913 resultados para global strategic networks of linkages


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Neuronal dynamics are fundamentally constrained by the underlying structural network architecture, yet much of the details of this synaptic connectivity are still unknown even in neuronal cultures in vitro. Here we extend a previous approach based on information theory, the Generalized Transfer Entropy, to the reconstruction of connectivity of simulated neuronal networks of both excitatory and inhibitory neurons. We show that, due to the model-free nature of the developed measure, both kinds of connections can be reliably inferred if the average firing rate between synchronous burst events exceeds a small minimum frequency. Furthermore, we suggest, based on systematic simulations, that even lower spontaneous inter-burst rates could be raised to meet the requirements of our reconstruction algorithm by applying a weak spatially homogeneous stimulation to the entire network. By combining multiple recordings of the same in silico network before and after pharmacologically blocking inhibitory synaptic transmission, we show then how it becomes possible to infer with high confidence the excitatory or inhibitory nature of each individual neuron.

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La présente thèse s'intitule "Développent et Application des Méthodologies Computationnelles pour la Modélisation Qualitative". Elle comprend tous les différents projets que j'ai entrepris en tant que doctorante. Plutôt qu'une mise en oeuvre systématique d'un cadre défini a priori, cette thèse devrait être considérée comme une exploration des méthodes qui peuvent nous aider à déduire le plan de processus regulatoires et de signalisation. Cette exploration a été mue par des questions biologiques concrètes, plutôt que par des investigations théoriques. Bien que tous les projets aient inclus des systèmes divergents (réseaux régulateurs de gènes du cycle cellulaire, réseaux de signalisation de cellules pulmonaires) ainsi que des organismes (levure à fission, levure bourgeonnante, rat, humain), nos objectifs étaient complémentaires et cohérents. Le projet principal de la thèse est la modélisation du réseau de l'initiation de septation (SIN) du S.pombe. La cytokinèse dans la levure à fission est contrôlée par le SIN, un réseau signalant de protéines kinases qui utilise le corps à pôle-fuseau comme échafaudage. Afin de décrire le comportement qualitatif du système et prédire des comportements mutants inconnus, nous avons décidé d'adopter l'approche de la modélisation booléenne. Dans cette thèse, nous présentons la construction d'un modèle booléen étendu du SIN, comprenant la plupart des composantes et des régulateurs du SIN en tant que noeuds individuels et testable expérimentalement. Ce modèle utilise des niveaux d'activité du CDK comme noeuds de contrôle pour la simulation d'évènements du SIN à différents stades du cycle cellulaire. Ce modèle a été optimisé en utilisant des expériences d'un seul "knock-out" avec des effets phénotypiques connus comme set d'entraînement. Il a permis de prédire correctement un set d'évaluation de "knock-out" doubles. De plus, le modèle a fait des prédictions in silico qui ont été validées in vivo, permettant d'obtenir de nouvelles idées de la régulation et l'organisation hiérarchique du SIN. Un autre projet concernant le cycle cellulaire qui fait partie de cette thèse a été la construction d'un modèle qualitatif et minimal de la réciprocité des cyclines dans la S.cerevisiae. Les protéines Clb dans la levure bourgeonnante présentent une activation et une dégradation caractéristique et séquentielle durant le cycle cellulaire, qu'on appelle communément les vagues des Clbs. Cet évènement est coordonné avec la courbe d'activation inverse du Sic1, qui a un rôle inhibitoire dans le système. Pour l'identification des modèles qualitatifs minimaux qui peuvent expliquer ce phénomène, nous avons sélectionné des expériences bien définies et construit tous les modèles minimaux possibles qui, une fois simulés, reproduisent les résultats attendus. Les modèles ont été filtrés en utilisant des simulations ODE qualitatives et standardisées; seules celles qui reproduisaient le phénotype des vagues ont été gardées. L'ensemble des modèles minimaux peut être utilisé pour suggérer des relations regulatoires entre les molécules participant qui peuvent ensuite être testées expérimentalement. Enfin, durant mon doctorat, j'ai participé au SBV Improver Challenge. Le but était de déduire des réseaux spécifiques à des espèces (humain et rat) en utilisant des données de phosphoprotéines, d'expressions des gènes et des cytokines, ainsi qu'un réseau de référence, qui était mis à disposition comme donnée préalable. Notre solution pour ce concours a pris la troisième place. L'approche utilisée est expliquée en détail dans le dernier chapitre de la thèse. -- The present dissertation is entitled "Development and Application of Computational Methodologies in Qualitative Modeling". It encompasses the diverse projects that were undertaken during my time as a PhD student. Instead of a systematic implementation of a framework defined a priori, this thesis should be considered as an exploration of the methods that can help us infer the blueprint of regulatory and signaling processes. This exploration was driven by concrete biological questions, rather than theoretical investigation. Even though the projects involved divergent systems (gene regulatory networks of cell cycle, signaling networks in lung cells), as well as organisms (fission yeast, budding yeast, rat, human), our goals were complementary and coherent. The main project of the thesis is the modeling of the Septation Initiation Network (SIN) in S.pombe. Cytokinesis in fission yeast is controlled by the SIN, a protein kinase signaling network that uses the spindle pole body as scaffold. In order to describe the qualitative behavior of the system and predict unknown mutant behaviors we decided to adopt a Boolean modeling approach. In this thesis, we report the construction of an extended, Boolean model of the SIN, comprising most SIN components and regulators as individual, experimentally testable nodes. The model uses CDK activity levels as control nodes for the simulation of SIN related events in different stages of the cell cycle. The model was optimized using single knock-out experiments of known phenotypic effect as a training set, and was able to correctly predict a double knock-out test set. Moreover, the model has made in silico predictions that have been validated in vivo, providing new insights into the regulation and hierarchical organization of the SIN. Another cell cycle related project that is part of this thesis was to create a qualitative, minimal model of cyclin interplay in S.cerevisiae. CLB proteins in budding yeast present a characteristic, sequential activation and decay during the cell cycle, commonly referred to as Clb waves. This event is coordinated with the inverse activation curve of Sic1, which has an inhibitory role in the system. To generate minimal qualitative models that can explain this phenomenon, we selected well-defined experiments and constructed all possible minimal models that, when simulated, reproduce the expected results. The models were filtered using standardized qualitative ODE simulations; only the ones reproducing the wave-like phenotype were kept. The set of minimal models can be used to suggest regulatory relations among the participating molecules, which will subsequently be tested experimentally. Finally, during my PhD I participated in the SBV Improver Challenge. The goal was to infer species-specific (human and rat) networks, using phosphoprotein, gene expression and cytokine data and a reference network provided as prior knowledge. Our solution to the challenge was selected as in the final chapter of the thesis.

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Tutkimuksen tarkoituksena oli tunnistaa nykyiset sekä potentiaaliset avainasiakkaat case yritykselle. Avainasiakkaat tunnistettiin Chevertonin tunnistamis- ja valintamatriisin avulla, jossa asiakkaan sijoittumista matriisiin arvioidaan asiakkaan houkuttelevuuden sekä toimittajan suhteellisten vahvuuksien avulla. Kriteereiksi avainasiakkaiden tunnistamiseen valittiin asiakkaan vuotuinen ostovolyymi, asiakkaan business-potentiaali sekä case-yrityksen toimittajaosuus. Asiakkaat luokiteltiin avainasiakkaisiin, kehitettäviin avainasiakkaisiin, ylläpidettäviin asiakkaisiin sekä satunnaisiin asiakkaisiin. Tutkimus tarjosi lähtökohdan case-yrityksen uusille avainasiakaspäälliköille sekä osoitti suunnan tulevaisuuden tutkimustarpeille. Aktiivisen tiedonvaihdannan kautta eri myyntikonttoreiden johtohenkilöstön sekä myös yrityksen eri funktionaalisten divisioonien välillä voidaan saavuttaa kilpailuetua kun lähestytään asiakasta toimintojaan järkiperäisesti koordinoineena toimittajana samalla kun asiakkaat keskittävät ostojaan. Jotta yrityksen tavoitteet, markkinamahdollisuudet sekä resurssit olisivat hyvin tasapainossa, tulisi myös asiakaskannattavuutta sekä asiakkaiden strategista merkittävyyttä arvioida ja mitata säännöllisesti tässä tutkimuksessa käytettyjen tunnistuskriteereiden lisäksi.

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The concerted action of ppGpp and DksA in transcription has been widely documented. In disparity with this model, phenotypic studies showed that ppGpp and DksA might also have independent and opposing roles in gene expression in Escherichia coli. In this study we used a transcriptomic approach to compare the global transcriptional patterns of gene expression in strains deficient in ppGpp (ppGpp0) and/or DksA ( dksA). Approximately 6 and 7% of all genes were significantly affected by more than twofold in ppGpp- and DksAdeficient strains, respectively, increasing to 13% of all genes in the ppGpp0 dksA strain. Although the data indicate that most of the affected genes were copositively or conegatively regulated by ppGpp and DksA, some genes that were independently and/or differentially regulated by the two factors were found. The large functional group of chemotaxis and flagellum synthesis genes were notably differentially affected, with all genes being upregulated in the DksA-deficient strain but 60% of them being downregulated in the ppGpp-deficient strain. Revealingly, mutations in the antipausing Gre factors suppress the upregulation observed in the DksA-deficient strain, emphasizing the importance of the secondary channel of the RNA polymerase for regulation and fine-tuning of gene expression in E. coli.

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Cooperation and coordination are desirable behaviors that are fundamental for the harmonious development of society. People need to rely on cooperation with other individuals in many aspects of everyday life, such as teamwork and economic exchange in anonymous markets. However, cooperation may easily fall prey to exploitation by selfish individuals who only care about short- term gain. For cooperation to evolve, specific conditions and mechanisms are required, such as kinship, direct and indirect reciprocity through repeated interactions, or external interventions such as punishment. In this dissertation we investigate the effect of the network structure of the population on the evolution of cooperation and coordination. We consider several kinds of static and dynamical network topologies, such as Baraba´si-Albert, social network models and spatial networks. We perform numerical simulations and laboratory experiments using the Prisoner's Dilemma and co- ordination games in order to contrast human behavior with theoretical results. We show by numerical simulations that even a moderate amount of random noise on the Baraba´si-Albert scale-free network links causes a significant loss of cooperation, to the point that cooperation almost vanishes altogether in the Prisoner's Dilemma when the noise rate is high enough. Moreover, when we consider fixed social-like networks we find that current models of social networks may allow cooperation to emerge and to be robust at least as much as in scale-free networks. In the framework of spatial networks, we investigate whether cooperation can evolve and be stable when agents move randomly or performing Le´vy flights in a continuous space. We also consider discrete space adopting purposeful mobility and binary birth-death process to dis- cover emergent cooperative patterns. The fundamental result is that cooperation may be enhanced when this migration is opportunistic or even when agents follow very simple heuristics. In the experimental laboratory, we investigate the issue of social coordination between indi- viduals located on networks of contacts. In contrast to simulations, we find that human players dynamics do not converge to the efficient outcome more often in a social-like network than in a random network. In another experiment, we study the behavior of people who play a pure co- ordination game in a spatial environment in which they can move around and when changing convention is costly. We find that each convention forms homogeneous clusters and is adopted by approximately half of the individuals. When we provide them with global information, i.e., the number of subjects currently adopting one of the conventions, global consensus is reached in most, but not all, cases. Our results allow us to extract the heuristics used by the participants and to build a numerical simulation model that agrees very well with the experiments. Our findings have important implications for policymakers intending to promote specific, desired behaviors in a mobile population. Furthermore, we carry out an experiment with human subjects playing the Prisoner's Dilemma game in a diluted grid where people are able to move around. In contrast to previous results on purposeful rewiring in relational networks, we find no noticeable effect of mobility in space on the level of cooperation. Clusters of cooperators form momentarily but in a few rounds they dissolve as cooperators at the boundaries stop tolerating being cheated upon. Our results highlight the difficulties that mobile agents have to establish a cooperative environment in a spatial setting without a device such as reputation or the possibility of retaliation. i.e. punishment. Finally, we test experimentally the evolution of cooperation in social networks taking into ac- count a setting where we allow people to make or break links at their will. In this work we give particular attention to whether information on an individual's actions is freely available to poten- tial partners or not. Studying the role of information is relevant as information on other people's actions is often not available for free: a recruiting firm may need to call a job candidate's refer- ences, a bank may need to find out about the credit history of a new client, etc. We find that people cooperate almost fully when information on their actions is freely available to their potential part- ners. Cooperation is less likely, however, if people have to pay about half of what they gain from cooperating with a cooperator. Cooperation declines even further if people have to pay a cost that is almost equivalent to the gain from cooperating with a cooperator. Thus, costly information on potential neighbors' actions can undermine the incentive to cooperate in dynamical networks.

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The concerted action of ppGpp and DksA in transcription has been widely documented. In disparity with this model, phenotypic studies showed that ppGpp and DksA might also have independent and opposing roles in gene expression in Escherichia coli. In this study we used a transcriptomic approach to compare the global transcriptional patterns of gene expression in strains deficient in ppGpp (ppGpp0) and/or DksA ( dksA). Approximately 6 and 7% of all genes were significantly affected by more than twofold in ppGpp- and DksAdeficient strains, respectively, increasing to 13% of all genes in the ppGpp0 dksA strain. Although the data indicate that most of the affected genes were copositively or conegatively regulated by ppGpp and DksA, some genes that were independently and/or differentially regulated by the two factors were found. The large functional group of chemotaxis and flagellum synthesis genes were notably differentially affected, with all genes being upregulated in the DksA-deficient strain but 60% of them being downregulated in the ppGpp-deficient strain. Revealingly, mutations in the antipausing Gre factors suppress the upregulation observed in the DksA-deficient strain, emphasizing the importance of the secondary channel of the RNA polymerase for regulation and fine-tuning of gene expression in E. coli.

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Ordered weighted averaging (OWA) operators and their extensions are powerful tools used in numerous decision-making problems. This class of operator belongs to a more general family of aggregation operators, understood as discrete Choquet integrals. Aggregation operators are usually characterized by indicators. In this article four indicators usually associated with the OWA operator are extended to discrete Choquet integrals: namely, the degree of balance, the divergence, the variance indicator and Renyi entropies. All of these indicators are considered from a local and a global perspective. Linearity of indicators for linear combinations of capacities is investigated and, to illustrate the application of results, indicators of the probabilistic ordered weighted averaging -POWA- operator are derived. Finally, an example is provided to show the application to a specific context.

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Mountain ecosystems have been less adversely affected by invasions of non-native plants than most other ecosystems, partially because most invasive plants in the lowlands are limited by climate and cannot grow under harsher high-elevation conditions. However, with ongoing climate change, invasive species may rapidly move upwards and threaten mid- then high-elevation mountain ecosystems. We evaluated this threat by predicting current and future potential distributions of 48 invasive plant species distributed in Switzerland (CH) and New South Wales (NSW), two areas where climate interacts differently with the elevation gradient. Using a species distribution modeling approach combining two scales, which builds on high-resolution data (< 250 m) but accounts for the global climatic niche of species, we found that different environmental drivers limit the elevation range of invasive species in the two regions, leading to region-specific species responses to climate change. Whereas the optimal suitability for plant invaders is predicted to markedly shift from the lowland to the montane or subalpine zone in CH, such an upward shift is far less pronounced in NSW where montane and subalpine elevations are currently already suitable. Non-native species able to invade the upper reaches of mountains in a future climate will be cold-tolerant in the Swiss Alps but preferring wet soils in the Australian Alps. Other plant traits were only marginally associated with elevation limits. These results demonstrate that a more systematic consideration of future distributions of invasive species is required in conservation plans of not yet invaded mountainous ecosystems.

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The question of why some firms perform better in managing their alliances has raised interest among scholars and managers. Whereas inter-firm factors influencing the alliance performance such as strategic fit between partners and the existence of complementarities have been studied extensively, research on firm-level antecedents is rather scarce. Therefore this study investigates the role of firm’s alliance capability in the alliance success equation. Particularly it analyses the specialized mechanisms and processes set up by firm in order to facilitate alliancerelated know-how leverage organization-wise. Evidence from a cross-industry sample of R&D intensive Finnish companies supports the fact that firms which have invested in institutionalizing alliance capabilities outperform their counterparts in alliance portfolio management. Results also suggest that firms need to adjust alliance management tools depending on the alliance portfolio size, prior experience with inter-firm partnerships and the strategic importance of alliances. Furthermore, absorptive capacity is found to be crucial for successful alliance management, its role being complementary to that of alliance capability. Finally, firms that have successful alliances also enjoy higher financial, market and innovation performance.

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Ecological network patterns are influenced by diverse processes that operate at different temporal rates. Here we analyzed whether the coupled effect of local abundance variation, seasonally phenotypic plastic responses, and species evolutionary adaptations might act in concert to shape network patterns. We studied the temporal variation in three interaction properties of bird species (number of interactions per species, interaction strength, and interaction asymmetry) in a temporal sequence of 28 plant frugivore interaction networks spanning two years in a Mediterranean shrubland community. Three main hypotheses dealing with the temporal variation of network properties were tested, examining the effects of abundance, switching behavior between alternative food resources, and morphological traits in determining consumer interaction patterns. Our results demonstrate that temporal variation in consumer interaction patterns is explained by short-term variation in resource and bird abundances and seasonal dietary switches between alternative resources (fleshy fruits and insects). Moreover, differences in beak morphology are associated with differences in switching behavior between resources, suggesting an important role of foraging adaptations in determining network patterns. We argue that beak shape adaptations might determine generalist and specialist feeding behaviors and thus the positions of consumer species within the network. Finally, we provide a preliminary framework to interpret phylogenetic signal in plant animal networks. Indeed, we show that the strength of the phylogenetic signal in networks depends on the relative importance of abundance, behavioral, and morphological variables. We show that these variables strongly differ in their phylogenetic signal. Consequently, we suggest that moderate and significant phylogenetic effects should be commonly observed in networks of species interactions. Read More: http://www.esajournals.org/doi/abs/10.1890/07-1939.1

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The mobile networks of earlier and current generations, or 2G and 3G networks, provide users voice and packet services with higher transmission rates and good quality over the same core network. When developing the next generation of mobile networks the current quality of services needs to be maintained. This thesis concentrates on the next generation mobile network, especially on the evolution of the packet network part. The new mobile network has requirements for the common packet backbone network, Mobile Packet Backbone Network, which is additionally discussed in this study. The next generation mobile network, called LTE/SAE, is currently under testing. The test system is called Container Trial System. It is a mini sized LTE/SAE site. The LTE/SAE is studied in this thesis concentrating on the evolved packet core, the SAE part of the composition. The empirical part of the study compares the LTE/SAE Container Trial System and commercial network designs and additionally produces documentation for internal personnel and customers. The research is performed by comparing the documentations and specifications of both the Container Trial System and commercial network. Since the LTE commercial network is not yet constructed, the comparison is done theoretically. The purpose is furthermore to find out if there are any design issues that could be done differently in the next version of the Container Trial System.

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Tutkimuksen tavoitteena on tuottaa malli globaalin tietoliikenneverkkojen palvelutuotannon toteuttamiseksi metsäteollisuuden yrityksessä. Pääongelmana on selvittää miten tietoliikenneverkkojen palvelutuotanto on toteutettava ottaen huomioon tarvittavat toimijat, kustannustehokkuus ja tiedonhallinta. Ongelmaa lähestyttiin IT- johtamisen, ulkoistamisen, yhteistyöverkostojen, prosessien, yhteisten työkalujen ja standardoinnin näkökulmista. Yrityksen tietoliikenneverkkojen nykytilaa ja tavoitetilaa tutkittiin laadullisella kyselytutkimuksella. Tutkimuksen perusteella päädyttiin malliin, jossa tietoliikenneverkkojen palvelutuotannon laadukkuuteen ja tehokkuuteen vaikuttavat oleellisesti toimijat, yhteiset työkalut, standardointi kaikilla tasoilla ja harkittu ja laskelmoitu ulkoistaminen. Keskeiseen rooliin nousivat standardit prosessit ja niitä tukevat yhteiset työkalut, jotka on toteutettu keskitetysti ja kriittisten osien osalta myös paikallisesti. Prosessien ja työkalujen tulee tukea tiedonhallintaa luonnollisena osana päivittäistä toimintaa. Toimijoiden rajapinnat on oltava yksiselitteisesti määritelty ja toimijoiden välillä on kyettävä kommunikoimaan yhteisillä työkaluilla ja jakamaan tietoa avoimesti.

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Valtiot soveltavat yleisesti puolustusvälinehankintojensa yhteydessä vastakauppamenettelyä, jota kutsutaan offsetiksi. Tämän laadullisen tapaustutkimuksen tavoitteena on selvittää minkälaista verkottumista suora offset edellyttää myyjäyritykseltä ja mitä vaikutuksia verkottumisella on myyjäyritykseen. Offsetvaatimusten ja paikallisyhteistyön vuoksi tapahtuvalla verkottumisella on monia vaikutuksia myyjäyritykseen, joista pääosan voidaan sanoa olevan liiketaloudellisessa mielessä negatiivisia. Huomioitavaa kuitenkin on, että ilman offsetia ei voida voittaa hankkeita ja näin generoida liiketoimintaa. Suoran offsetin verkostoituminen perustuu ratkaisuliiketoiminnan eli arvopajan kautta tuotettuun lisäarvoon loppuasiakkaalle. Tällaista verkostotoimintaa harjoittavaa yritystä voidaan kutsua asiakaskeskeisen verkoston ansaitsijaksi joka kasvattaa ansaintaansa tuottamansa korkeamman lisäarvon kautta. Offsetin luonteesta johtuen erilaisten mittausjärjestelmien rakentaminen voi nousta haasteeksi.

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The main outcome of the master thesis is innovative solution, which can support a choice of business process modeling methodology. Potential users of this tool are people with background in business process modeling and possibilities to collect required information about organization’s business processes. Master thesis states the importance of business process modeling in implementation of strategic goals of organization. It is made by revealing the place of the concept in Business Process Management (BPM) and its particular case Business Process Reengineering (BPR). In order to support the theoretical outcomes of the thesis a case study of Northern Dimension Research Centre (NORDI) in Lappeenranta University of Technology was conducted. On its example several solutions are shown: how to apply business process modeling methodologies in practice; in which way business process models can be useful for BPM and BPR initiatives; how to apply proposed innovative solution for a choice of business process modeling methodology.

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The study examines the internationalisation process of a contemporary SME firm and explores the impact of its business network on this development. The objective of the study is to understand SME internationalisation and its dynamics from a network perspective. The purpose of this research project is to describe and explore the development process of a firm and its business network by identifying the changes, critical events and influence factors that form this development. It is a qualitative case study, which focuses on a Finnish focal firm and its respective business network as it expands into the Greek market. It is a longitudinal research process, which covers a period of time from 1994 to 2004. The empirical study concentrates on the paper trading and converting business. The study builds on the network theory and the framework provided by Johanson and Mattsson's (1988) model on network internationalisation. The incremental internationalisation theories and network theories form the theoretical focus. The research project is organised according to a process view. The focal firm evolves from a domestically-oriented small subsidiary into an internationally experienced company, which has activities in several market areas and numerous business networks in various market segments and product categories. The findings illustrate the importance of both the domestic and foreign business network context in a firm's internationalisation process. The results of the study suggest theoretical modifications on a firm's internationalisation process by broadening the perspective and incorporating the strategic context of a firm. The findings suggest that internationalisation process is a non-linear process, which does not have a deterministic order in its development. The findings emphasise the significance of relational networks, both managerial and entrepreneurial, for establishing position in foreign markets. It implies that a firm's evolution is significantly influenced by its business network and by critical events. Business networks gain coherence due to common goals and they use accumulated capabilities to exploit market opportunities. The business network sets constraints and provides opportunities, which makes the related decision making strategically important. The firm co-evolves with its business network. The research project provides an instrumental case study with a description of an SME internationalisation process. It contributes to existing knowledge by illustrating dynamics in an international business network and by pinpointing the importance of suppliers, customers, partners, ownerships and competition to the internationalisation process.