QSAR modeling: um novo pacote computacional open source para gerar e validar modelos QSAR

QSAR modeling is a novel computer program developed to generate and validate QSAR or QSPR (quantitative structure- activity or property relationships) models. With QSAR modeling, users can build partial least squares (PLS) regression models, perform variable selection with the ordered predictors selection (OPS) algorithm, and validate models by using y-randomization and leave-N-out cross validation. An additional new feature is outlier detection carried out by simultaneous comparison of sample leverage with the respective Studentized residuals. The program was developed using Java version 6, and runs on any operating system that supports Java Runtime Environment version 6. The use of the program is illustrated. This program is available for download at lqta.iqm.unicamp.br.

Mobiilin työajanhallinnan ohjelmistokehitys

Työajan seuranta ja kohdistaminen oikeisiin kustannuslajeihin on yrityksen suorituskyvyn ja kasvun kannalta usein välttämättömyys. Tässä työssä tutkitaan mobiiliteknologioiden mahdollisuuksia ja soveltuvuutta tuottaa palveluita työajan hallinnointiin, valitaan sopiva arkkitehtuuri ja kehitetään Java ME –teknologialla prototyyppi, joka on helposti integroitavissa yrityksen nykyisiin palvelinpuolen järjestelmiin ja tietokantoihin. Työn sovellusosuudessa kuvataan prototyypin ohjelmoinnissa käytetyt työkalut, menetelmät, ongelmakohdat sekä niiden ratkaisut. Suunnitelluissa käyttötapauksissa tapahtumatiedot syötetään manuaalisesti puhelimen käyttöliittymän kautta tai automatisoidummin kerätään kustannuskohdistetietoa työkohteisiin sijoitetuista NFC-tageista. Työaikaleimaamista testattiin emulaattorilla ja oikealla matkapuhelimella. Lopputuloksena asiakkaan työajanhallinnan tapahtumat siirtyvät langattomasti ja reaaliaikaisesti yrityksen webpalvelimelle JSON-formaatissa.

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.

Perfis temporais NDVI MODIS, na cana-soca, de maturação tardia

Este artigo descreve o desenvolvimento de um banco de dados relacional e de uma ferramenta para a visualização de perfis temporais do NDVI MODIS, a partir dos dados do produto MOD09Q1, referente ao fator de refletância bidirecional de superfície relativa ao comprimento de onda do vermelho e do infravermelho-próximo, composição temporal em mosaicos de 8 dias, e a banda de controle de qualidade, dos talhões de cana-de-açúcar no Estado de São Paulo, para analisar a maturação da cana-soca Tardia. Das fazendas de cana-de-açúcar são obtidos os dados de históricos sobre produtividade, solo, variedade, localização de cada pixel para cada microrregião monitorada. Todos os dados são integrados em um banco de dados desenvolvido em PostgreSQL. O aplicativo foi implementado usando a linguagem Java e permitiu uma forma rápida e automática para analisar padrões fenológicos na cana-de-açúcar. Concluiu-se que o perfil temporal do NDVI MODIS obtido a partir do produto MOD09Q1 é capaz de subsidiar o monitoramento das mudanças fenológicas na cultura da cana-de-açúcar.

Analyyttista geometriaa GeoGebralla

GeoGebra on ilmainen, Java-pohjainen, dynaaminen matematiikkaohjelmisto, jossa geometriaan on yhdistetty algebraa, funktio-oppia sekä diferentiaali- ja integraalilaskentaa. Tämän tutkielman aiheena on matematiikkaohjelma GeoGebran käyttö lukion analyyttisen geometrian opetuksessa, jonka keskeisimpiä tavoitteita on saada oppilas ymmärtämään algebrallisten ja geometristen käsitteiden välisiä yhteyksiä. Lukion analyyttisen geometrian kurssin keskeisistä aihealueista on tässä tutkielmassa valittu käsiteltäviksi piste, suora ja jana koordinaatistossa sekä pistejoukon yhtälöt. Pistejoukon yhtälöistä tarkemmin käsitellään suorien ja kartioleikkausten yhtälöitä. Tutkielmassa esitellään GeoGebra-ohjelman käyttömahdollisuuksia analyyttisen geometrian opetuksessa ja laaditaan monipuolisia opetuskäyttöön soveltuvia dynaamisia GeoGebra-konstruktioita. Käsiteltyihin analyyttisen geometrian aiheisiin on laadittu myös harjoitustehtäviä ratkaisuineen. Kaikki GeoGebra-konstruktiot ovat vapaasti käytettävissä dynaamisina tiedostoina sekä liitteenä olevalla cd-rom-levyllä että osoitteessa https://sites.google. com/site/analyyttistageometriaageogebra/. Sähköinen materiaali on saatavilla sekä GeoGebran omassa tallennusmuodossa (.ggb) että html-muodossa. Html-tiedostot avautuvat Java-sovelluksina suoraan verkkoselaimeen, joten niiden käyttö on helppoa myös ilman erityistä GeoGebran käytön osaamista.

Warning system based on theoretical-experimental study of dispersion of soluble pollutants in rivers

Information about capacity of transport and dispersion of soluble pollutants in natural streams are important in the management of water resources, especially in planning preventive measures to minimize the problems caused by accidental or intentional waste, in public health and economic activities that depend on the use of water. Considering this importance, this study aimed to develop a warning system for rivers, based on experimental techniques using tracers and analytical equations of one-dimensional transport of soluble pollutants conservative, to subsidizing the decision-making in the management of water resources. The system was development in JAVA programming language and MySQL database can predict the travel time of pollutants clouds from a point of eviction and graphically displays the temporal distribution of concentrations of passage clouds, in a particular location, downstream from the point of its launch.

Social tagging within task management

Social tagging evolved in response to a need to tag heterogeneous objects, the automated tagging of which is usually not feasible by current technological means. Social tagging can be used for more flexible competence management within organizations. The profiles of employees can be built in the form of groups of tags, as employees tag each other, based on their familiarity of each other’s expertise. This can serve as a replacement for the more traditional competence management approaches, which usually become outdated due to social and organizational hurdles, and obsolete data. These limitations can be overcome by people tagging, as the information revealed by such tags is usually based on most recent employee interaction and knowledge. Task management as part of personal information management aims at the support of users’ individual task handling. This can include collaborating with other individuals, sharing one’s knowledge, both functional and process-related, and distributing documents and web resources. In this context, Task patterns can be used as templates that collect information and experience around tasks associated to it during run time, facilitating agility. The effective collaboration among contributors necessitates the means to find the appropriate individuals to work with on the task, and this can be made possible by using social tagging to describe individual competencies. The goal of this study is to support finding and tagging people within task management, through the effective exploitation of the work/task context. This involves the utilization of knowledge of the workers’ expertise, nature of the task/task pattern and information available from the documents and web resources attached to the task. Vice versa, task management provides an excellent environment for social tagging due to the task context that already provides suitable tags. The study also aims at assisting users of the task management solution with the collaborative construction of light-weight ontology by inferring semantic relations between tags. The thesis project aims at an implementation of people finding & tagging within the java application for task management that consumes web services, which provide the required ontology for the organization.

ANATI QUANTI: software de análises quantitativas para estudos em anatomia vegetal

Em diversos estudos interdisciplinares em que a Anatomia Vegetal é utilizada, análises quantitativas complementares são necessárias. Geralmente, a avaliação micromorfométrica é feita manualmente e/ou utilizando programas computacionais de análise de imagens não específicos. Este trabalho teve como objetivo desenvolver um programa específico para Anatomia Vegetal quantitativa e testar sua eficiência e aceitação por usuários. A solução foi elaborada na linguagem Java, visando maior mobilidade em relação ao sistema operacional a ser usado. O software desenvolvido foi denominado ANATI QUANTI e testado pelos alunos, pesquisadores e professores do Laboratório de Anatomia Vegetal da Universidade Federal de Viçosa (UFV). Todos os entrevistados receberam fotos para efetuarem medições no ANATI QUANTI e comparar com os resultados obtidos utilizando o software disponível. Os voluntários, através de questionários previamente formulados, destacaram as principais vantagens e desvantagens do programa desenvolvido em relação ao software disponível. Além de ser mais específico, simples e ágil do que o software disponível, o ANATI QUANTI é confiável, atendendo à expectativa dos entrevistados. Entretanto, há necessidade de acrescentar recursos adicionais, como a inserção de novas escalas, o que aumentaria a gama de usuários. O ANATI QUANTI já está em uso nas pesquisas desenvolvidas por usuários na UFV. Por ser um software livre e de código aberto, será disponibilizado na internet gratuitamente.

Kramerius - Fedora based open source system for a digital library

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

SimpleREST -RESTful DSpace API

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Natiivin Android-pelin käyttöliittymän skaalautuminen ja suorituskyvyn optimointi

Tässä työssä esiteltiin Android laitteisto- ja sovellusalustana sekä kuvattiin, kuinka Android-pelisovelluksen käyttöliittymä voidaan pitää yhtenäisenä eri näyttölaitteilla skaalauskertoimien ja ankkuroinnin avulla. Toisena osiona työtä käsiteltiin yksinkertaisia tapoja, joilla pelisovelluksien suorituskykyä voidaan parantaa. Näistä tarkempiin mittauksiin valittiin matalatarkkuuksinen piirtopuskuri ja näkymättömissä olevien kappaleiden piilotus. Mittauksissa valitut menetelmät vaikuttivat demosovelluksen suorituskykyyn huomattavasti. Tässä työssä rajauduttiin Android-ohjelmointiin Java-kielellä ilman ulkoisia kirjastoja, jolloin työn tuloksia voi helposti hyödyntää mahdollisimman monessa eri käyttökohteessa.

Developing an introductory object-oriented programming course

The state of the object-oriented programming course in Lappeenranta University of Technology had reached the point, where it required changes to provide better learning opportunities and thus the learning outcomes. Based on the student feedback the course was partially dated and ineffective. The components of the course were analysed and the ineffective elements were removed and new methods were introduced to improve the course. The major changes included the change from traditional teaching methods to reverse classroom method and the use of Java as the programming language. The changes were measured by the student feedback, lecturer’s observations and comparison to previous years. The feedback suggested that the changes were successful; the course received higher overall grade than before.

Implementation of Quantitative Reaction-based Model Refinement

Building a computational model for complex biological systems is an iterative process. It starts from an abstraction of the process and then incorporates more details regarding the specific biochemical reactions which results in the change of the model fit. Meanwhile, the model’s numerical properties such as its numerical fit and validation should be preserved. However, refitting the model after each refinement iteration is computationally expensive resource-wise. There is an alternative approach which ensures the model fit preservation without the need to refit the model after each refinement iteration. And this approach is known as quantitative model refinement. The aim of this thesis is to develop and implement a tool called ModelRef which does the quantitative model refinement automatically. It is both implemented as a stand-alone Java application and as one of Anduril framework components. ModelRef performs data refinement of a model and generates the results in two different well known formats (SBML and CPS formats). The development of this tool successfully reduces the time and resource needed and the errors generated as well by traditional reiteration of the whole model to perform the fitting procedure.

Telemedicina: Desenvolvimento de um sistema para atendimento à distância de pacientes com doença renal crônica pré-dialítica

ResumoIntrodução:O foco no tratamento da doença renal crônica (DRC) é evitar a sua progressão com o uso do controle clínico otimizado. O uso de tecnologias leves apresenta-se como forma promissora de cuidado em saúde. A internet oferece a oportunidade de instrumentalizar o médico em seu contato profissional com o usuário.Objetivo:Desenvolver um sistema web para o atendimento a distância de pacientes com DRC nos estágios não dialíticos e clinicamente estáveis.Métodos:Desenvolvido um sistema utilizando a linguagem Java, banco de dados MySQL e framework PrimeFaces; disponibilizado em um servidor de aplicações Glassfish.Resultados:O acesso inicial é realizado pelo nefrologista, que cadastra os pacientes com suas informações pessoais e dados de acesso. Após ser cadastrado, o paciente (ou médico de família) pode inserir os dados de sua consulta e estes serão, na sequência, repassados ao nefrologista para avaliação. O formulário com os dados de interesse é pré-determinado, mas ainda há possibilidade de acrescentar informações de forma livre. O sistema possibilita, adicionalmente, que haja troca de mensagens entre os médicos e os pacientes. Além disso, os usuários recebem mensagens via e-mail alertando-os de suas tarefas. O sigilo é garantido por senhas individuais para médicos e pacientes.Conclusão:Essa ferramenta possibilitará aumentar a área de abrangência dos nefrologistas, diminuir os custos e aproximar o paciente ao seu médico da atenção básica, utilizando o Programa de Saúde de Família como interface entre o paciente e a atenção secundária nefrológica.

Measuring software security from the design of software

The vast majority of our contemporary society owns a mobile phone, which has resulted in a dramatic rise in the amount of networked computers in recent years. Security issues in the computers have followed the same trend and nearly everyone is now affected by such issues. How could the situation be improved? For software engineers, an obvious answer is to build computer software with security in mind. A problem with building software with security is how to define secure software or how to measure security. This thesis divides the problem into three research questions. First, how can we measure the security of software? Second, what types of tools are available for measuring security? And finally, what do these tools reveal about the security of software? Measuring tools of these kind are commonly called metrics. This thesis is focused on the perspective of software engineers in the software design phase. Focus on the design phase means that code level semantics or programming language specifics are not discussed in this work. Organizational policy, management issues or software development process are also out of the scope. The first two research problems were studied using a literature review while the third was studied using a case study research. The target of the case study was a Java based email server called Apache James, which had details from its changelog and security issues available and the source code was accessible. The research revealed that there is a consensus in the terminology on software security. Security verification activities are commonly divided into evaluation and assurance. The focus of this work was in assurance, which means to verify one’s own work. There are 34 metrics available for security measurements, of which five are evaluation metrics and 29 are assurance metrics. We found, however, that the general quality of these metrics was not good. Only three metrics in the design category passed the inspection criteria and could be used in the case study. The metrics claim to give quantitative information on the security of the software, but in practice they were limited to evaluating different versions of the same software. Apart from being relative, the metrics were unable to detect security issues or point out problems in the design. Furthermore, interpreting the metrics’ results was difficult. In conclusion, the general state of the software security metrics leaves a lot to be desired. The metrics studied had both theoretical and practical issues, and are not suitable for daily engineering workflows. The metrics studied provided a basis for further research, since they pointed out areas where the security metrics were necessary to improve whether verification of security from the design was desired.