Raise All Ships: Cooperative Repository Strategies in a Boot-Strap Culture

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

DSpace-CRIS tutorial

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

INSPIRE: contributions to Invenio from the leading High Energy Physics (HEP) platform

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

APIs and Datasets everywhere

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

Biomedical Event Extraction with Machine Learning

Biomedical natural language processing (BioNLP) is a subfield of natural language processing, an area of computational linguistics concerned with developing programs that work with natural language: written texts and speech. Biomedical relation extraction concerns the detection of semantic relations such as protein-protein interactions (PPI) from scientific texts. The aim is to enhance information retrieval by detecting relations between concepts, not just individual concepts as with a keyword search. In recent years, events have been proposed as a more detailed alternative for simple pairwise PPI relations. Events provide a systematic, structural representation for annotating the content of natural language texts. Events are characterized by annotated trigger words, directed and typed arguments and the ability to nest other events. For example, the sentence “Protein A causes protein B to bind protein C” can be annotated with the nested event structure CAUSE(A, BIND(B, C)). Converted to such formal representations, the information of natural language texts can be used by computational applications. Biomedical event annotations were introduced by the BioInfer and GENIA corpora, and event extraction was popularized by the BioNLP'09 Shared Task on Event Extraction. In this thesis we present a method for automated event extraction, implemented as the Turku Event Extraction System (TEES). A unified graph format is defined for representing event annotations and the problem of extracting complex event structures is decomposed into a number of independent classification tasks. These classification tasks are solved using SVM and RLS classifiers, utilizing rich feature representations built from full dependency parsing. Building on earlier work on pairwise relation extraction and using a generalized graph representation, the resulting TEES system is capable of detecting binary relations as well as complex event structures. We show that this event extraction system has good performance, reaching the first place in the BioNLP'09 Shared Task on Event Extraction. Subsequently, TEES has achieved several first ranks in the BioNLP'11 and BioNLP'13 Shared Tasks, as well as shown competitive performance in the binary relation Drug-Drug Interaction Extraction 2011 and 2013 shared tasks. The Turku Event Extraction System is published as a freely available open-source project, documenting the research in detail as well as making the method available for practical applications. In particular, in this thesis we describe the application of the event extraction method to PubMed-scale text mining, showing how the developed approach not only shows good performance, but is generalizable and applicable to large-scale real-world text mining projects. Finally, we discuss related literature, summarize the contributions of the work and present some thoughts on future directions for biomedical event extraction. This thesis includes and builds on six original research publications. The first of these introduces the analysis of dependency parses that leads to development of TEES. The entries in the three BioNLP Shared Tasks, as well as in the DDIExtraction 2011 task are covered in four publications, and the sixth one demonstrates the application of the system to PubMed-scale text mining.

Replikoitavan palvelinjärjestelmän toteuttaminen julkisen liikenteen avoimen datan jakeluun

Tässä diplomityössä tutkittiin, miten toteuttaa replikoitava palvelinjärjestelmä julkisen liikenteen avoimen datan jakeluun. Tutkimuksessa selvitettiin, onko vastaavanlaisia järjestelmiä suunniteltu aiemmin, vai pitääkö järjestelmä suunnitella itse. Projektissa käytettiin avoimen lähdekoodin OneBusAway-ohjelmistokokonaisuutta. Projektin avulla osoitettiin, että kyseinen ohjelmisto toimi yliopiston testikäytössä hyvin. Ohjelmiston avulla pystytään jakelemaan staattista ja reaaliaikaista dataa, ja se on replikoitavissa kunnasta toiseen maailmanlaajuisesti. Tulevaisuudessa olisi kuitenkin hyvä selvittää, miten ohjelmistosta puuttuva reittihakuominaisuus kannattaisi toteuttaa, sekä olisiko REST- rajapinta mahdollista muuttaa sellaiseksi, että se noudattaisi julkisen liikenteen standardeja.

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.

pp-Blast: a "pseudo-parallel" Blast

We have developed a software called pp-Blast that uses the publicly available Blast package and PVM (parallel virtual machine) to partition a multi-sequence query across a set of nodes with replicated or shared databases. Benchmark tests show that pp-Blast running in a cluster of 14 PCs outperformed conventional Blast running in large servers. In addition, using pp-Blast and the cluster we were able to map all human cDNAs onto the draft of the human genome in less than 6 days. We propose here that the cost/benefit ratio of pp-Blast makes it appropriate for large-scale sequence analysis. The source code and configuration files for pp-Blast are available at http://www.ludwig.org.br/biocomp/tools/pp-blast.

Sulautetun ohjausjärjestelmän kehittäminen 3D-tulostimelle

Kandidaatintyössä tutkittiin Adam Klodowskin tutkimuksessa käytetyn menetelmän soveltuvuutta 3D-tulostimen mekanismiin. Tutkimustyö liittyy RepRap-projektiin, jonka tavoitteena on valmistaa 3D-tulostin 3D-tulostetuista osista. Mekaniikasta oli luotu matemaattinen malli, jota tutkittiin simuloinnin avulla. Työssä toteutettiin täysin yksilöity sulautettu ohjausjärjestelmä kyseiselle mekanismille ja tutkittiin järjestelmän soveltuvuutta käytäntöön. Tavoitteena oli vähentää komponenttien lukumäärää ja pienentää laitteiston vaatimaa tilaa.

CloudSimDisk: Energy-Aware Storage Simulation in CloudSim

Cloud Computing paradigm is continually evolving, and with it, the size and the complexity of its infrastructure. Assessing the performance of a Cloud environment is an essential but strenuous task. Modeling and simulation tools have proved their usefulness and powerfulness to deal with this issue. This master thesis work contributes to the development of the widely used cloud simulator CloudSim and proposes CloudSimDisk, a module for modeling and simulation of energy-aware storage in CloudSim. As a starting point, a review of Cloud simulators has been conducted and hard disk drive technology has been studied in detail. Furthermore, CloudSim has been identified as the most popular and sophisticated discrete event Cloud simulator. Thus, CloudSimDisk module has been developed as an extension of CloudSim v3.0.3. The source code has been published for the research community. The simulation results proved to be in accordance with the analytic models, and the scalability of the module has been presented for further development.

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.

Tekemisen meininki: Suomalainen maker-kulttuuri

Tutkimuksen tavoitteena on selvittää, millaista on kansainvälinen tekemisen alakulttuuri, jota kutsutaan nimellä maker, ja miten se toteutuu Suomessa. Maker -kulttuuri on 2000-luvulla syntynyt itse tekemisen alakulttuuri, jossa hyödynnetään ennakkoluulottomasti kehittynyttä teknologiaa, avoimia työtiloja sekä kansainvälistä virtuaalista ja fyysistä yhteisöä. Pyrkimyksenä on kuvailla ja kartoittaa ilmiötä, josta ei aikaisemmin ole tehty tutkimusta Suomessa. Tutkimuksen viitekehyksessä kansainvälinen maker-kulttuuri sijoitetaan perinteisen käsityöprosessin ympäristöihin. Teoria rakentuu maker-kulttuurin kansainvälisestä tutkimuksesta ja suomalaisesta käsityötutkimuksesta. Tutkimusote on fenomenografinen ja aineistonkeruumenetelmänä käytettiin teemahaastattelua. Tutkimuksessa haastateltiin yhtätoista (11) maker-kulttuurin asiantuntijaa. Aineisto analysoitiin aineistolähtöisellä sisällönanalyysillä. Suomalaisesta maker- kulttuurista nousi tutkimuksessa esiin kolme keskeistä näkökulmaa: 1. Yhteisö vahvistaa sosiaalista pääomaa, levittää osaamista sekä jakaa käsityöllisen prosessin. 2. Avoimet työtilat, informaatioteknologian yleistyminen sekä modernin tuotantoteknologian kehittyminen ja halventuminen ovat luoneet ympäristön, jossa maker-kulttuuri kasvaa ja kehittyy. 3. Oppiminen ja henkilökohtainen kompetenssi ovat keskeisiä kokonaisen käsityöprosessin osatekijöitä. Oma-aloitteisuutta ja yrittämistä arvostetaan, ja niitä vahvistetaan vertaistuella. Teknologisen pystyvyyden kehittäminen ja osaamisen jakaminen ovat keskeisiä tavoitteita. Tämän tutkimuksen tulosten mukaan suomalaisessa maker-kulttuurissa teknologista kompetenssia, sen vahvistamista ja jakamista arvostetaan. Muualla maailmassa teknologista kompetenssia pidetään enemmänkin lähtökohtana ja itseisarvona, jonka kautta maker-kulttuurista kiinnostutaan. Tulevaa valtakunnallista perusopetuksen opetussuunnitelmauudistusta 2016 silmällä pitäen jatkotutkimusta voisi tehdä peruskoulun käsityönopetuksen ja maker -kulttuurin kohtaamisesta sekä maker-kulttuurista ilmiölähtöisen oppimisen kenttänä. Asiasanat: maker, hackerspace, makerspace, FabLab,hacker, open source, avoimet työtilat, digitaalinen valmistaminen, digital fabrication, kokonainen käsityö

Fusion of Data from Quadcopter’s Inertial Measurement Unit Using Complementary Filter

A quadcopter is a helicopter with four rotors, which is mechanically simple device, but requires complex electrical control for each motor. Control system needs accurate information about quadcopter’s attitude in order to achieve stable flight. The goal of this bachelor’s thesis was to research how this information could be obtained. Literature review revealed that most of the quadcopters, whose source-code is available, use a complementary filter or some derivative of it to fuse data from a gyroscope, an accelerometer and often also a magnetometer. These sensors combined are called an Inertial Measurement Unit. This thesis focuses on calculating angles from each sensor’s data and fusing these with a complementary filter. On the basis of literature review and measurements using a quadcopter, the proposed filter provides sufficiently accurate attitude data for flight control system. However, a simple complementary filter has one significant drawback – it works reliably only when the quadcopter is hovering or moving at a constant speed. The reason is that an accelerometer can’t be used to measure angles accurately if linear acceleration is present. This problem can be fixed using some derivative of a complementary filter like an adaptive complementary filter or a Kalman filter, which are not covered in this thesis.

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.