Student's watcher : comparison between ASP.NET and PHP+CSS

"Student’s Watcher” is a small Web application which wants to show in a visual, simple and fast way, the evolution of the students. The main project table displays such things as marks and comments about students. We can add a comment for each mark to explain why this mark. The objective is to be able to know if some student has a problem, how is going his year, marks in other courses, or even, to know if he has a bad week in a different subjects. We can see the evolution of students in past years to do an objective comparison. It also allows inserting global comments of student, we have a list of these, and all professors can add new ones, where we can see more general valuations. “Student’s Watcher” was begun in ASP.net, but finally my project would be developed in PHP, HTML and CSS. This project wants to be a comparison between two of most important languages used nowadays, ASPX and PHP

Aplicatiu web per la gestió de l’Associació Cultural Pubills

S'ha creat un aplicatiu web autogestionable per a l'Associació Cultural Pubills de Valls de Torroella que millora l’existent. El nou aplicatiu disposa de noves funcionalitats com el fòrum, notícies, secció d’arxius multimèdia i botiga virtual. L'aplicatiu ha estat desenvolupat des de zero utilitzant programari lliure i els principals llenguatges de programació web actuals. Projecte disponible a http://www.pubills.com.

Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'.

Background: The variety of DNA microarray formats and datasets presently available offers an unprecedented opportunity to perform insightful comparisons of heterogeneous data. Cross-species studies, in particular, have the power of identifying conserved, functionally important molecular processes. Validation of discoveries can now often be performed in readily available public data which frequently requires cross-platform studies.Cross-platform and cross-species analyses require matching probes on different microarray formats. This can be achieved using the information in microarray annotations and additional molecular biology databases, such as orthology databases. Although annotations and other biological information are stored using modern database models ( e. g. relational), they are very often distributed and shared as tables in text files, i.e. flat file databases. This common flat database format thus provides a simple and robust solution to flexibly integrate various sources of information and a basis for the combined analysis of heterogeneous gene expression profiles.Results: We provide annotationTools, a Bioconductor-compliant R package to annotate microarray experiments and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file databases. First, annotationTools contains a specialized set of functions for mining this widely used database format in a systematic manner. It thus offers a straightforward solution for annotating microarray experiments. Second, building on these basic functions and relying on the combination of information from several databases, it provides tools to easily perform cross-species analyses of gene expression data.Here, we present two example applications of annotationTools that are of direct relevance for the analysis of heterogeneous gene expression profiles, namely a cross-platform mapping of probes and a cross-species mapping of orthologous probes using different orthology databases. We also show how to perform an explorative comparison of disease-related transcriptional changes in human patients and in a genetic mouse model.Conclusion: The R package annotationTools provides a simple solution to handle microarray annotation and orthology tables, as well as other flat molecular biology databases. Thereby, it allows easy integration and analysis of heterogeneous microarray experiments across different technological platforms or species.

MyHits: improvements to an interactive resource for analyzing protein sequences.

The MyHits web site (http://myhits.isb-sib.ch) is an integrated service dedicated to the analysis of protein sequences. Since its first description in 2004, both the user interface and the back end of the server were improved. A number of tools (e.g. MAFFT, Jacop, Dotlet, Jalview, ESTScan) were added or updated to improve the usability of the service. The MySQL schema and its associated API were revamped and the database engine (HitKeeper) was separated from the web interface. This paper summarizes the current status of the server, with an emphasis on the new services.

Gestió d'un portal web d'intercanvi de coneixement

En aquest món on ens ha tocat viure i patir canvis tan durs amb la crisi econòmica que patim, que ens ha fet passar de lligar els gossos amb llonganisses a vigilar en les despeses del dia a dia per poder arribar just a final de mes, és el moment de reinventar-se. És per aquest motiu que presento aquesta idea, on el seu objectiu és desenvolupar una pàgina web que esdevingui un punt de trobada entre usuaris que volen transmetre o ampliar el seu coneixement i oferir-los la possibilitat que entre ells puguin compartir les seves habilitats i destreses. El web consistirà en un panell d’activitats on els usuaris un cop s’hagin registrat puguin crear les activitats que vulguin aprendre o bé ensenyar, tot demanant, si ho desitgen, quelcom a canvi. Aleshores la resta d’usuaris si els interessa l’activitat, poden acceptar la demanda o bé fer una proposta pròpia. A partir d’aquí els usuaris s’han de posar d’acord a l’hora de dur a terme l’activitat. El web disposarà d’una part pels usuaris amb permisos d’administrador perquè puguin gestionar el portal. Aquest projecte s’ha desenvolupat amb el framework de PHP Codeigniter, el qual utilitza la programació per capes MVC, la qual separa la programació en tres parts: el Model, la Vista i el Controlador. També s’han utilitzat els llenguatges HTML5 i CSS3, i jQuery, que és una llibreria de JavaScript. Com a sistema gestor de base de dades s’ha utilitzat el MySQL.

EuroPhenome: a repository for high-throughput mouse phenotyping data.

The broad aim of biomedical science in the postgenomic era is to link genomic and phenotype information to allow deeper understanding of the processes leading from genomic changes to altered phenotype and disease. The EuroPhenome project (http://www.EuroPhenome.org) is a comprehensive resource for raw and annotated high-throughput phenotyping data arising from projects such as EUMODIC. EUMODIC is gathering data from the EMPReSSslim pipeline (http://www.empress.har.mrc.ac.uk/) which is performed on inbred mouse strains and knock-out lines arising from the EUCOMM project. The EuroPhenome interface allows the user to access the data via the phenotype or genotype. It also allows the user to access the data in a variety of ways, including graphical display, statistical analysis and access to the raw data via web services. The raw phenotyping data captured in EuroPhenome is annotated by an annotation pipeline which automatically identifies statistically different mutants from the appropriate baseline and assigns ontology terms for that specific test. Mutant phenotypes can be quickly identified using two EuroPhenome tools: PhenoMap, a graphical representation of statistically relevant phenotypes, and mining for a mutant using ontology terms. To assist with data definition and cross-database comparisons, phenotype data is annotated using combinations of terms from biological ontologies.

Taajuusmuuttajan ohjelmiston testaus

Tämän diplomityön tavoitteena oli kehittää menetelmiä ja ohjeitataajuusmuuttajan sulautetun ohjelmiston kehityksen aikaiseen testaukseen. Soveltuvia menetelmiä etsittiin tutkimalla laajasti kirjallisuutta sekä selvittämälläyrityksen testauskäytäntöä. Tutkittuja kirjallisuudesta löytyneitä menetelmä olivat testauskehykset, simulointi ja staattinen sekä automaattinen testaus. Kirjallisuudesta etsittiin myös menetelmiä, joiden avulla testausprosessia voidaan helpottaa tai muuten parantaa. Tällaisista menetelmistä tutkittiin muun muassa testidatan valintaa, testauslähtöistä kehitystä sekä testattavuuden parantamista. Lisäksi selvitettiin uudelleenkäytettävien testien ohjelmointiin soveltuvia ohjelmointikieliä. Haastatteluiden ja dokumentaation avulla saatiin hyvä käsitys yrityksessä vallitsevasta testauskäytännöstä sekä sen ongelmakohdista. Testauksen ongelmiksi havaittiin testausprosessin järjestelmällisyyden puute sekä tarve suunnittelijoiden testauskoulutukseen. Testausprosessin parantamiseksi esitetään moduulitestauskehyksen käyttöönottoa. Lisäksi suunnittelijoiden testauskoulutuksella arvioidaan olevan suuri vaikutus koko testausprosessiin. Testitapausten suunnitteluun esitetään menetelmiä, joiden avulla voidaan suunnitella kattavampia testejä.

Protection of publicly distributed software components

The nature of client-server architecture implies that some modules are delivered to customers. These publicly distributed commercial software components are under risk, because users (and simultaneously potential malefactors) have physical access to some components of the distributed system. The problem becomes even worse if interpreted programming languages are used for creation of client side modules. The language Java, which was designed to be compiled into platform independent byte-code is not an exception and runs the additional risk. Along with advantages like verifying the code before execution (to ensure that program does not produce some illegal operations)Java has some disadvantages. On a stage of byte-code a java program still contains comments, line numbers and some other instructions, which can be used for reverse-engineering. This Master's thesis focuses on protection of Java code based client-server applications. I present a mixture of methods to protect software from tortious acts. Then I shall realize all the theoretical assumptions in a practice and examine their efficiency in examples of Java code. One of the criteria's to evaluate the system is that my product is used for specialized area of interactive television.

Implementació de programari de pràctiques d'introducció a la química quàntica i d'introducció a la programació en live CDs utilitzables pels alumnes fora de les aules

L'objectiu d'aquest projecte és desenvolupar live CDs per tal de facilitar als alumnes de les assignatures obligatòries del Departament de Química Física que inclouen pràctiques amb ordinadors el treball fora de les aules, com a complement del realitzar durant les sessions de pràctiques.

Tuning Performance of Multi-threaded programs

Diplomityö tarkastelee säikeistettyä ohjelmointia rinnakkaisohjelmoinnin ylemmällä hierarkiatasolla tarkastellen erityisesti hypersäikeistysteknologiaa. Työssä tarkastellaan hypersäikeistyksen hyviä ja huonoja puolia sekä sen vaikutuksia rinnakkaisalgoritmeihin. Työn tavoitteena oli ymmärtää Intel Pentium 4 prosessorin hypersäikeistyksen toteutus ja mahdollistaa sen hyödyntäminen, missä se tuo suorituskyvyllistä etua. Työssä kerättiin ja analysoitiin suorituskykytietoa ajamalla suuri joukko suorituskykytestejä eri olosuhteissa (muistin käsittely, kääntäjän asetukset, ympäristömuuttujat...). Työssä tarkasteltiin kahdentyyppisiä algoritmeja: matriisioperaatioita ja lajittelua. Näissä sovelluksissa on säännöllinen muistinkäyttökuvio, mikä on kaksiteräinen miekka. Se on etu aritmeettis-loogisissa prosessoinnissa, mutta toisaalta huonontaa muistin suorituskykyä. Syynä siihen on nykyaikaisten prosessorien erittäin hyvä raaka suorituskyky säännöllistä dataa käsiteltäessä, mutta muistiarkkitehtuuria rajoittaa välimuistien koko ja useat puskurit. Kun ongelman koko ylittää tietyn rajan, todellinen suorituskyky voi pudota murto-osaan huippusuorituskyvystä.

A System-Level Simulation Model for a Protocol Processor

As the development of integrated circuit technology continues to follow Moore’s law the complexity of circuits increases exponentially. Traditional hardware description languages such as VHDL and Verilog are no longer powerful enough to cope with this level of complexity and do not provide facilities for hardware/software codesign. Languages such as SystemC are intended to solve these problems by combining the powerful expression of high level programming languages and hardware oriented facilities of hardware description languages. To fully replace older languages in the desing flow of digital systems SystemC should also be synthesizable. The devices required by modern high speed networks often share the same tight constraints for e.g. size, power consumption and price with embedded systems but have also very demanding real time and quality of service requirements that are difficult to satisfy with general purpose processors. Dedicated hardware blocks of an application specific instruction set processor are one way to combine fast processing speed, energy efficiency, flexibility and relatively low time-to-market. Common features can be identified in the network processing domain making it possible to develop specialized but configurable processor architectures. One such architecture is the TACO which is based on transport triggered architecture. The architecture offers a high degree of parallelism and modularity and greatly simplified instruction decoding. For this M.Sc.(Tech) thesis, a simulation environment for the TACO architecture was developed with SystemC 2.2 using an old version written with SystemC 1.0 as a starting point. The environment enables rapid design space exploration by providing facilities for hw/sw codesign and simulation and an extendable library of automatically configured reusable hardware blocks. Other topics that are covered are the differences between SystemC 1.0 and 2.2 from the viewpoint of hardware modeling, and compilation of a SystemC model into synthesizable VHDL with Celoxica Agility SystemC Compiler. A simulation model for a processor for TCP/IP packet validation was designed and tested as a test case for the environment.

Gestió d'un portal web d'intercanvi de coneixement

En aquest món on ens ha tocat viure i patir canvis tan durs amb la crisi econòmica que patim, que ens ha fet passar de lligar els gossos amb llonganisses a vigilar en les despeses del dia a dia per poder arribar just a final de mes, és el moment de reinventar-se. És per aquest motiu que presento aquesta idea, on el seu objectiu és desenvolupar una pàgina web que esdevingui un punt de trobada entre usuaris que volen transmetre o ampliar el seu coneixement i oferir-los la possibilitat que entre ells puguin compartir les seves habilitats i destreses. El web consistirà en un panell d’activitats on els usuaris un cop s’hagin registrat puguin crear les activitats que vulguin aprendre o bé ensenyar, tot demanant, si ho desitgen, quelcom a canvi. Aleshores la resta d’usuaris si els interessa l’activitat, poden acceptar la demanda o bé fer una proposta pròpia. A partir d’aquí els usuaris s’han de posar d’acord a l’hora de dur a terme l’activitat. El web disposarà d’una part pels usuaris amb permisos d’administrador perquè puguin gestionar el portal. Aquest projecte s’ha desenvolupat amb el framework de PHP Codeigniter, el qual utilitza la programació per capes MVC, la qual separa la programació en tres parts: el Model, la Vista i el Controlador. També s’han utilitzat els llenguatges HTML5 i CSS3, i jQuery, que és una llibreria de JavaScript. Com a sistema gestor de base de dades s’ha utilitzat el MySQL.

Introducing Continuous Integration for C and C++ Software Development Projects on Linux Platform

Software integration is a stage in a software development process to assemble separate components to produce a single product. It is important to manage the risks involved and being able to integrate smoothly, because software cannot be released without integrating it first. Furthermore, it has been shown that the integration and testing phase can make up 40 % of the overall project costs. These issues can be mitigated by using a software engineering practice called continuous integration. This thesis work presents how continuous integration is introduced to the author's employer organisation. This includes studying how the continuous integration process works and creating the technical basis to start using the process on future projects. The implemented system supports software written in C and C++ programming languages on Linux platform, but the general concepts can be applied to any programming language and platform by selecting the appropriate tools. The results demonstrate in detail what issues need to be solved when the process is acquired in a corporate environment. Additionally, they provide an implementation and process description suitable to the organisation. The results show that continuous integration can reduce the risks involved in a software process and increase the quality of the product as well.

Pilvisovelluskehitys Google App Engine -pilvisovellusalustalla

Tämä Diplomityö keskittyy tutkimaan pilvisovelluskehitystä Google App Engine – pilvisovellusalustalle perustuen kuusi –vaiheiseen vesiputousmalliin sekä tutkimaan Google App Engine -pilvisovellusalustan tarjoamia mahdollisuuksia ja rajoituksia sovelluskehityksen muodossa. Tutkimuksen perusteella kuusi –vaiheinen vesiputousmalli soveltuu pilvisovelluskehitykseen,mikäli vaatimusmäärittely on tarkka jo sovelluskehityksen alkuvaiheessa. Tutkimuksen tuloksena syntyi vaatimusmäärittely MikkoMail –pilvisovellukselle. Vaatimusmäärittelyn pohjalta luotiin MikkoMail –pilvisovellus Google App Engine –pilvisovellusalustalle. Google App Engine –pilvisovellusalusta tukee vain Python- ja Java –ohjelmointikieliä eikä sisällä lainkaan ulkoista tietokantapalveluiden tukea. Tästä syystä Google App Engine -pilvisovellusalusta soveltuu pieniin, keskisuuriin ja pilottiprojektinomaisiin sovelluskehitysprojekteihin.

Cohesion Metrics for Improving Software Quality

Abstract Software product metrics aim at measuring the quality of software. Modu- larity is an essential factor in software quality. In this work, metrics related to modularity and especially cohesion of the modules, are considered. The existing metrics are evaluated, and several new alternatives are proposed. The idea of cohesion of modules is that a module or a class should consist of related parts. The closely related principle of coupling says that the relationships between modules should be minimized. First, internal cohesion metrics are considered. The relations that are internal to classes are shown to be useless for quality measurement. Second, we consider external relationships for cohesion. A detailed analysis using design patterns and refactorings confirms that external cohesion is a better quality indicator than internal. Third, motivated by the successes (and problems) of external cohesion metrics, another kind of metric is proposed that represents the quality of modularity of software. This metric can be applied to refactorings related to classes, resulting in a refactoring suggestion system. To describe the metrics formally, a notation for programs is developed. Because of the recursive nature of programming languages, the properties of programs are most compactly represented using grammars and formal lan- guages. Also the tools that were used for metrics calculation are described.