Advanced Islandora Workshop

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

Panel: Leveraging Agile & Resourcing for Success - Hydramata, Avalon, Fedora 4 and Islandora

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

Islandora Sync: Enabling Administrators and Developers

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

Service oriented archive based on Fedora Commons

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

Envia – a repository for environmental information access and discovery

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

How to Hack the DSpace Community

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

A museum object repository using LIDO schema

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

Large-eddy simulation of wind flows over complex terrains for wind energy applications

Wind energy has obtained outstanding expectations due to risks of global warming and nuclear energy production plant accidents. Nowadays, wind farms are often constructed in areas of complex terrain. A potential wind farm location must have the site thoroughly surveyed and the wind climatology analyzed before installing any hardware. Therefore, modeling of Atmospheric Boundary Layer (ABL) flows over complex terrains containing, e.g. hills, forest, and lakes is of great interest in wind energy applications, as it can help in locating and optimizing the wind farms. Numerical modeling of wind flows using Computational Fluid Dynamics (CFD) has become a popular technique during the last few decades. Due to the inherent flow variability and large-scale unsteadiness typical in ABL flows in general and especially over complex terrains, the flow can be difficult to be predicted accurately enough by using the Reynolds-Averaged Navier-Stokes equations (RANS). Large- Eddy Simulation (LES) resolves the largest and thus most important turbulent eddies and models only the small-scale motions which are more universal than the large eddies and thus easier to model. Therefore, LES is expected to be more suitable for this kind of simulations although it is computationally more expensive than the RANS approach. With the fast development of computers and open-source CFD software during the recent years, the application of LES toward atmospheric flow is becoming increasingly common nowadays. The aim of the work is to simulate atmospheric flows over realistic and complex terrains by means of LES. Evaluation of potential in-land wind park locations will be the main application for these simulations. Development of the LES methodology to simulate the atmospheric flows over realistic terrains is reported in the thesis. The work also aims at validating the LES methodology at a real scale. In the thesis, LES are carried out for flow problems ranging from basic channel flows to real atmospheric flows over one of the most recent real-life complex terrain problems, the Bolund hill. All the simulations reported in the thesis are carried out using a new OpenFOAM® -based LES solver. The solver uses the 4th order time-accurate Runge-Kutta scheme and a fractional step method. Moreover, development of the LES methodology includes special attention to two boundary conditions: the upstream (inflow) and wall boundary conditions. The upstream boundary condition is generated by using the so-called recycling technique, in which the instantaneous flow properties are sampled on aplane downstream of the inlet and mapped back to the inlet at each time step. This technique develops the upstream boundary-layer flow together with the inflow turbulence without using any precursor simulation and thus within a single computational domain. The roughness of the terrain surface is modeled by implementing a new wall function into OpenFOAM® during the thesis work. Both, the recycling method and the newly implemented wall function, are validated for the channel flows at relatively high Reynolds number before applying them to the atmospheric flow applications. After validating the LES model over simple flows, the simulations are carried out for atmospheric boundary-layer flows over two types of hills: first, two-dimensional wind-tunnel hill profiles and second, the Bolund hill located in Roskilde Fjord, Denmark. For the twodimensional wind-tunnel hills, the study focuses on the overall flow behavior as a function of the hill slope. Moreover, the simulations are repeated using another wall function suitable for smooth surfaces, which already existed in OpenFOAM® , in order to study the sensitivity of the flow to the surface roughness in ABL flows. The simulated results obtained using the two wall functions are compared against the wind-tunnel measurements. It is shown that LES using the implemented wall function produces overall satisfactory results on the turbulent flow over the two-dimensional hills. The prediction of the flow separation and reattachment-length for the steeper hill is closer to the measurements than the other numerical studies reported in the past for the same hill geometry. The field measurement campaign performed over the Bolund hill provides the most recent field-experiment dataset for the mean flow and the turbulence properties. A number of research groups have simulated the wind flows over the Bolund hill. Due to the challenging features of the hill such as the almost vertical hill slope, it is considered as an ideal experimental test case for validating micro-scale CFD models for wind energy applications. In this work, the simulated results obtained for two wind directions are compared against the field measurements. It is shown that the present LES can reproduce the complex turbulent wind flow structures over a complicated terrain such as the Bolund hill. Especially, the present LES results show the best prediction of the turbulent kinetic energy with an average error of 24.1%, which is a 43% smaller than any other model results reported in the past for the Bolund case. Finally, the validated LES methodology is demonstrated to simulate the wind flow over the existing Muukko wind farm located in South-Eastern Finland. The simulation is carried out only for one wind direction and the results on the instantaneous and time-averaged wind speeds are briefly reported. The demonstration case is followed by discussions on the practical aspects of LES for the wind resource assessment over a realistic inland wind farm.

Pipeline for macro- and microarray analyses

The pipeline for macro- and microarray analyses (PMmA) is a set of scripts with a web interface developed to analyze DNA array data generated by array image quantification software. PMmA is designed for use with single- or double-color array data and to work as a pipeline in five classes (data format, normalization, data analysis, clustering, and array maps). It can also be used as a plugin in the BioArray Software Environment, an open-source database for array analysis, or used in a local version of the web service. All scripts in PMmA were developed in the PERL programming language and statistical analysis functions were implemented in the R statistical language. Consequently, our package is a platform-independent software. Our algorithms can correctly select almost 90% of the differentially expressed genes, showing a superior performance compared to other methods of analysis. The pipeline software has been applied to 1536 expressed sequence tags macroarray public data of sugarcane exposed to cold for 3 to 48 h. PMmA identified thirty cold-responsive genes previously unidentified in this public dataset. Fourteen genes were up-regulated, two had a variable expression and the other fourteen were down-regulated in the treatments. These new findings certainly were a consequence of using a superior statistical analysis approach, since the original study did not take into account the dependence of data variability on the average signal intensity of each gene. The web interface, supplementary information, and the package source code are available, free, to non-commercial users at http://ipe.cbmeg.unicamp.br/pub/PMmA.

Nichesourcing The Uralic Languages For The Benefit Of Linguistic Research And Lingual Societies

The emerging technologies have recently challenged the libraries to reconsider their role as a mere mediator between the collections, researchers, and wider audiences (Sula, 2013), and libraries, especially the nationwide institutions like national libraries, haven’t always managed to face the challenge (Nygren et al., 2014). In the Digitization Project of Kindred Languages, the National Library of Finland has become a node that connects the partners to interplay and work for shared goals and objectives. In this paper, I will be drawing a picture of the crowdsourcing methods that have been established during the project to support both linguistic research and lingual diversity. The National Library of Finland has been executing the Digitization Project of Kindred Languages since 2012. The project seeks to digitize and publish approximately 1,200 monograph titles and more than 100 newspapers titles in various, and in some cases endangered Uralic languages. Once the digitization has been completed in 2015, the Fenno-Ugrica online collection will consist of 110,000 monograph pages and around 90,000 newspaper pages to which all users will have open access regardless of their place of residence. The majority of the digitized literature was originally published in the 1920s and 1930s in the Soviet Union, and it was the genesis and consolidation period of literary languages. This was the era when many Uralic languages were converted into media of popular education, enlightenment, and dissemination of information pertinent to the developing political agenda of the Soviet state. The ‘deluge’ of popular literature in the 1920s to 1930s suddenly challenged the lexical orthographic norms of the limited ecclesiastical publications from the 1880s onward. Newspapers were now written in orthographies and in word forms that the locals would understand. Textbooks were written to address the separate needs of both adults and children. New concepts were introduced in the language. This was the beginning of a renaissance and period of enlightenment (Rueter, 2013). The linguistically oriented population can also find writings to their delight, especially lexical items specific to a given publication, and orthographically documented specifics of phonetics. The project is financially supported by the Kone Foundation in Helsinki and is part of the Foundation’s Language Programme. One of the key objectives of the Kone Foundation Language Programme is to support a culture of openness and interaction in linguistic research, but also to promote citizen science as a tool for the participation of the language community in research. In addition to sharing this aspiration, our objective within the Language Programme is to make sure that old and new corpora in Uralic languages are made available for the open and interactive use of the academic community as well as the language societies. Wordlists are available in 17 languages, but without tokenization, lemmatization, and so on. This approach was verified with the scholars, and we consider the wordlists as raw data for linguists. Our data is used for creating the morphological analyzers and online dictionaries at the Helsinki and Tromsø Universities, for instance. In order to reach the targets, we will produce not only the digitized materials but also their development tools for supporting linguistic research and citizen science. The Digitization Project of Kindred Languages is thus linked with the research of language technology. The mission is to improve the usage and usability of digitized content. During the project, we have advanced methods that will refine the raw data for further use, especially in the linguistic research. How does the library meet the objectives, which appears to be beyond its traditional playground? The written materials from this period are a gold mine, so how could we retrieve these hidden treasures of languages out of the stack that contains more than 200,000 pages of literature in various Uralic languages? The problem is that the machined-encoded text (OCR) contains often too many mistakes to be used as such in research. The mistakes in OCRed texts must be corrected. For enhancing the OCRed texts, the National Library of Finland developed an open-source code OCR editor that enabled the editing of machine-encoded text for the benefit of linguistic research. This tool was necessary to implement, since these rare and peripheral prints did often include already perished characters, which are sadly neglected by the modern OCR software developers, but belong to the historical context of kindred languages and thus are an essential part of the linguistic heritage (van Hemel, 2014). Our crowdsourcing tool application is essentially an editor of Alto XML format. It consists of a back-end for managing users, permissions, and files, communicating through a REST API with a front-end interface—that is, the actual editor for correcting the OCRed text. The enhanced XML files can be retrieved from the Fenno-Ugrica collection for further purposes. Could the crowd do this work to support the academic research? The challenge in crowdsourcing lies in its nature. The targets in the traditional crowdsourcing have often been split into several microtasks that do not require any special skills from the anonymous people, a faceless crowd. This way of crowdsourcing may produce quantitative results, but from the research’s point of view, there is a danger that the needs of linguists are not necessarily met. Also, the remarkable downside is the lack of shared goal or the social affinity. There is no reward in the traditional methods of crowdsourcing (de Boer et al., 2012). Also, there has been criticism that digital humanities makes the humanities too data-driven and oriented towards quantitative methods, losing the values of critical qualitative methods (Fish, 2012). And on top of that, the downsides of the traditional crowdsourcing become more imminent when you leave the Anglophone world. Our potential crowd is geographically scattered in Russia. This crowd is linguistically heterogeneous, speaking 17 different languages. In many cases languages are close to extinction or longing for language revitalization, and the native speakers do not always have Internet access, so an open call for crowdsourcing would not have produced appeasing results for linguists. Thus, one has to identify carefully the potential niches to complete the needed tasks. When using the help of a crowd in a project that is aiming to support both linguistic research and survival of endangered languages, the approach has to be a different one. In nichesourcing, the tasks are distributed amongst a small crowd of citizen scientists (communities). Although communities provide smaller pools to draw resources, their specific richness in skill is suited for complex tasks with high-quality product expectations found in nichesourcing. Communities have a purpose and identity, and their regular interaction engenders social trust and reputation. These communities can correspond to research more precisely (de Boer et al., 2012). Instead of repetitive and rather trivial tasks, we are trying to utilize the knowledge and skills of citizen scientists to provide qualitative results. In nichesourcing, we hand in such assignments that would precisely fill the gaps in linguistic research. A typical task would be editing and collecting the words in such fields of vocabularies where the researchers do require more information. For instance, there is lack of Hill Mari words and terminology in anatomy. We have digitized the books in medicine, and we could try to track the words related to human organs by assigning the citizen scientists to edit and collect words with the OCR editor. From the nichesourcing’s perspective, it is essential that altruism play a central role when the language communities are involved. In nichesourcing, our goal is to reach a certain level of interplay, where the language communities would benefit from the results. For instance, the corrected words in Ingrian will be added to an online dictionary, which is made freely available for the public, so the society can benefit, too. This objective of interplay can be understood as an aspiration to support the endangered languages and the maintenance of lingual diversity, but also as a servant of ‘two masters’: research and society.

Current State of Ontology Matching. A Survey of Ontology and Schema Matching

Ontology matching is an important task when data from multiple data sources is integrated. Problems of ontology matching have been studied widely in the researchliterature and many different solutions and approaches have been proposed alsoin commercial software tools. In this survey, well-known approaches of ontologymatching, and its subtype schema matching, are reviewed and compared. The aimof this report is to summarize the knowledge about the state-of-the-art solutionsfrom the research literature, discuss how the methods work on different application domains, and analyze pros and cons of different open source and academic tools inthe commercial world.

Les logiciels libres sous l'angle de la responsabilité civile

Distribués sous des licences permissives qui assurent des droits d'utilisation, de modification et de redistribution aux licenciés, l'élaboration des logiciels libres est fondée sur un modèle de développement décentralisé. Ces caractéristiques posent de nombreux défis au milieu juridique, particulièrement en ce qui a trait à la responsabilité civile. Ainsi, les développeurs se demandent dans quelles circonstances leur responsabilité civile peut être engagée suite à la défaillance de leur logiciel libre. De la même façon, ils questionnent la possibilité d'appliquer cette responsabilité à un nombre important de développeurs dispersés aux quatre coins du globe. L'analyse présentée montre que le droit, tel qu'il existe actuellement, est en mesure de résoudre la majorité des problèmes relatifs à la détermination et l'application de la responsabilité civile en matière de logiciels libres. Les règles de la responsabilité civile représentent donc un risque potentiel pour les développeurs de logiciels libres, même s'ils sont relativement bien protégés par les contextes juridiques et factuels.

Développement logiciel par transformation de modèles

La recherche en génie logiciel a depuis longtemps tenté de mieux comprendre le processus de développement logiciel, minimalement, pour en reproduire les bonnes pratiques, et idéalement, pour pouvoir le mécaniser. On peut identifier deux approches majeures pour caractériser le processus. La première approche, dite transformationnelle, perçoit le processus comme une séquence de transformations préservant certaines propriétés des données à l’entrée. Cette idée a été récemment reprise par l’architecture dirigée par les modèles de l’OMG. La deuxième approche consiste à répertorier et à codifier des solutions éprouvées à des problèmes récurrents. Les recherches sur les styles architecturaux, les patrons de conception, ou les cadres d’applications s’inscrivent dans cette approche. Notre travail de recherche reconnaît la complémentarité des deux approches, notamment pour l’étape de conception: dans le cadre du développement dirigé par les modèles, nous percevons l’étape de conception comme l’application de patrons de solutions aux modèles reçus en entrée. Il est coutume de définir l’étape de conception en termes de conception architecturale, et conception détaillée. La conception architecturale se préoccupe d’organiser un logiciel en composants répondant à un ensemble d’exigences non-fonctionnelles, alors que la conception détaillée se préoccupe, en quelque sorte, du contenu de ces composants. La conception architecturale s’appuie sur des styles architecturaux qui sont des principes d’organisation permettant d’optimiser certaines qualités, alors que la conception détaillée s’appuie sur des patrons de conception pour attribuer les responsabilités aux classes. Les styles architecturaux et les patrons de conception sont des artefacts qui codifient des solutions éprouvées à des problèmes récurrents de conception. Alors que ces artefacts sont bien documentés, la décision de les appliquer reste essentiellement manuelle. De plus, les outils proposés n’offrent pas un support adéquat pour les appliquer à des modèles existants. Dans cette thèse, nous nous attaquons à la conception détaillée, et plus particulièrement, à la transformation de modèles par application de patrons de conception, en partie parce que les patrons de conception sont moins complexes, et en partie parce que l’implémentation des styles architecturaux passe souvent par les patrons de conception. Ainsi, nous proposons une approche pour représenter et appliquer les patrons de conception. Notre approche se base sur la représentation explicite des problèmes résolus par ces patrons. En effet, la représentation explicite du problème résolu par un patron permet : (1) de mieux comprendre le patron, (2) de reconnaître l’opportunité d’appliquer le patron en détectant une instance de la représentation du problème dans les modèles du système considéré, et (3) d’automatiser l’application du patron en la représentant, de façon déclarative, par une transformation d’une instance du problème en une instance de la solution. Pour vérifier et valider notre approche, nous l’avons utilisée pour représenter et appliquer différents patrons de conception et nous avons effectué des tests pratiques sur des modèles générés à partir de logiciels libres.

Système de listes de vérification interactives du niveau de conformité des maquettes avec les recommandations des fabricants de plateformes mobiles

L'ensemble de mon travail a été réalisé grâce a l'utilisation de logiciel libre.

Investigating the Impact of Personal, Temporal and Participation Factors on Code Review Quality

La révision du code est un procédé essentiel quelque soit la maturité d'un projet; elle cherche à évaluer la contribution apportée par le code soumis par les développeurs. En principe, la révision du code améliore la qualité des changements de code (patches) avant qu'ils ne soient validés dans le repertoire maître du projet. En pratique, l'exécution de ce procédé n'exclu pas la possibilité que certains bugs passent inaperçus. Dans ce document, nous présentons une étude empirique enquétant la révision du code d'un grand projet open source. Nous investissons les relations entre les inspections des reviewers et les facteurs, sur les plans personnel et temporel, qui pourraient affecter la qualité de telles inspections.Premiérement, nous relatons une étude quantitative dans laquelle nous utilisons l'algorithme SSZ pour détecter les modifications et les changements de code favorisant la création de bogues (bug-inducing changes) que nous avons lié avec l'information contenue dans les révisions de code (code review information) extraites du systéme de traçage des erreurs (issue tracking system). Nous avons découvert que les raisons pour lesquelles les réviseurs manquent certains bogues était corrélées autant à leurs caractéristiques personnelles qu'aux propriétés techniques des corrections en cours de revue. Ensuite, nous relatons une étude qualitative invitant les développeurs de chez Mozilla à nous donner leur opinion concernant les attributs favorables à la bonne formulation d'une révision de code. Les résultats de notre sondage suggèrent que les développeurs considèrent les aspects techniques (taille de la correction, nombre de chunks et de modules) autant que les caractéristiques personnelles (l'expérience et review queue) comme des facteurs influant fortement la qualité des revues de code.