The Human Language Project

This is a "white paper" proposing the construction of a "universal corpus" containing digitizations of the world's languages. The proposed corpus is community-built and community-owned.http://deepblue.lib.umich.edu/bitstream/2027.42/64990/1/proposal.pd

Modelling bacterial regulatory networks with Petri nets

To exploit the vast data obtained from high throughput molecular biology, a variety of modelling and analysis techniques must be fully utilised. In this thesis, Petri nets are investigated within the context of computational systems biology, with the specific focus of facilitating the creation and analysis of models of biological pathways. The analysis of qualitative models of genetic networks using safe Petri net techniques was investigated with particular reference to model checking. To exploit existing model repositories a mapping was presented for the automatic translation of models encoded in the Systems Biology Markup Language (SBML) into the Petri Net framework. The mapping is demonstrated via the conversion and invariant analysis of two published models of the glycolysis pathway. Dynamic stochastic simulations of biological systems suffer from two problems: computational cost; and lack of kinetic parameters. A new stochastic Petri net simulation tool, NASTY was developed which addresses the prohibitive real-time computational costs of simulations by using distributed job scheduling. In order to manage and maximise the usefulness of simulation results a new data standard, TSML was presented. The computational power of NASTY provided the basis for the development of a genetic algorithm for the automatic parameterisation of stochastic models. This parameter estimation technique was evaluated on a published model of the general stress response of E. coli. An attempt to enhance the parameter estimation process using sensitivity analysis was then investigated. To explore the scope and limits of applying the Petri net techniques presented, a realistic case study investigated how the Pho and aB regulons interact to mitigate phosphate stress in Bacillus subtilis. This study made use of a combination of qualitative and quantitative Petri net techniques and was able to confirm an existing experimental hypothesis.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Modelling bacterial regulatory networks with Petri nets

To exploit the vast data obtained from high throughput molecular biology, a variety of modelling and analysis techniques must be fully utilised. In this thesis, Petri nets are investigated within the context of computational systems biology, with the specific focus of facilitating the creation and analysis of models of biological pathways. The analysis of qualitative models of genetic networks using safe Petri net techniques was investigated with particular reference to model checking. To exploit existing model repositories a mapping was presented for the automatic translation of models encoded in the Systems Biology Markup Language (SBML) into the Petri Net framework. The mapping is demonstrated via the conversion and invariant analysis of two published models of the glycolysis pathway. Dynamic stochastic simulations of biological systems suffer from two problems: computational cost; and lack of kinetic parameters. A new stochastic Petri net simulation tool, NASTY was developed which addresses the prohibitive real-time computational costs of simulations by using distributed job scheduling. In order to manage and maximise the usefulness of simulation results a new data standard, TSML was presented. The computational power of NASTY provided the basis for the development of a genetic algorithm for the automatic parameterisation of stochastic models. This parameter estimation technique was evaluated on a published model of the general stress response of E. coli. An attempt to enhance the parameter estimation process using sensitivity analysis was then investigated. To explore the scope and limits of applying the Petri net techniques presented, a realistic case study investigated how the Pho and aB regulons interact to mitigate phosphate stress in Bacillus subtilis. This study made use of a combination of qualitative and quantitative Petri net techniques and was able to confirm an existing experimental hypothesis.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Coping with evolution in information systems: a database perspective

Business organisations today are faced with the complex problem of dealing with evolution in their software information systems. This effectively concerns the accommodation and facilitation of change, in terms of both changing user requirements and changing technological requirements. An approach that uses the software development life-cycle as a vehicle to study the problem of evolution is adopted. This involves the stages of requirements analysis, system specification, design, implementation, and finally operation and maintenance. The problem of evolution is one requiring proactive as well as reactive solutions for any given application domain. Measuring evolvability in conceptual models and the specification of changing requirements are considered. However, even "best designs" are limited in dealing with unanticipated evolution, and require implementation phase paradigms that can facilitate an evolution correctly (semantic integrity), efficiently (minimal disruption of services) and consistently (all affected parts are consistent following the change). These are also discussedComputingM. Sc. (Information Systems

A theory and model for the evolution of software services

Software services are subject to constant change and variation. To control service development, a service developer needs to know why a change was made, what are its implications and whether the change is complete. Typically, service clients do not perceive the upgraded service immediately. As a consequence, service-based applications may fail on the service client side due to changes carried out during a provider service upgrade. In order to manage changes in a meaningful and effective manner service clients must therefore be considered when service changes are introduced at the service provider's side. Otherwise such changes will most certainly result in severe application disruption. Eliminating spurious results and inconsistencies that may occur due to uncontrolled changes is therefore a necessary condition for the ability of services to evolve gracefully, ensure service stability, and handle variability in their behavior. Towards this goal, this work presents a model and a theoretical framework for the compatible evolution of services based on well-founded theories and techniques from a number of disparate fields.

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio