454 research outputs found
Enhancing systems biology models through semantic data integration
Studying and modelling biology at a systems level requires a large amount of data of different experimental types. Historically, each of these types is stored in its own distinct format, with its own internal structure for holding the data produced by those experiments. While the use of community data standards can reduce the need for specialised, independent formats by providing a common syntax, standards uptake is not universal and a single standard cannot yet describe all biological data. In the work described in this thesis, a variety of integrative methods have been developed to reuse and restructure already extant systems biology data. SyMBA is a simple Web interface which stores experimental metadata in a published, common format. The creation of accurate quantitative SBML models is a time-intensive manual process. Modellers need to understand both the systems they are modelling and the intricacies of the SBML format. However, the amount of relevant data for even a relatively small and well-scoped model can be overwhelming. Saint is a Web application which accesses a number of external Web services and which provides suggested annotation for SBML and CellML models. MFO was developed to formalise all of the knowledge within the multiple SBML specification documents in a manner which is both human and computationally accessible. Rule-based mediation, a form of semantic data integration, is a useful way of reusing and re-purposing heterogeneous datasets which cannot, or are not, structured according to a common standard. This method of ontology-based integration is generic and can be used in any context, but has been implemented specifically to integrate systems biology data and to enrich systems biology models through the creation of new biological annotations. The work described in this thesis is one step towards the formalisation of biological knowledge useful to systems biology. Experimental metadata has been transformed into common structures, a Web application has been created for the retrieval of data appropriate to the annotation of systems biology models and multiple data models have been formalised and made accessible to semantic integration techniques.EThOS - Electronic Theses Online ServiceBBSRCEPSRCGBUnited Kingdo
Ontologies for Bioinformatics
The past twenty years have witnessed an explosion of biological data in diverse database formats governed by heterogeneous infrastructures. Not only are semantics (attribute terms) different in meaning across databases, but their organization varies widely. Ontologies are a concept imported from computing science to describe different conceptual frameworks that guide the collection, organization and publication of biological data. An ontology is similar to a paradigm but has very strict implications for formatting and meaning in a computational context. The use of ontologies is a means of communicating and resolving semantic and organizational differences between biological databases in order to enhance their integration. The purpose of interoperability (or sharing between divergent storage and semantic protocols) is to allow scientists from around the world to share and communicate with each other. This paper describes the rapid accumulation of biological data, its various organizational structures, and the role that ontologies play in interoperability
Biohacking and code convergence : a transductive ethnography
Cette thĂšse se dĂ©ploie dans un espace de discours et de pratiques revendicatrices, Ă lâinter- section des cultures amateures informatiques et biotechniques, euro-amĂ©ricaines contempo- raines. La problĂ©matique se dessinant dans ce croisement culturel examine des mĂ©taphores et analogies au coeur dâun traffic intense, au milieu de voies de commmunications imposantes, reliant les technologies informatiques et biotechniques comme lieux dâexpression mĂ©diatique. Lâexamen retrace les lignes de force, les mĂ©diations expressives en ces lieux Ă travers leurs manifestations en tant que codes âĂ la fois informatiques et gĂ©nĂ©tiquesâ et reconnaĂźt les caractĂšres analogiques dâexpressivitĂ© des codes en tant que processus de convergence.
Ămergeant lentement, Ă partir des annĂ©es 40 et 50, les visions convergentes des codes ont facilitĂ© lâentrĂ©e des ordinateurs personnels dans les marchĂ©s, ainsi que dans les garages de hackers, alors que des bricoleurs de lâinformatique sâen rĂ©clamaient comme espace de libertĂ© dâinformation âet surtout dâinnovation. Plus de cinquante ans plus tard, lâanalogie entre codes informatiques et gĂ©nĂ©tiques sert de moteur aux revendications de libertĂ©, informant cette fois les nouvelles applications de la biotechnologie de marchĂ©, ainsi que lâactivitĂ© des biohackers, ces bricoleurs de garage en biologie synthĂ©tique. Les pratiques du biohacking sont ainsi comprises comme des individuations : des tentatives continues de rĂ©soudre des frictions, des tensions travaillant les revendications des cultures amateures informatiques et biotechniques.
Une des maniĂšres de moduler ces tensions sâincarne dans un processus connu sous le nom de forking, entrevu ici comme lâexpĂ©rience dâune bifurcation. Autrement dit, le forking est ici dĂ©finit comme passage vers un seuil critique, dĂ©clinant la technologie et la biologie sur plusieurs modes. Le forking informe âcâest-Ă -dire permet et contraintâ diffĂ©rentes vi- sions collectives de lâouverture informationnelle. Le forking intervient aussi sur les plans des iii semio-matĂ©rialitĂ©s et pouvoirs dâaction investis dans les pratiques biotechniques et informa- tiques. Pris comme processus de co-constitution et de diffĂ©rentiation de lâaction collective, les mouvements de bifurcation invitent les trois questions suivantes : 1) Comment le forking catalyse-t-il la solution des tensions participant aux revendications des pratiques du bioha- cking ? 2) Dans ce processus de solution, de quelles maniĂšres les revendications changent de phase, bifurquent et se transforment, parfois au point dâaltĂ©rer radicalement ces pratiques ? 3) Quels nouveaux problĂšmes Ă©mergent de ces solutions ?
Lâeffort de recherche a trouvĂ© ces questions, ainsi que les plans correspondants dâaction sĂ©mio-matĂ©rielle et collective, incarnĂ©es dans trois expĂ©riences ethnographiques rĂ©parties sur trois ans (2012-2015) : la premiĂšre dans un laboratoire de biotechnologie communautaire new- yorkais, la seconde dans lâĂ©mergence dâun groupe de biotechnologie amateure Ă MontrĂ©al, et la troisiĂšme Ă Cork, en Irlande, au sein du premier accĂ©lĂ©rateur dâentreprises en biologie synthĂ©tique au monde. La logique de lâenquĂȘte nâest ni strictement inductive ou dĂ©ductive, mais transductive. Elle emprunte Ă la philosophie de la communication et de lâinformation de Gilbert Simondon et dĂ©couvre lâĂ©pistĂ©mologie en tant quâacte de crĂ©ation opĂ©rant en milieux relationnels. Lâheuristique transductive offre des rencontres inusitĂ©es entre les mĂ©taphores et les analogies des codes. Ces rencontres Ă©tonnantes ont amĂ©nagĂ© lâexpĂ©rience de la conver- gence des codes sous forme de jeux dâĂ©critures. Elles se sont retrouvĂ©es dans la recherche ethnographique en tant que processus transductifs.This dissertation examines creative practices and discourses intersecting computer and biotech cultures. It queries influential metaphors and analogies on both sides of the inter- section, and their positioning of biotech and information technologies as expression media. It follows mediations across their incarnations as codes, both computational and biological, and situates their analogical expressivity and programmability as a process of code conver- gence. Converging visions of technological freedom facilitated the entrance of computers in 1960âs Western hobbyist hacker circles, as well as in consumer markets. Almost fifty years later, the analogy drives claims to freedom of information âand freedom of innovationâ from biohacker hobbyist groups to new biotech consumer markets. Such biohacking practices are understood as individuations: as ongoing attempts to resolve frictions, tensions working through claims to freedom and openness animating software and biotech cultures.
Tensions get modulated in many ways. One of them, otherwise known as âforking,â refers here to a critical bifurcation allowing for differing iterations of biotechnical and computa- tional configurations. Forking informs âthat is, simultaneously affords and constrainsâ differing collective visions of openness. Forking also operates on the materiality and agency invested in biotechnical and computational practices. Taken as a significant process of co- constitution and differentiation in collective action, bifurcation invites the following three questions: 1) How does forking solve tensions working through claims to biotech freedom? 2) In this solving process, how can claims bifurcate and transform to the point of radically altering biotech practices? 3) what new problems do these solutions call into existence?
This research found these questions, and both scales of material action and agency, in- carnated in three extensive ethnographical journeys spanning three years (2012-2015): the first in a Brooklyn-based biotech community laboratory, the second in the early days of a biotech community group in Montreal, and the third in the worldâs first synthetic biology startup accelerator in Cork, Ireland. The inquiryâs guiding empirical logic is neither solely deductive or inductive, but transductive. It borrows from Gilbert Simondonâs philosophy of communication and information to experience epistemology as an act of analogical creation involving the radical, irreversible transformation of knower and known. Transductive heuris- tics offer unconvential encounters with practices, metaphors and analogies of code. In the end, transductive methods acknowledge code convergence as a metastable writing games, and ethnographical research itself as a transductive process
Social shaping of digital publishing: exploring the interplay between culture and technology
The processes and forms of electronic publishing have been changing since the advent of the Web. In recent years, the open access movement has been a major driver of scholarly communication, and change is also evident in other fields such as e-government and e-learning. Whilst many changes are driven by technological advances, an altered social reality is also pushing the boundaries of digital publishing. With 23 articles and 10 posters, Elpub 2012 focuses on the social shaping of digital publishing and explores the interplay between culture and technology. This book contains the proceedings of the conference, consisting of 11 accepted full articles and 12 articles accepted as extended abstracts. The articles are presented in groups, and cover the topics: digital scholarship and publishing; special archives; libraries and repositories; digital texts and readings; and future solutions and innovations. Offering an overview of the current situation and exploring the trends of the future, this book will be of interest to all those whose work involves digital publishing
Integration strategies and data analysis methods for plant systems biology
Understanding how function relates to multiple layers of inactions between biological entities is one of the key goals of bioinformatics research, in particular in such areas as systems biology. However, the realisation of this objective is hampered by the sheer volume and multi-level heterogeneity of potentially relevant information. This work addressed this issue by developing a set of integration pipelines and analysis methods as part of an Ondex data integration framework. The integration process incorporated both relevant data from a set of publically available databases and information derived from predicted approaches, which were also implemented as part of this work.
These methods were used to assemble integrated datasets that were of relevance to the study of the model plant species Arabidopsis thaliana and applicable for the network-driven analysis. A particular attention was paid to the evaluation and comparison of the different sources of these data. Approaches were implemented for the identification and characterisation of functional modules in integrated networks and used to study and compare networks constructed from different types of data. The benefits of data integration were also demonstrated in three different bioinformatics research scenarios. The analysis of the constructed datasets has also resulted in a better understanding of the functional role of genes identified in a study of a nitrogen uptake mutant and allowed to select candidate genes for further exploration
Fungi Media: A Post-Internet Performance of Bodily Mutations as an Enactment of Alternative Sexualities
This theory-practice PhD project investigates post-Internet performance art, i.e. art which is visually inspired by mutations of human bodies on the Internet, to stage a form of bodily decomposition in real-life spaces. As a framing device for my thesis, I propose the concept of âfungi mediaâ. This concept builds on the vital role of fungi in the decomposition of individual organismsâ bodies to highlight the role of media, including the Internet, in breaking down and reassembling human and nonhuman bodies into complex ecologies. Body performance that engages with fungi on a visual and material level is used in this project to explore the possibility of enacting alternative sexualities and non-normative lifestyles within the present-day context of the decomposing world. Those alternative sexualities are described in the thesis as âfungosexualâ. This formulation repositions queer sexualities in the context of the original meaning of the term âqueerâ, which is ârotâ, and which stands for a fungiinduced process of decomposition. With this, I explore the foundational importance of rot for both breaking down and sustaining bodies, relationships and life as such. Using the mutability of fungal life as a model, I also look at lifeâs mutation beyond sexual reproduction and beyond binary gender roles. In line with its theory-practice aspect, the PhD has a dual methodology. On the one hand, it uses a humanities framework (drawn from philosophies of posthumanism and new materialism, media theory, and theories of sexuality and the body) to engage, critically and creatively, with bioscience research into microbes and fungi. On the other, it mobilises the concept of âfungi mediaâ for my own performance art and curatorial work. The performance space used for my research, which is a London squat inhabited by both artists and fungi, serves as an important actor in these performances. My overall aim with this thesis is to position bodily mutation unfolding on and off the Internet as a performative form of dark vitalism. This philosophical-artistic approach offers strategies for urban dwelling, which transcend normative family and sexual life to embrace a hybrid fungosexuality
Using Real-Time Data Flux In Art â The Mediation Of A Situation As It Unfolds: RoadMusic â An Experimental Case Study.
The practice driving this research is called RoadMusic. The project uses a small computer based system installed in a car that composes music from the flux of information it captures about the journey as it unfolds. It uses a technique known as sonification that consists of mapping data to sound. In the case of RoadMusic, this data capture is realtime, external to the computer and mobilised with the user. This dissertation investigates ways in which such a sonification can become an artistic form.
To interrogate the specificity of an art of real-time it considers philosophical theories of the fundamental nature of time and immediacy and the ways in which the human mind âmakes senseâ of this flux. After extending this scrutiny via theories of system and environment, it proceeds to extract concepts and principles leading to a possible art of real-time flux. Time, immediacy and the everyday are recurring questions in art and music, this study reviews practices that address these questions, essentially through three landmark composers of the twentieth century: Iannis Xenakis, John Cage and Murray Schafer. To gain precision in regards to the nature of musical listening it then probes theories of audio cognition and reflects on ways in which these can apply to real-time composing. The art of sonifying data extracted from the environment is arguably only as recent as the computer programs it depends on. This study reviews different practices that contribute towards a corpus of sonification-art, paying special attention to those practices where this process takes place in real-time. This is extended by an interrogation of the effect that mobility has on our listening experience.
RoadMusic is now a fully functional device generating multi-timbral music from immediate data about its surroundings. This dissertation argues that this process can be an alternative to mainstream media systems; it describes how RoadMusicâs programs function and the ways in which they have evolved to incorporate the ideas developed in this thesis. It shows how RoadMusic is now developing beyond my own personal practice and how it intends to reach a wider audience
Integration strategies and data analysis methods for plant systems biology
Understanding how function relates to multiple layers of inactions between biological entities is one of the key goals of bioinformatics research, in particular in such areas as systems biology. However, the realisation of this objective is hampered by the sheer volume and multi-level heterogeneity of potentially relevant information. This work addressed this issue by developing a set of integration pipelines and analysis methods as part of an Ondex data integration framework. The integration process incorporated both relevant data from a set of publically available databases and information derived from predicted approaches, which were also implemented as part of this work.
These methods were used to assemble integrated datasets that were of relevance to the study of the model plant species Arabidopsis thaliana and applicable for the network-driven analysis. A particular attention was paid to the evaluation and comparison of the different sources of these data. Approaches were implemented for the identification and characterisation of functional modules in integrated networks and used to study and compare networks constructed from different types of data. The benefits of data integration were also demonstrated in three different bioinformatics research scenarios. The analysis of the constructed datasets has also resulted in a better understanding of the functional role of genes identified in a study of a nitrogen uptake mutant and allowed to select candidate genes for further exploration
- âŠ