Technological advancements in mass spectrometry allowing quantification of almost complete proteomes make proteomics a key platform for generating unique functional molecular data. Furthermore, the integrative analysis of genomic and proteomic data, termed proteogenomics, has emerged as a new field revealing insights into gene expression regulation, cell signalling, and disease processes. However, the lack of software tools for high-throughput integration and unbiased modification and variant detection hinder efforts for large-scale proteogenomics studies. The main objectives of this work are to address these issues by developing and applying new software tools and data analysis methods. Firstly, I address mapping of peptide sequences to reference genomes. I introduce a novel tool for high-throughput mapping and highlight its unique features facilitating quantitative and post-translational modification mapping alongside accounting for amino acid substitutions. The performance is benchmarked. Furthermore, I offer an additional tool that permits generation of web accessible hubs of genome wide mappings. To enable unbiased identification of post-translational modifications and amino acid substitutions for high resolution mass spectrometry data, I present algorithmic updates the mass tolerant blind spectrum comparison tool ’MS SMiV’. I demonstrate the applicability of the changes by benchmarking against a published mass tolerant database search of a high resolution tandem mass spectrometry dataset. I then present the application of ‘MS SMiV’ on a panel of 50 colorectal cancer cell lines. I show that the adaption of ‘MS SMiV’ outperforms traditional sequence database based identification of single amino acid variants. Furthermore, I highlight the utility of mass tolerant spectrum matching in combination with isobaric labelled quantitative proteomics in distinguishing between post-translational modifications and amino acid variants of similar mass. In the last part of this work I integrate both tools with a high-throughput proteogenomic identification pipeline and apply it to a pilot study of chondrocytes derived from 12 osteoarthritic individuals. I show the value of this approach in identifying variation between individuals and molecular levels and highlight them with individual examples. I show that multi-plexed proteogenomics can be used to infer genotypes of individuals.

A presente tese tem como objetivo produzir subsídios para a construção de um referencial teórico-metodológico sobre a utilização dos objetos de aprendizagem no contexto das comunidades virtuais auto-organizadas para a produção de software livre e de código aberto. Utiliza-se como metodologia a etnografia virtual (HINE, 2000) em conjunto com a teoria analítica da ação mediada (WERTSCH, 1991) e a análise de conteúdo (BARDIN, 2000). A coleta de dados foi efetuada, em duas fases, nos fóruns de discussão de quatro (4) comunidades, além de uma comunidade incubadora de desenvolvimento de projetos de software livre e de código aberto. Constata-se que os objetos de aprendizagem mediam o processo de solução de problemas, uma vez que 100% dos problemas da amostra analisada foram resolvidos, apesar da ausência de um padrão de conformidade desses objetos. Esta limitação é superada em razão do perfil específico imperante dos membros ativos da comunidade, pois estes possuem elevado nível de comportamento colaborativo/cooperativo, iniciativa voluntária, desprendimento, obstinação, capacidade de autoaprendizagem, autonomia, independência, disciplina, responsabilidade e comprometimento com prazos, qualidade dos produtos e outras exigências estabelecidas pela comunidade. Outro fator de relevância é que as comunidades são ricas em interação humana, o que qualifica o processo do significado da mediação e o ambiente de colaboração, nas ações referentes à localização, montagem e contextualização dos objetos de aprendizagem. Os significativos resultados atingidos por estas comunidades têm impactado, sobremaneira, as grandes organizações de produção de software, levando-as a rever suas estratégias corporativas, boas práticas de desenvolvimento, gestão de pessoas, equipes e projetos. Por outro lado, infere-se que a sustentabilidade de tais comunidades não pode estar assentada somente em atributos e habilidades pessoais, principalmente pelo fato de que a localização dos objetos de aprendizagem para a solução de problemas baseia-se no conhecimento tácito de seus membros. Necessário se faz agregar inovações na forma e funcionalidade de tais comunidades (padrão de conformidade, métodos e ferramentas tecnológicas), com vistas a possibilitar uma efetiva e universal acessibilidade do conhecimento produzido para a solução mais eficiente dos problemas, bem como incorporar membros com comportamentos e habilidades diversos. Os resultados desta pesquisa contribuem para as inovações futuras, no campo teórico e prático, na definição de um padrão de conformidade para a especificação, indexação, uso, combinação e avaliação dos objetos de aprendizagem, além de motivar a mudança de comportamento, cultura e forma de aprender. / The present thesis aims to produce subsidies for the development of a theoreticalmethodological referential on the use of learning objects in the context of self-organized virtual communities for the development of free and open source software. The methodologies used were the virtual ethnography (HINE, 2000), together with the mediated action analytical theory (WERTSCH, 1991) and content analysis (BARDIN, 2000). Data was collected in two phases: from the discussion forums of (4) four communities, and from an incubator community for the development of free and open source software projects. The learning objects appear to mediate the problem solution processes, since all the problems of the analyzed sample were solved, despite the lack of a standard of compliance of those objects. This limitation is overcome due to the specific dominant profile of the active members of the community, who display a high level of collaborative behavior, voluntary initiative, detachment, obstinacy, auto-learning capacity, autonomy, independence, discipline, responsibility and commitment to deadlines, product quality and other requirements established by the community. Another relevant aspect is that the communities are abundant in human interaction, what qualifies the mediation significance process and the collaborative environment in the actions referring to location, assembling and contextualization of the learning objects. The meaningful results obtained by those communities have led great software production organizations to review their corporate strategies, good developmental practices, staff, people and project management. On the other hand, it is inferred that the sustainability of those communities can not be maintained only by personal attributes and abilities, specially because the location of the learning objects for problem solution is based on the tacit knowledge of their members. It is necessary to aggregate innovation into the nature and functionality of those communities (standard compliance, technological methods and tools), to not only enable an effective and universal accessibility to knowledge leading to more efficient problem solution, but also to incorporate members with diverse behavior and abilities. The results of the present research contribute to future innovation in both theoretical and practical fields in the definition of a pattern of conformity for the specification, indexation, use, combination and evaluation of learning objects, in addition to motivating a change of behavior, culture and way of learning.

Des logiciels Open Source à Wikipédia, la production par les pairs mobilise des centaines de milliers de contributeurs de par le monde. C’est une source importante de création de valeur dans les secteurs très compétitifs de l’information et de la technologie, ainsi qu’une source majeure d’innovation. Au-delà même de son importance économique, l’émergence de la production par les pairs représente une opportunité d’éclairer un certain nombre de questions anciennes et particulièrement ardues dans la littérature d’un jour nouveau. Compte-tenu de la nature souvent non conventionnelle des incitations au travail dans les environnements de production par les pairs, ceux-ci sont particulièrement adaptés à l’étude de l’impact des préférences économiques non standard sur la production de biens publics, à l’analyse de leur rôle en tant que motivations au travail, ainsi qu’à l’évaluation de leurs conséquences en termes d’économie organisationnelle.Ce travail de thèse s'appuie sur un outil d’expérimentation en ligne original (développé et évalué dans le chapitre 1) pour combiner expériences en ligne à large échelle et méthodes computationnelles (i.e. l’extraction systématique de données sur le comportement de terrain des sujets) afin de (i) mener le tout premier test de terrain exhaustif de la théorie de la production privée de biens publics, (ii) étudier l’importance des préférences sociales en tant que motivations au travail au sein d’organisations productives réelles et (iii) procéder aux premiers tests de terrain documentant des comportements endogènes d’appariement des agents économiques au sein d’équipes productives en fonction de leur type coopératif. / From Open Source Software to Wikipedia, peer production involves hundreds of thousands of contributors worldwide. It is an important source of value creation in the most competitive sectors of information and technology, as well as a major source of innovation. Beyond its economic significance, the emergence of peer production also represents an opportunity to shed new lights on a number of longstanding but notably difficult questions in the literature. Given the unconventional nature of many of the work incentives at play in peer production environments, those are particularly well suited for researching the impact of non standard economic preferences on public goods provision, studying their role as work incentives, and assessing their consequences in terms of organizational economics.This Ph.D. work leverages a novel online experimentation tool (developed and assessed in Chapter 1) to combine large-scale online experiments and computational methods (i.e. the systematic extraction of data on subjects’ field behavior) to respectively (i) provide the first comprehensive field test of the theory of the private provision of public goods, (ii) study the importance of social preferences as work motives within real-world productive organizations and(iii) report the first field evidence of endogenous sorting behavior of economic agents within productive teams based on their cooperative types.

En milieu urbain, la concurrence entre les enjeux de préservation de la biodiversité et de la densification du territoire est particulièrement développée. Dans une optique d’aide à la décision, une meilleure connaissance des zones les plus conflictuelles est requise. Face au constat d’insuffisance et d’inadéquation des données et des méthodes nécessaires à la cartographie des Trames vertes urbaines, notre travail s’intègre en premier lieu dans une démarche technique. Celle-ci est centrée sur la mise en place d’une méthode de traitement d’images satellitaires Très Haute Résolution Spatiale Pléiades (THRS) pour l’extraction de la végétation arborée et herbacée à l’échelle fine d’une emprise urbaine. D’abord appliquée à des données fictives, cette méthode est ensuite déployée sur quatre territoires (Toulouse, Muret, Pierrefite-Nestalas et Strasbourg). Bien que fondée sur une approche pixel, la simplicité de la méthode, qui s’appuie sur des outils libres, et les résultats obtenus (indice Kappa supérieur à 85 %) garantissent sa reproductibilité sur de vastes territoires plus ou moins urbanisés. Cette donnée de végétation est ensuite exploitée pour modéliser les connectivités écologiques potentielles du paysage urbain et périurbain toulousain. L’approche mobilise la théorie des graphes et permet d’évaluer l’impact d’un aménagement urbain sur la biodiversité. Le cas du Boulevard Urbain Nord de Toulouse est étudié. La cartographie proposée des réservoirs de biodiversité, hiérarchisés à l’aide de métriques de connectivité, est avant tout indicative. Elle est finalement confrontée à des documents d’urbanisme (Plans Locaux d’Urbanisme) afin d’obtenir une meilleure visibilité des territoires à enjeux environnementaux et urbanistiques. En fonction des enjeux fixés par les acteurs du territoire et à travers le filtre applicatif, cette thèse propose un outil robuste d’analyse et d’aide à la décision pour la gestion et la planification du territoire. / In urban areas, competition between land development and ecological conservation is intense. To assist decision making, a better knowledge of those areas of interest is required. Regarding inadequacy data and methods needed for ecological network mapping in urban areas, the aim of our study is to develop a method for semi-automatic vegetation extraction with Very High Spatial Resolution Pleiades imagery (VHSR). Initially applied to training samples, the process is then be deployed to four French study areas (Toulouse, Muret, Pierrefite-Nestalas and Strasbourg). The reproducibility of this method over large urbanized areas is ensured by its simplicity and the results of a pixel-based classification (kappa coefficient higher than 85 %). This extraction workflow uses free or open-source software. This vegetation data is then used in order to model potential ecological connectivity in Toulouse’s urban and peri-urban areas. Impacts on biodiversity due to urban planning are assessed using graph theory. The “Boulevard Urbain Nord de Toulouse” project, a road infrastructure, is studied. Graph metrics have been calculated to assess the level of connectivity at habitat patches and landscape scales. We classified the importance of the patches which is cross-tabulated with planning documents (PLU, a local town planning) in order to locate conflict urban areas: between biodiversity preservation and urbanization. Depending on the issues set out by local actors and through the application filter, this thesis proposes a robust analytical tool and decision-making aid for landscape management and land planning.

The thesis focuses on analysis and the selection of an appropriate project management tool for web based projects. The theoretical part characterizes project management, level of project management in IT environment and web based projects with their specifics. Within the web based projects, it characterizes the possibilities of development and delivery of the Web applications and the methodology used in the development -- rigorous and agile methodologies. The work focuses on the description of agile methodologies in managing software development and their usage in the management of web based projects. Procedures and ways of managing agile methodologies are reflected in the definition of requirements for functionality analyzed among the project management tools in the practical part. The practical part focuses on the description and characteristics of a sample of project management tools used in web based projects and analyzes the selection of the most appropriate one. Evaluation of project management tools is based on the level of compliance with the pre-defined functionalities and comparison of the cost of acquisition and operation for a 3 years period. The functionality of the selected project management tools is evaluated on the basis of meeting the level 8 defined areas. The cost for the project tools are evaluated in the methods of acquisition, which offers their suppliers - On-Premise, On-Demand with proprietary tools and Open Source Software tools under the GNU General Public License.

No description available.

The dissertation focuses on the use of free software in Czech libraries. Both real practice and librarians' attitudes to this type of software are analyzed. The main goal of the dissertation has been to evaluate the attitudes of Czech libraries to free software, to analyze its use in practice, to design information and communications strategy for free software project and to implement it using Evergreen as an example project. In order to achieve the goals, both qualitative and quantitative research methods have been used. These included a survey, web data gathering and analysis and also case studies. The devised and implemented information and communications strategy consists of eight main parts (setting up a local community, creating communication tools, organizing seminars, Czech localization, the creation of first common catalogues, making documentation publicly available, active involvement in the international community and establishing a legal entity to improve awareness about free software among librarians) which are complemented with a SWOT analysis evaluating the strategy implementation.

This diploma thesis deals with the issue of acquisition and selection of software developers with an emphasis on current trends in this area. With regard to demand of labour market for software developers, HR professionals are required to take an innovative approach in their acquisition and selection. The personnel officers are also expected to have a basic orientation in technical terms and an overview of used technologies. The aim of this thesis is to identify significant changes in the acquisition and selection of software developers with an emphasis on current trends. The thesis presents the specifics of work in the software development industry, the position of the software developer within the ICT professions system, the category of software developers or the competency model of a software development worker. The theoretical sources are mainly current foreign articles. The thesis is supplemented by its own empirical survey, which verifies the experience of software developers with the application of the latest trends in the process of recruitment and selection of employers in the Czech Republic.

Providing citizens with the robust and suitable tools to effectively participate in the planning process is a necessity nowadays. Also, changes in the capabilities and popularity of new technologies have dramatically raised the number of technology-based tools that are potentially available for enhancing public participation in the planning process. This study explores both the theoretical aspect of collaborative planning and the effects that Web-based Public Participatory GIS (WPPGIS) applications and Information and Communication Technologies (ICT) has on the planning process. Findings indicate that the WPPGIS applications have the potential for increasing participation. It is also found that besides the contextual elements like the attitudes of planners and decision makers, the technological features such as proper user interface, price of software, technical and literacy skills are seen as crucial hindrances to bridging the planning process and technology-based solutions. This research also attempts to combine IAP2 Public Participation Spectrum and technological functionalities into a single framework to understand the implementation of WPPGIS applications in Stockholm, the capital of Sweden. Finally, based on the given criteria and assessment of the reviewed applications, this study concludes with the design and implementation of a prototype WPPGIS application using Open-Source Technologies (OST).

Les blessures musculo-squelettiques du membre supérieur représentent un problème de santé publique dans le secteur de la manutention. En plus d’affecter la qualité de vie du travailleur, ces lésions entraînent une perte de temps de travail et une augmentation des coûts de production. Alors que nous avons des évidences épidémiologiques que les femmes manutentionnaires sont plus nombreuses que les hommes à souffrir de douleurs à l’épaule, la littérature fait défaut d’indices biomécaniques qui expliquent l'origine de cette différence. L'objectif général de cette thèse était d'améliorer l'évaluation des techniques de manutention du membre supérieur, avec trois objectifs spécifiques : (1) développer des indices cinématiques, électromyographiques et musculo-squelettiques synthétiques pour évaluer et différencier des techniques de manutention du membre supérieur ; (2) développer un logiciel libre d'analyse biomécanique ; et (3) utiliser les indices et le logiciel développés pour décrire les différences biomécaniques entre des femmes et des hommes manutentionnaires. Nous avons récolté des données de cinématique, d'électromyographie et de force sur 30 femmes et 30 hommes réalisant une tâche de manutention qui consistait à déplacer une boîte de 6 et 12 kg entre la hauteur des hanches et la hauteur des yeux. À partir de ces données, nous avons développé des indicateurs synthétiques : un indicateur cinématique utile pour identifier des techniques de manutention problématiques et plus généralement les fonctions articulaires ; des indicateurs électromyographiques qui permettent d'estimer la quantité d'activation musculaire et la co-contraction musculaire ; et des indicateurs musculo-squelettiques qui permettent d'estimer les contraintes musculaires totales et les contraintes appliquées à l'articulation glénohumérale. Nous avons implémenté ces indicateurs avec pyomeca, notre logiciel libre d'analyse biomécanique. Mis à disposition de la communauté biomécanique, pyomeca supporte des tâches utiles dans le quotidien d'un chercheur biomécanique, mais également des routines biomécaniques plus avancées, axées sur la mécanique du corps rigide et le traitement de signal. Ce dernier se démarque des logiciels biomécaniques existants parce que c'est une solution libre, conviviale, spécialisée et sûre. Nous avons ensuite appliqué les indices synthétiques pour décrire les différences biomécaniques entre les femmes et les hommes participant à notre expérimentation. L'indicateur cinématique a montré que les femmes employaient une technique de manutention moins sécuritaire, avec une plus grande contribution glénohumérale, une faible contribution des membres inférieurs et une boite plus éloignée du tronc. Ces différences de technique se sont répercutées sur les indicateurs électromyographiques et musculo-squelettiques, avec des activations musculaires deux fois plus importantes comparativement aux hommes et une moindre stabilité de l'articulation glénohumérale. Ces différences pourraient contribuer à expliquer la prévalence de blessure du membre supérieur plus élevée chez les femmes manutentionnaires. Cette thèse a donc permis de développer des indicateurs synthétiques et un logiciel libre d'analyse biomécanique qui pourraient permettre aux ergonomes d'évaluer l'exposition aux risques de blessures du membre supérieur pendant une tâche de travail dynamique. Appliqués à une population spécifique, ces indicateurs suggèrent qu'il est crucial d'accorder une attention particulière au sexe pendant l'évaluation d'une tâche de travail au-dessus des épaules. / Work-related upper limb musculoskeletal disorders represent a public health challenge in the material handling industry. In addition to affecting the worker's quality of life, these injuries result in lost work time and increased production costs. While we have epidemiological evidence that more female material handlers suffer from shoulder pain than men, the literature is lacking biomechanical indicators that explain the origin of this difference. The general objective of this thesis was to improve the evaluation of upper limb handling techniques, with three specific objectives~: (1) to develop synthetic kinematic, electromyographic and musculoskeletal indicators to evaluate and differentiate upper limb handling techniques~; (2) to develop an open source biomechanical analysis software~; and (3) to use the developed indicators and software to describe the biomechanical differences between female and male workers. We collected kinematics, electromyography and force data on 30 women and 30 men performing a handling task that consisted in lifting a 6 and 12~kg box from hip to eye level. From these data, we developed synthetic indicators~: a kinematic indicator useful to identify poor handling techniques and more generally joint functions~; two electromyographic indicators to quantify the amount of muscle activation and muscle co-contraction~; and two musculoskeletal indicators to estimate total muscle stress and stress applied to the glenohumeral joint. We have implemented these indicators with pyomeca, our open-source biomechanical analysis software. Available to the biomechanical community, pyomeca provide basic operations useful in the daily workflow of a biomechanical researcher, but also more advanced biomechanical routines geared towards rigid body mechanics and signal processing. pyomeca stands from existing biomechanical software because it is an open-source, user-friendly, specialized and secure solution. We then applied our synthetic indicators to describe the biomechanical differences between the women and men participating in our experiment. The kinematic indicator showed that women used a poor handling technique, with a higher glenohumeral contribution, a low contribution from the lower limbs and a box further away from the trunk. These differences in technique affected the electromyographic and musculoskeletal indicators, with twice as much muscle activation compared to men and less glenohumeral stability. These results may contribute to the sex difference in the prevalence of upper limb musculoskeletal disorders. This thesis has enabled the development of biomechanical indicators and an open-source software that could allow ergonomists to assess the upper limb exposure during a dynamic lifting task. Applied to a specific population, these indicators argue for a careful consideration of sex during ergonomics intervention, particularly during overhead work.