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

A generic framework for process execution and secure multi-party transaction authorization

Process execution engines are not only an integral part of workflow and business process management systems but are increasingly used to build process-driven applications. In other words, they are potentially used in all kinds of software across all application domains. However, contemporary process engines and workflow systems are unsuitable for use in such diverse application scenarios for several reasons. The main shortcomings can be observed in the areas of interoperability, versatility, and programmability. Therefore, this thesis makes a step away from domain specific, monolithic workflow engines towards generic and versatile process runtime frameworks, which enable integration of process technology into all kinds of software. To achieve this, the idea and corresponding architecture of a generic and embeddable process virtual machine (ePVM), which supports defining process flows along the theoretical foundation of communicating extended finite state machines, are presented. The architecture focuses on the core process functionality such as control flow and state management, monitoring, persistence, and communication, while using JavaScript as a process definition language. This approach leads to a very generic yet easily programmable process framework. A fully functional prototype implementation of the proposed framework is provided along with multiple example applications. Despite the fact that business processes are increasingly automated and controlled by information systems, humans are still involved, directly or indirectly, in many of them. Thus, for process flows involving sensitive transactions, a highly secure authorization scheme supporting asynchronous multi-party transaction authorization must be available within process management systems. Therefore, along with the ePVM framework, this thesis presents a novel approach for secure remote multi-party transaction authentication - the zone trusted information channel (ZTIC). The ZTIC approach uniquely combines multiple desirable properties such as the highest level of security, ease-of-use, mobility, remote administration, and smooth integration with existing infrastructures into one device and method. Extensively evaluating both, the ePVM framework and the ZTIC, this thesis shows that ePVM in combination with the ZTIC approach represents a unique and very powerful framework for building workflow systems and process-driven applications including support for secure multi-party transaction authorization

Pristup integraciji tehničkih prostora zasnovan na preslikavanjima iinženjerstvu vođenom modelima

In order to automate development of integration adapters in industrial settings, a model-driven approach to adapter specification is devised. In this approach, a domain-specific modeling language is created to allow specification of mappings between integrated technical spaces. Also proposed is the mapping automation engine that comprises reuse and alignment algorithms. Based on mapping specifications, executable adapters are automatically generated and executed. Results of approach evaluations indicate that it is possible to use a model-driven approach to successfully integrate technical spaces and increase the automation by reusing domainspecific mappings from previously created adapters.За потребе повећања степена аутоматизације развоја адаптера за интеграцију у индустријском окружењу, осмишљен је моделом вођен приступ развоју адаптера. У оквиру овог приступа развијен је наменски језик за спецификацију пресликавања између техничких простора који су предмет интеграције. Приступ обухвата и алгоритме за поравнање и поновно искориштење претходно креираних пресликавања са циљем аутоматизације процеса спецификације. На основу креираних пресликавања, могуће je аутоматски генерисати извршиви код адаптера. У испитивањима приступа, показано је да је могуће успешно применити моделом вођен приступ у интеграцији техничких простора као и да је могуће успешно повећати степен аутоматизације поновним искоришћењем претходно креираних пресликавања.Za potrebe povećanja stepena automatizacije razvoja adaptera za integraciju u industrijskom okruženju, osmišljen je modelom vođen pristup razvoju adaptera. U okviru ovog pristupa razvijen je namenski jezik za specifikaciju preslikavanja između tehničkih prostora koji su predmet integracije. Pristup obuhvata i algoritme za poravnanje i ponovno iskorištenje prethodno kreiranih preslikavanja sa ciljem automatizacije procesa specifikacije. Na osnovu kreiranih preslikavanja, moguće je automatski generisati izvršivi kod adaptera. U ispitivanjima pristupa, pokazano je da je moguće uspešno primeniti modelom vođen pristup u integraciji tehničkih prostora kao i da je moguće uspešno povećati stepen automatizacije ponovnim iskorišćenjem prethodno kreiranih preslikavanja

A service orientated architecture and wireless sensor network approach applied to the measurement and visualisation of a micro injection moulding process. Design, development and testing of an ESB based micro injection moulding platform using Google Gadgets and business processes for the integration of disparate hardware systems on the factory shop floor

Factory shop floors of the future will see a significant increase in interconnected devices for monitoring and control. However, if a Service Orientated Architecture (SOA) is implemented on all such devices then this will result in a large number of permutations of services and composite services. These services combined with other business level components can pose a huge challenge to manage as it is often difficult to keep an overview of all the devices, equipment and services. This thesis proposes an SOA based novel assimilation architecture for integrating disparate industrial hardware based processes and business processes of an enterprise in particular the plastics machinery environment. The key benefits of the proposed architecture are the reduction of complexity when integrating disparate hardware platforms; managing the associated services as well as allowing the Micro Injection Moulding (µIM) process to be monitored on the web through service and data integration. An Enterprise Service Bus (ESB) based middleware layer integrates the Wireless Sensor Network (WSN) based environmental and simulated machine process systems with frontend Google Gadgets (GGs) based web visualisation applications. A business process framework is proposed to manage and orchestrate the resulting services from the architecture. Results from the analysis of the WSN kits in terms of their usability and reliability showed that the Jennic WSN was easy to setup and had a reliable communication link in the polymer industrial environment with the PER being below 0.5%. The prototype Jennic WSN based µIM process monitoring system had limitations when monitoring high-resolution machine data, therefore a novel hybrid integration architecture was proposed. The assimilation architecture was implemented on a distributed server based test bed. Results from test scenarios showed that the architecture was highly scalable and could potentially allow a large number of disparate sensor based hardware systems and services to be hosted, managed, visualised and linked to form a cohesive business process

Experimental Object-Oriented Modelling

This thesis examines object-oriented modelling in experimental system development. Object-oriented modelling aims at representing concepts and phenomena of a problem domain in terms of classes and objects. Experimental system development seeks active experimentation in a system development project through, e.g., technical prototyping and active user involvement. We introduce and examine "experimental object-oriented modelling" as the intersection of these practices

Combining SOA and BPM Technologies for Cross-System Process Automation

This paper summarizes the results of an industry case study that introduced a cross-system business process automation solution based on a combination of SOA and BPM standard technologies (i.e., BPMN, BPEL, WSDL). Besides discussing major weaknesses of the existing, custom-built, solution and comparing them against experiences with the developed prototype, the paper presents a course of action for transforming the current solution into the proposed solution. This includes a general approach, consisting of four distinct steps, as well as specific action items that are to be performed for every step. The discussion also covers language and tool support and challenges arising from the transformation