siirretyä prosessorille keskusmuistista, levyjärjestelmistä ja toisista laskentasolmuista. Tyypillinen benchmark-ohjelma sisältää paljon laskentaa tarvitsevan matemaattisen algoritmin, jota käytetään tieteellisissä ohjelmistoissa. Benchmarkista riippuen tulosten ymmärtäminen ja hyödyntäminen voi olla haasteellista.

Algorithms and cryptographic protocols using elliptic curves

En els darrers anys, la criptografia amb corbes el.líptiques ha adquirit una importància creixent, fins a arribar a formar part en la actualitat de diferents estàndards industrials. Tot i que s'han dissenyat variants amb corbes el.líptiques de criptosistemes clàssics, com el RSA, el seu màxim interès rau en la seva aplicació en criptosistemes basats en el Problema del Logaritme Discret, com els de tipus ElGamal. En aquest cas, els criptosistemes el.líptics garanteixen la mateixa seguretat que els construïts sobre el grup multiplicatiu d'un cos finit primer, però amb longituds de clau molt menor. Mostrarem, doncs, les bones propietats d'aquests criptosistemes, així com els requeriments bàsics per a que una corba sigui criptogràficament útil, estretament relacionat amb la seva cardinalitat. Revisarem alguns mètodes que permetin descartar corbes no criptogràficament útils, així com altres que permetin obtenir corbes bones a partir d'una de donada. Finalment, descriurem algunes aplicacions, com són el seu ús en Targes Intel.ligents i sistemes RFID, per concloure amb alguns avenços recents en aquest camp.

Coscheduling techniques and monitoring tools for non-dedicated cluster computing

Our efforts are directed towards the understanding of the coscheduling mechanism in a NOW system when a parallel job is executed jointly with local workloads, balancing parallel performance against the local interactive response. Explicit and implicit coscheduling techniques in a PVM-Linux NOW (or cluster) have been implemented. Furthermore, dynamic coscheduling remains an open question when parallel jobs are executed in a non-dedicated Cluster. A basis model for dynamic coscheduling in Cluster systems is presented in this paper. Also, one dynamic coscheduling algorithm for this model is proposed. The applicability of this algorithm has been proved and its performance analyzed by simulation. Finally, a new tool (named Monito) for monitoring the different queues of messages in such an environments is presented. The main aim of implementing this facility is to provide a mean of capturing the bottlenecks and overheads of the communication system in a PVM-Linux cluster.

Teaching fundamentals of computing theory: a constructivist approach

A Fundamentals of Computing Theory course involves different topics that are core to the Computer Science curricula and whose level of abstraction makes them difficult both to teach and to learn. Such difficulty stems from the complexity of the abstract notions involved and the required mathematical background. Surveys conducted among our students showed that many of them were applying some theoretical concepts mechanically rather than developing significant learning. This paper shows a number of didactic strategies that we introduced in the Fundamentals of Computing Theory curricula to cope with the above problem. The proposed strategies were based on a stronger use of technology and a constructivist approach. The final goal was to promote more significant learning of the course topics.

Soft Computing Methods in Metallurgy

In metallurgic plants a high quality metal production is always required. Nowadays soft computing applications are more often used for automation of manufacturing process and quality control instead of mechanical techniques. In this thesis an overview of soft computing methods presents. As an example of soft computing application, an effective model of fuzzy expert system for the automotive quality control of steel degassing process was developed. The purpose of this work is to describe the fuzzy relations as quality hypersurfaces by varying number of linguistic variables and fuzzy sets.

Evolutionary computing in search-based software engineering

This master’s thesis aims to study and represent from literature how evolutionary algorithms are used to solve different search and optimisation problems in the area of software engineering. Evolutionary algorithms are methods, which imitate the natural evolution process. An artificial evolution process evaluates fitness of each individual, which are solution candidates. The next population of candidate solutions is formed by using the good properties of the current population by applying different mutation and crossover operations. Different kinds of evolutionary algorithm applications related to software engineering were searched in the literature. Applications were classified and represented. Also the necessary basics about evolutionary algorithms were presented. It was concluded, that majority of evolutionary algorithm applications related to software engineering were about software design or testing. For example, there were applications about classifying software production data, project scheduling, static task scheduling related to parallel computing, allocating modules to subsystems, N-version programming, test data generation and generating an integration test order. Many applications were experimental testing rather than ready for real production use. There were also some Computer Aided Software Engineering tools based on evolutionary algorithms.

Use of scenario analysis in studying emerging technology – Case Grid computing

Tutkimuksen selvitettiin miten skenaarioanalyysia voidaan käyttää uuden teknologian tutkimisessa. Työssä havaittiin, että skenaarioanalyysin soveltuvuuteen vaikuttaa eniten teknologisen muutoksen taso ja saatavilla olevan tiedon luonne. Skenaariomenetelmä soveltuu hyvin uusien teknologioiden tutkimukseen erityisesti radikaalien innovaatioiden kohdalla. Syynä tähän on niihin liittyvä suuri epävarmuus, kompleksisuus ja vallitsevan paradigman muuttuminen, joiden takia useat muut tulevaisuuden tutkimuksen menetelmät eivät ole tilanteessa käyttökelpoisia. Työn empiirisessä osiossa tutkittiin hilaverkkoteknologian tulevaisuutta skenaarioanalyysin avulla. Hilaverkot nähtiin mahdollisena disruptiivisena teknologiana, joka radikaalina innovaationa saattaa muuttaa tietokonelaskennan nykyisestä tuotepohjaisesta laskentakapasiteetin ostamisesta palvelupohjaiseksi. Tällä olisi suuri vaikutus koko nykyiseen ICT-toimialaan erityisesti tarvelaskennan hyödyntämisen ansiosta. Tutkimus tarkasteli kehitystä vuoteen 2010 asti. Teorian ja olemassa olevan tiedon perusteella muodostettiin vahvaan asiantuntijatietouteen nojautuen neljä mahdollista ympäristöskenaariota hilaverkoille. Skenaarioista huomattiin, että teknologian kaupallinen menestys on vielä monen haasteen takana. Erityisesti luottamus ja lisäarvon synnyttäminen nousivat tärkeimmiksi hilaverkkojen tulevaisuutta ohjaaviksi tekijöiksi.

Trust region versus line search for computing the optical flow

We consider the numerical treatment of the optical flow problem by evaluating the performance of the trust region method versus the line search method. To the best of our knowledge, the trust region method is studied here for the first time for variational optical flow computation. Four different optical flow models are used to test the performance of the proposed algorithm combining linear and nonlinear data terms with quadratic and TV regularization. We show that trust region often performs better than line search; especially in the presence of non-linearity and non-convexity in the model.