Sustaining your Open Source project through training: a Hydra case study

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

Building Successful, Open Repository Software Ecosystems: Technology and Community

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

Tarvitaanko verkkodokumenttien kuvailussa käsityötä? : osa 2 : tietoyhteisöt ja suodatusmekanismit

Summary

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.

AVR-pohjainen mobiilirobotti

Kandidaatintyön aineena oli rakentaa autonomisesti pyörillä liikkuva, esteitä väistelevä mobiilirobotti käyttäen Arduino-kehitysympäristöä prototyypin valmistamiseen. Rakensin robotin alusta alkaen itse eli työhön sisältyi robotin mekaniikan kokoaminen, elektroniikan suunnittelu ja rakentaminen sekä toimintaälyn ohjelmointi mikroprosessorille eteenpäin kulkemiseen ja esteiden väistämiseen. Arduinon ytimenä on Atmelin AVR-sarjaan kuuluva ATMega328-mikroprosessori. Robotin ympäristön havainnointi tapahtuu käyttämällä ultraäänisensoria. Robotti oli mielenkiintoinen projekti toteuttaa ja toimi kokonaisuutena katsottuna odotetulla tavalla.

Panossyöttökasvatusprosessin automatisointi

Tutkimuskäyttöön tarkoitettujen rekombinanttiproteiinien tuottaminen fermentoimalla on yleinen menetelmä bioteollisuudessa. Mikrobit kasvatetaan fermentorissa, joka tarjoaa kontrolloidun kasvuympäristön ja sopivat tuotto-olosuhteet halutulle tuotteelle. Eräs fermentointimuodoista on korkeatuottoinen ja pitkäkestoinen panossyöttökasvatus, jossa saavutetaan panoskavatusta merkittävästi korkeampi solutiheys jatkamalla panosvaiheen jälkeen kasvua rajoittavan substraatin syöttöä. Laboratoriomittakaavassa fermentorikasvatusten tilavuudet vaihtelevat litrasta kymmeniin ja niissä kasvatusta seurataan sekä ohjataan joko fermentorista tai tietokoneesta. Tyypillisessä fermentointiprosessissa operaattori tarkkailee muun muassa vaahdonkorkeutta sekä käynnistää pumppuja olosuhteiden muuttuessa. Tällaiset tehtävät ovat teollisen mittakaavan laitteistoissa usein automatisoituja. Diplomityön tarkoituksena oli päivittää kahden Turun yliopiston biotekniikan laboratoriossa sijaitsevan BioFlo® -sarjan pöytäfermentorin MS-DOS -pohjainen tietokoneohjausohjelma nykyaikaiseksi ja lisätä siihen etäseuranta ja -ohjaus. Ohjelmaan oli tarkoitus liittää erillinen optinen solutiheysanturi, jonka lukemien häiriötä haluttiin myös vähentää signaalinkäsittelyllä. Lisäksi vaahdonestoaineen ja indusorin lisäykset haluttiin automatisoida panossyöttökasvatuksessa. Vaahdonkorkeuden havaitsemisen mahdollisuutta konenäön menetelmin haluttiin selvittää, jotta vaahdonestoaineen automaattiset lisäykset voitaisiin toteuttaa nettikameran syötteen perusteella. Koekasvatuksilla osoitettiin päivitetyn ohjausohjelman toimivan panos- ja panossyöttömuodoilla. Uuden käyttöliittymän avulla pystyttiin automatisoimaan panoskasvatuksen lisäykset ja syöttönopeuden muutokset sekä tunnistamaan kasvatusliuosten vaahdonkorkeutta vaahdonestoaineen lisäykseen riittävällä kahden senttimetrin tarkkuudella. Lisäksi käyttöliittymä mahdollisti kasvatuksen ohjauksen ja seurauksen myös etänä. Työssä kehitetty ohjausohjelma julkaistiin avoimena ohjelmana ilman etä- ja nettikameratoimintoja. Ohjelma toimii hyvin BioFlo® -sarjan fermentorien käyttöliittymänä, mutta avoimen lähdekoodin ansiosta kuka tahansa voi hyödyntää ohjelmaa pohjana myös uusissa projekteissa tai muissa fermentorimalleissa.

Project for Active and Robot Vision Course

Tässä työssä raportoidaan harjoitustyön kehittäminen ja toteuttaminen Aktiivisen- ja robottinäön kurssille. Harjoitustyössä suunnitellaan ja toteutetaan järjestelmä joka liikuttaa kappaleita robottikäsivarrella kolmiuloitteisessa avaruudessa. Kappaleidenpaikkojen määrittämiseen järjestelmä käyttää digitaalisia kuvia. Tässä työssä esiteltävässä harjoitustyötoteutuksessa käytettiin raja-arvoistusta HSV-väriavaruudessa kappaleiden segmentointiin kuvasta niiden värien perusteella. Segmentoinnin tuloksena saatavaa binäärikuvaa suodatettiin mediaanisuotimella kuvan häiriöiden poistamiseksi. Kappaleen paikkabinäärikuvassa määritettiin nimeämällä yhtenäisiä pikseliryhmiä yhtenäisen alueen nimeämismenetelmällä. Kappaleen paikaksi määritettiin suurimman nimetyn pikseliryhmän paikka. Kappaleiden paikat kuvassa yhdistettiin kolmiuloitteisiin koordinaatteihin kalibroidun kameran avulla. Järjestelmä liikutti kappaleita niiden arvioitujen kolmiuloitteisten paikkojen perusteella.

Making the impact on research and society: a case study - open repository and crowdsourcing solutions developed for the Finno-Ugric Digitization Pilot Project at the National Library of Finland

Jussi-Pekka Hakkaraisen esitys 24. Kansainvälisessä tieteen-, teknologian ja lääketieteen historian kongressissa (24th International Congress of History of Science, Technology and Medicine) Manchesterissa 26.7.2013

Project Success through Effective Decisions: Case Studies on Project Goal Setting, Success Evaluation and Managerial Decision Making

The objective of the thesis is to structure and model the factors that contribute to and can be used in evaluating project success. The purpose of this thesis is to enhance the understanding of three research topics. The goal setting process, success evaluation and decision-making process are studied in the context of a project, business unitand its business environment. To achieve the objective three research questionsare posed. These are 1) how to set measurable project goals, 2) how to evaluateproject success and 3) how to affect project success with managerial decisions.The main theoretical contribution comes from deriving a synthesis of these research topics which have mostly been discussed apart from each other in prior research. The research strategy of the study has features from at least the constructive, nomothetical, and decision-oriented research approaches. This strategy guides the theoretical and empirical part of the study. Relevant concepts and a framework are composed on the basis of the prior research contributions within the problem area. A literature review is used to derive constructs of factors withinthe framework. They are related to project goal setting, success evaluation, and decision making. On the basis of this, the case study method is applied to complement the framework. The empirical data includes one product development program, three construction projects, as well as one organization development, hardware/software, and marketing project in their contexts. In two of the case studiesthe analytic hierarchy process is used to formulate a hierarchical model that returns a numerical evaluation of the degree of project success. It has its origin in the solution idea which in turn has its foundation in the notion of projectsuccess. The achieved results are condensed in the form of a process model thatintegrates project goal setting, success evaluation and decision making. The process of project goal setting is analysed as a part of an open system that includes a project, the business unit and its competitive environment. Four main constructs of factors are suggested. First, the project characteristics and requirements are clarified. The second and the third construct comprise the components of client/market segment attractiveness and sources of competitive advantage. Together they determine the competitive position of a business unit. Fourth, the relevant goals and the situation of a business unit are clarified to stress their contribution to the project goals. Empirical evidence is gained on the exploitation of increased knowledge and on the reaction to changes in the business environment during a project to ensure project success. The relevance of a successful project to a company or a business unit tends to increase the higher the reference level of project goals is set. However, normal performance or sometimes performance below this normal level is intentionally accepted. Success measures make project success quantifiable. There are result-oriented, process-oriented and resource-oriented success measures. The study also links result measurements to enablers that portray the key processes. The success measures can be classified into success domains determining the areas on which success is assessed. Empiricalevidence is gained on six success domains: strategy, project implementation, product, stakeholder relationships, learning situation and company functions. However, some project goals, like safety, can be assessed using success measures that belong to two success domains. For example a safety index is used for assessing occupational safety during a project, which is related to project implementation. Product safety requirements, in turn, are connected to the product characteristics and thus to the product-related success domain. Strategic success measures can be used to weave the project phases together. Empirical evidence on their static nature is gained. In order-oriented projects the project phases are oftencontractually divided into different suppliers or contractors. A project from the supplier's perspective can represent only a part of the ¿whole project¿ viewed from the client's perspective. Therefore static success measures are mostly used within the contractually agreed project scope and duration. Proof is also acquired on the dynamic use of operational success measures. They help to focus on the key issues during each project phase. Furthermore, it is shown that the original success domains and success measures, their weights and target values can change dynamically. New success measures can replace the old ones to correspond better with the emphasis of the particular project phase. This adjustment concentrates on the key decision milestones. As a conclusion, the study suggests a combination of static and dynamic success measures. Their linkage to an incentive system can make the project management proactive, enable fast feedback and enhancethe motivation of the personnel. It is argued that the sequence of effective decisions is closely linked to the dynamic control of project success. According to the used definition, effective decisions aim at adequate decision quality and decision implementation. The findings support that project managers construct and use a chain of key decision milestones to evaluate and affect success during aproject. These milestones can be seen as a part of the business processes. Different managers prioritise the key decision milestones to a varying degree. Divergent managerial perspectives, power, responsibilities and involvement during a project offer some explanation for this. Finally, the study introduces the use ofHard Gate and Soft Gate decision milestones. The managers may use the former milestones to provide decision support on result measurements and ad hoc critical conditions. In the latter milestones they may make intermediate success evaluation also on the basis of other types of success measures, like process and resource measures.

Designing a modular, open and expandable Bluetooth-platform

Lähitulevaisuudessa langattomien järjestelmien kaupalliset mahdollisuudet tulevat olemaan valtavia. Tutkiaksemme tulevia tarpeita, tässä diplomityössä esitellään kuinka voidaan suunnitella ja toteuttaa avoin langaton asiakas-palvelin järjestelmä. Järjestelmänä päätettiin käyttää Bluetooth:ia. Tutkituista langattomista standardeista Bluetooth sopii parhaiten akkukäyttöiselle laitteelle, jonka tulee olla monipuolinen. Lisäksi Bluetooth:iin on liitetty suuria kaupallisia odotuksia ja yksi työn tavoitteista olikin tutkia, ovatko nämä odotukset realistisia. Bluetooth:iin havaittiin liittyvän paljon ylimainontaa ja, sen todettiin olevan monimutkainen. Sillä on kuitenkin paljon ominaisuuksia ja erilaisten käyttöprofiilien avulla sitä voidaan käyttää monenlaisiin tehtäviin. Suunniteltu järjestelmä ajaa socket-palvelinta Bluetooth-yhteyden päällä. Tietyntyyppiseen liikenteeseen erikoistuneet socket:t tarjoavat vaaditun laajennattavuuden. Palvelin toteutetiin Linux-säikeenä ja se hallitsee Bluetooth protokollapinoa sekä sovelluksia, joita suoritetaan palvelimella. Näiden sovelluksien palvelut ovat muiden käytössä Bluetooth:n kautta.

Knowledge creation and transfer in an iterative project environment

This Master’s Thesis examines knowledge creation and transfer processes in an iterative project environment. The aim is to understand how knowledge is created and transferred during an actual iterative implementation project which takes place in International Business Machines (IBM). The second aim is to create and develop new working methods that support more effective knowledge creation and transfer for future iterative implementation projects. The research methodology in this thesis is qualitative. Using focus group interviews as a research method provides qualitative information and introduces the experiences of the individuals participating in the project. This study found that the following factors affect knowledge creation and transfer in an iterative, multinational, and multi-organizational implementation project: shared vision and common goal, trust, open communication, social capital, and network density. All of these received both theoretical and empirical support. As for future projects, strengthening these factors was found to be the key for more effective knowledge creation and transfer.

Novel Robot Solutions for Carrying out Field Joint Welding and Machining in the Assembly of the Vacuum Vessel of ITER

It is necessary to use highly specialized robots in ITER (International Thermonuclear Experimental Reactor) both in the manufacturing and maintenance of the reactor due to a demanding environment. The sectors of the ITER vacuum vessel (VV) require more stringent tolerances than normally expected for the size of the structure involved. VV consists of nine sectors that are to be welded together. The vacuum vessel has a toroidal chamber structure. The task of the designed robot is to carry the welding apparatus along a path with a stringent tolerance during the assembly operation. In addition to the initial vacuum vessel assembly, after a limited running period, sectors need to be replaced for repair. Mechanisms with closed-loop kinematic chains are used in the design of robots in this work. One version is a purely parallel manipulator and another is a hybrid manipulator where the parallel and serial structures are combined. Traditional industrial robots that generally have the links actuated in series are inherently not very rigid and have poor dynamic performance in high speed and high dynamic loading conditions. Compared with open chain manipulators, parallel manipulators have high stiffness, high accuracy and a high force/torque capacity in a reduced workspace. Parallel manipulators have a mechanical architecture where all of the links are connected to the base and to the end-effector of the robot. The purpose of this thesis is to develop special parallel robots for the assembly, machining and repairing of the VV of the ITER. The process of the assembly and machining of the vacuum vessel needs a special robot. By studying the structure of the vacuum vessel, two novel parallel robots were designed and built; they have six and ten degrees of freedom driven by hydraulic cylinders and electrical servo motors. Kinematic models for the proposed robots were defined and two prototypes built. Experiments for machine cutting and laser welding with the 6-DOF robot were carried out. It was demonstrated that the parallel robots are capable of holding all necessary machining tools and welding end-effectors in all positions accurately and stably inside the vacuum vessel sector. The kinematic models appeared to be complex especially in the case of the 10-DOF robot because of its redundant structure. Multibody dynamics simulations were carried out, ensuring sufficient stiffness during the robot motion. The entire design and testing processes of the robots appeared to be complex tasks due to the high specialization of the manufacturing technology needed in the ITER reactor, while the results demonstrate the applicability of the proposed solutions quite well. The results offer not only devices but also a methodology for the assembly and repair of ITER by means of parallel robots.

Trolley R&D project for a small portal log yard crane

This master’s thesis was done for Andritz Inc. Atlanta Georgia. The purpose of the thesis was to develop a new trolley for a small portal log yard crane. In the beginning of the thesis the basic principles of the systematic design processes have been described, along which the design work of the trolley has proceeded. The second literature part consists of the design and dimensioning of the welded steel structures under fatigue loading. The design work of the trolley consists of the engineering and the selection of the mechanical components and the design of the load carrying structure for the trolley. The realization of the steel structure of the trolley is based on the fatigue and static dimensioning. The fatigue dimensioning is grounded in the life expectations estimated for the trolley and the static dimensioning is based on the CMAA guidelines. The computer aided element method was utilized in the design of the steel structure. The effective notch method and the hot spot method were used in the fatigue calculations. The trolley structure was carried out by using the sheet metal parts in order to manufacture the structure as effective and low cost way as possible. The corner stone of the dimensioning of the trolley structure was the utilization of the open profiles made of welded or cold formed sheet metals, which provide better weldability, weld inspection, access for repairs and corrosion protection. As a last part of the thesis a new trolley traveling system was developed. The distribution of the wheel loads of the trolley bogies on the main girder was also studied, which led to an innovative suspension arrangement between the trolley leg and the bogie. The new bogie solution increases the service life of the main girder of the crane and improves the stability of the bogies. The outcome of the thesis is an excellent trolley structure from the weight and the service life point of view.

Smart homes as service platforms. Research report of ÄLYKOP sub-project “Competitive advantage from customer value”

In this report, we summarize results of our part of the ÄLYKOP-project on customer value creation in the intersection of the health care, ICT, forest and energy industries. The research directs to describe how industry transformation and convergence create new possibilities, business opportunities and even new industries.The report consists of findings which are presented former in academic publications. The publication discusses on customer value, service provision and resource basis of the novel concepts through multiple theorethical frameworks. The report is divided into three maim sections which are theoretical background, discussion on health care industry and evaluations regarding novel smart home concepts. Transaction cost economics and Resource- Based view on the firm provides the theoretical basis to analyze the prescribed phenomena. The health care industry analysis describes the most important changes in the demand conditions of health care services, and explores the features that are likely to open new business opportunities for a solution provider. The third part of the report on the smart home business provides illustrations few potential concepts that can be considered to provide solutions to economical problems which arise from aging of population. The results provide several recommendations for the smart home platform developers in public and private sectors. By the analysis, public organizations dominate service provision and private markets are emergent state at present. We argue that public-private partnerships are nececssary for creating key suppliers. Indeed, paying attion on appropriate regulation, service specifications and technology standards would foster diffusion of new services. The dynamics of the service provision networks is driven by need for new capabiltities which are required for adapting business concepts to new competitive situation. Finally, the smart home framework revealed links between conventionally distant business areas such as health care and energy distribution. The platform integrates functionalities different for purposes which however apply same resource basis.