A cooperative framework for molecular biology database integration using image object selection

The theme and the concept of 'Molecular Biology Database Integration' and the problems associated with this concept initiated the idea for this Ph.D research. The available technologies facilitate to analyse the data independently and discretely but it fails to integrate the data resources for more meaningful information. This along with the integration issues created the scope for this Ph.D research. The research has reviewed the 'database interoperability' problems and it has suggested a framework for integrating the molecular biology databases. The framework has proposed to develop a cooperative environment to share information on the basis of common purpose for the molecular biology databases. The research has also reviewed other implementation and interoperability issues for laboratory based, dedicated and target specific database. The research has addressed the following issues: diversity of molecular biology databases schemas, schema constructs and schema implementation multi-database query using image object keying, database integration technologies using context graph, automated navigation among these databases. This thesis has introduced a new approach for database implementation. It has introduced an interoperable component database concept to initiate multidatabase query on gene mutation data. A number of data models have been proposed for gene mutation data which is the basis for integrating the target specific component database to be integrated with the federated information system. The proposed data models are: data models for genetic trait analysis, classification of gene mutation data, pathological lesion data and laboratory data. The main feature of this component database is non-overlapping attributes and it will follow non-redundant integration approach as explained in the thesis. This will be achieved by storing attributes which will not have the union or intersection of any attributes that exist in public domain molecular biology databases. Unlike data warehousing technique, this feature is quite unique and novel. The component database will be integrated with other biological data sources for sharing information in a cooperative environment. This involves developing new tools. The thesis explains the role of these new tools which are: meta data extractor, mapping linker, query generator and result interpreter. These tools are used for a transparent integration without creating any global schema of the participating databases. The thesis has also established the concept of image object keying for multidatabase query and it has proposed a relevant algorithm for matching protein spot in gel electrophoresis image. An object spot in gel electrophoresis image will initiate the query when it is selected by the user. It matches the selected spot with other similar spots in other resource databases. This image object keying method is an alternative to conventional multidatabase query which requires writing complex SQL scripts. This method also resolve the semantic conflicts that exist among molecular biology databases. The research has proposed a new framework based on the context of the web data for interactions with different biological data resources. A formal description of the resource context is described in the thesis. The implementation of the context into Resource Document Framework (RDF) will be able to increase the interoperability by providing the description of the resources and the navigation plan for accessing the web based databases. A higher level construct is developed (has, provide and access) to implement the context into RDF for web interactions. The interactions within the resources are achieved by utilising an integration domain to extract the required information with a single instance and without writing any query scripts. The integration domain allows to navigate and to execute the query plan within the resource databases. An extractor module collects elements from different target webs and unify them as a whole object in a single page. The proposed framework is tested to find specific information e.g., information on Alzheimer's disease, from public domain biology resources, such as, Protein Data Bank, Genome Data Bank, Online Mendalian Inheritance in Man and local database. Finally, the thesis proposes further propositions and plans for future work

Sapienz: Multi-objective automated testing for android applications

We introduce Sapienz, an approach to Android testing that uses multi-objective search-based testing to automatically explore and optimise test sequences, minimising length, while simultaneously maximising coverage and fault revelation. Sapienz combines random fuzzing, systematic and search-based exploration, exploiting seeding and multi-level instrumentation. Sapienz significantly outperforms (with large effect size) both the state-of-the-art technique Dynodroid and the widely-used tool, Android Monkey, in 7/10 experiments for coverage, 7/10 for fault detection and 10/10 for fault-revealing sequence length. When applied to the top 1, 000 Google Play apps, Sapienz found 558 unique, previously unknown crashes. So far we have managed to make contact with the developers of 27 crashing apps. Of these, 14 have confirmed that the crashes are caused by real faults. Of those 14, six already have developer-confirmed fixes

TEGDroid: Test Case Generation Approach for Android Apps Considering Context and GUI Events

The advancement in mobile technologies has led to the production of mobile devices (e.g. smartphone) with rich innovative features. This has enabled the development of mobile applications that offer users an advanced and extremely localized context-aware content. The recent dependence of people on mobile applications for various computational needs poses a significant concern on the quality of mobile applications. In order to build a high quality and more reliable applications, there is a need for effective testing techniques to test the applications. Most existing testing technique focuses on GUI events only without sufficient support for context events. This makes it difficult to identify other defects in the changes that can be inclined by context in which an application runs. This paper presents an approach named TEGDroid for generating test case for Android Apps considering both context and GUI Events. The GUI and context events are identified through the static analysis of bytecode, and the analysis of app’s permission from the XML file. An experiment was performed on real world mobile apps to evaluate TEGDroid. Our experimental results show that TEGDroid is effective in identifying context events and had 65%-91% coverage across the eight selected applications. To evaluate the fault detection capability of this approach, mutation testing was performed by introducing mutants to the applications. Results from the mutation analysis shows that 100% of the mutants were killed. This indicates that TEGDroid have the capability to detect faults in mobile apps

Overcoming Language Dichotomies: Toward Effective Program Comprehension for Mobile App Development

Mobile devices and platforms have become an established target for modern software developers due to performant hardware and a large and growing user base numbering in the billions. Despite their popularity, the software development process for mobile apps comes with a set of unique, domain-specific challenges rooted in program comprehension. Many of these challenges stem from developer difficulties in reasoning about different representations of a program, a phenomenon we define as a "language dichotomy". In this paper, we reflect upon the various language dichotomies that contribute to open problems in program comprehension and development for mobile apps. Furthermore, to help guide the research community towards effective solutions for these problems, we provide a roadmap of directions for future work.Comment: Invited Keynote Paper for the 26th IEEE/ACM International Conference on Program Comprehension (ICPC'18

Automating Regression Test Selection for Web Services

As Web services grow in maturity and use, so do the methods which are being used to test and maintain them. Regression Testing is a major component of most major testing systems but has only begun to be applied to Web services. The majority of the tools and techniques applying regression test to Web services are focused on test-case generation, thus ignoring the potential savings of regression test selection. Regression test selection optimizes the regression testing process by selecting a subset of all tests, while still maintaining some level of confidence about the system performing no worse than the unmodified system. A safe regression test selection technique implies that after selection, the level of confidence is as high as it would be if no tests were removed. Since safe regression test selection techniques generally involve code-based (white-box) testing, they cannot be directly applied to Web services due to their loosely-coupled, standards-based, and distributed nature. A framework which automates both the regression test selection and regression testing processes for Web services in a decentralized, end-to-end manner is proposed. As part of this approach, special consideration is given to the concurrency issues which may occur in an autonomous and decentralized system. The resulting synchronization method will be presented along with a set of algorithms which manage the regression testing and regression test selection processes throughout the system. A set of empirical results demonstrate the feasibility and benefit of the approach

The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web

Research in life sciences is increasingly being conducted in a digital and online environment. In particular, life scientists have been pioneers in embracing new computational tools to conduct their investigations. To support the sharing of digital objects produced during such research investigations, we have witnessed in the last few years the emergence of specialized repositories, e.g., DataVerse and FigShare. Such repositories provide users with the means to share and publish datasets that were used or generated in research investigations. While these repositories have proven their usefulness, interpreting and reusing evidence for most research results is a challenging task. Additional contextual descriptions are needed to understand how those results were generated and/or the circumstances under which they were concluded. Because of this, scientists are calling for models that go beyond the publication of datasets to systematically capture the life cycle of scientific investigations and provide a single entry point to access the information about the hypothesis investigated, the datasets used, the experiments carried out, the results of the experiments, the people involved in the research, etc. In this paper we present the Research Object (RO) suite of ontologies, which provide a structured container to encapsulate research data and methods along with essential metadata descriptions. Research Objects are portable units that enable the sharing, preservation, interpretation and reuse of research investigation results. The ontologies we present have been designed in the light of requirements that we gathered from life scientists. They have been built upon existing popular vocabularies to facilitate interoperability. Furthermore, we have developed tools to support the creation and sharing of Research Objects, thereby promoting and facilitating their adoption.Comment: 20 page

Machine-Readable Privacy Certificates for Services

Privacy-aware processing of personal data on the web of services requires managing a number of issues arising both from the technical and the legal domain. Several approaches have been proposed to matching privacy requirements (on the clients side) and privacy guarantees (on the service provider side). Still, the assurance of effective data protection (when possible) relies on substantial human effort and exposes organizations to significant (non-)compliance risks. In this paper we put forward the idea that a privacy certification scheme producing and managing machine-readable artifacts in the form of privacy certificates can play an important role towards the solution of this problem. Digital privacy certificates represent the reasons why a privacy property holds for a service and describe the privacy measures supporting it. Also, privacy certificates can be used to automatically select services whose certificates match the client policies (privacy requirements). Our proposal relies on an evolution of the conceptual model developed in the Assert4Soa project and on a certificate format specifically tailored to represent privacy properties. To validate our approach, we present a worked-out instance showing how privacy property Retention-based unlinkability can be certified for a banking financial service.Comment: 20 pages, 6 figure