On the quality of Web Services.

Web Services (WSs) are gaining increasing attention as programming components and so is their quality. WSs offer many benefits, like assured interoperability, and reusability. Conversely, they introduce a number of challenges as far as their quality is concerned, seen from the perspectives of two different stakeholders: (1) the developer/provider of WSs and (2) the consumer of WSs. Developers are usually concerned about the correctness of the WS's functionality which can be assessed by functional testing. Consumers of WSs are usually careful about the reliability of WSs they are depending on (in addition to other qualities). They need to know whether the WSs are available (i.e., up and running), accessible (i.e., they actually accept requests) while available and whether they successfully deliver responses for the incoming requests. Availability, Accessibility, and Successability of WSs are directly related to WS reliability. Assessing these three factors via testing is usually only feasible at late stages of the development life-cycle. If they can be predicted early during the development, they can provide valuable information that may positively influence the engineering of WSs with regards to their quality. In this thesis we focus on assessing the quality of WSs via testing and via prediction. Testing of WSs is addressed by an extensive systematic literature review that focuses on a special type of WSs, the semantic WSs. The main objective of the review is to capture the current state of the art of functional testing of semantic WSs and to identify possible approaches for deriving functional test cases from their requirement specifications. The review follows a predefined procedure that involves automatically searching 5 well-known digital libraries. After applying the selection criteria to the search results, a total of 34 studies were identified as relevant. Required information was extracted from the studies, synthesized and summarized. The results of the systematic literature review showed that it is possible to derive test cases from requirement specifications of semantic WSs based on the different testing approaches identified in the primary studies. In more than half of the identified approaches, test cases are derived from transformed specification models. Petri Nets (and its derivatives) is the mostly used transformation. To derive test cases, different techniques are applied to the specification models. Model checking is largely used for this purpose. Prediction of Availability, Accessibility, and Successability is addressed by a correlational study in which we focused on identifying possible relations between the quality attributes Availability, Accessibility, and Successability and other internal quality measures (e.g., cyclomatic complexity) that may allow building statistically significant predictive models for the three attributes. A total of 34 students interacted freely with 20 pre-selected WSs while internal and external quality measures are collected using a data collection framework designed and implemented specially for this purpose. The collected data are then analyzed using different statistical approaches. The correlational study conducted confirmed that it is possible to build statistically significant predictive models for Accessibility and Successability. A very large number of significant models was built using two different approaches, namely the binary logistic regression and the ordinal logistic regression. Many significant predictive models were selected out of the identified models based on special criteria that take into consideration the predictive power and the stability of the models. The selected models are validated using the bootstrap validation technique. The result of validation showed that only two models out of the selected models are well calibrated and expected to maintain their predictive power when applied to a future dataset. These two models are for predicting Accessibility based on the number of weighted methods (WM) and the number of lines of code (LOC) respectively. The approach and the findings presented in this work for building accurate predictive models for the WSs qualities Availability, Accessibility, and Successability may offer researchers and practitioners an opportunity to examine and build similar predictive models for other WSs qualities, thus allowing for early prediction of the targeted qualities and hence early adjustments during the development to satisfy any requirements imposed on the WSs with regards to the predicted qualities. Early prediction of WSs qualities may help leverage trust on the WSs and reduces development costs, hence increases their adoption

An E-Learning Semantic Grid for Life science Education

There are a lot of life science databases and services on the Internet nowadays, especially in life science e-science. In this paper, we will present an E-Learning Semantic Grid that integrates these resources provided by both teachers and scientists for life science education. It uses domain ontologies to integrate these heterogeneous life science database and service resources, and supports ontology-based e-learning data-sharing and service-coordination for life science teachers and students in an e-learning virtual organization. Our system provides life science students with semantically superior experience in learning activities, and also extends the function of life science e-science. It has a promising future in the domain of life science education

The consistent representation of scientific knowledge : investigations into the ontology of karyotypes and mitochondria

PhD ThesisOntologies are widely used in life sciences to model scienti c knowledge. The engineering of these ontologies is well-studied and there are a variety of methodologies and techniques, some of which have been re-purposed from software engineering methodologies and techniques. However, due to the complex nature of bio-ontologies, they are not resistant to errors and mistakes. This is especially true for more expressive and/or larger ontologies. In order to improve on this issue, we explore a variety of software engineering techniques that were re-purposed in order to aid ontology engineering. This exploration is driven by the construction of two light-weight ontologies, The Mitochondrial Disease Ontology and The Karyotype Ontology. These ontologies have speci c and useful computational goals, as well as providing exemplars for our methodology. This thesis discusses the modelling decisions undertaken as well as the overall success of each ontological model. Due to the added knowledge capture steps required for the mitochondrial knowledge, The Karyotype Ontology is further developed than The Mitochondrial Disease Ontology. Speci cally, this thesis explores the use of a pattern-driven and programmatic approach to bio-medical ontology engineering. During the engineering of our biomedical ontologies, we found many of the components of each model were similar in logical and textual de nitions. This was especially true for The Karyotype Ontology. In software engineering a common technique to avoid replication is to abstract through the use of patterns. Therefore we utilised localised patterns to model these highly repetitive models. There are a variety of possible tools for the encoding of these patterns, but we found ontology development using Graphical User Interface (GUI) tools to be time-consuming due to the necessity of manual GUI interaction when the ontology needed updating. With the development of Tawny- OWL, a programmatic tool for ontology construction, we are able to overcome this issue, with the added bene t of using a single syntax to express both simple and - i - patternised parts of the ontology. Lastly, we brie y discuss how other methodologies and tools from software engineering, namely unit tests, di ng, version control and Continuous Integration (CI) were re-purposed and how they aided the engineering of our two domain ontologies. Together, this knowledge increases our understanding in ontology engineering techniques. By re-purposing software engineering methodologies, we have aided construction, quality and maintainability of two novel ontologies, and have demonstrated their applicability more generally

An Activating Mutation in sos-1 Identifies Its Dbl Domain as a Critical Inhibitor of the Epidermal Growth Factor Receptor Pathway during Caenorhabditis elegans Vulval Development

Proper regulation of receptor tyrosine kinase (RTK)-Ras-mitogen-activated protein kinase (MAPK) signaling pathways is critical for normal development and the prevention of cancer. SOS is a dual-function guanine nucleotide exchange factor (GEF) that catalyzes exchange on Ras and Rac. Although the physiologic role of SOS and its CDC25 domain in RTK-mediated Ras activation is well established, the in vivo function of its Dbl Rac GEF domain is less clear. We have identified a novel gain-of-function missense mutation in the Dbl domain of Caenorhabditis elegans SOS-1 that promotes epidermal growth factor receptor (EGFR) signaling in vivo. Our data indicate that a major developmental function of the Dbl domain is to inhibit EGF-dependent MAPK activation. The amount of inhibition conferred by the Dbl domain is equal to that of established trans-acting inhibitors of the EGFR pathway, including c-Cbl and RasGAP, and more than that of MAPK phosphatase. In conjunction with molecular modeling, our data suggest that the C. elegans mutation, as well as an equivalent mutation in human SOS1, activates the MAPK pathway by disrupting an autoinhibitory function of the Dbl domain on Ras activation. Our work suggests that functionally similar point mutations in humans could directly contribute to disease

Deploying mutation impact text-mining software with the SADI Semantic Web Services framework

Background: Mutation impact extraction is an important task designed to harvest relevant annotations from scientific documents for reuse in multiple contexts. Our previous work on text mining for mutation impacts resulted in (i) the development of a GATE-based pipeline that mines texts for information about impacts of mutations on proteins, (ii) the population of this information into our OWL DL mutation impact ontology, and (iii) establishing an experimental semantic database for storing the results of text mining. Results: This article explores the possibility of using the SADI framework as a medium for publishing our mutation impact software and data. SADI is a set of conventions for creating web services with semantic descriptions that facilitate automatic discovery and orchestration. We describe a case study exploring and demonstrating the utility of the SADI approach in our context. We describe several SADI services we created based on our text mining API and data, and demonstrate how they can be used in a number of biologically meaningful scenarios through a SPARQL interface (SHARE) to SADI services. In all cases we pay special attention to the integration of mutation impact services with external SADI services providing information about related biological entities, such as proteins, pathways, and drugs. Conclusion: We have identified that SADI provides an effective way of exposing our mutation impact data suc

MOODY: An ontology-driven framework for standardizing multi-objective evolutionary algorithms

The application of semantic technologies, particularly ontologies, in the realm of multi-objective evolutionary algorithms is overlook despite their effectiveness in knowledge representation. In this paper, we introduce MOODY, an ontology specifically tailored to formalize these kinds of algorithms, encompassing their respective parameters, and multi-objective optimization problems based on a characterization of their search space landscapes. MOODY is designed to be particularly applicable in automatic algorithm configuration, which involves the search of the parameters of an optimization algorithm to optimize its performance. In this context, we observe a notable absence of standardized components, parameters, and related considerations, such as problem characteristics and algorithm configurations. This lack of standardization introduces difficulties in the selection of valid component combinations and in the re-use of algorithmic configurations between different algorithm implementations. MOODY offers a means to infuse semantic annotations into the configurations found by automatic tools, enabling efficient querying of the results and seamless integration across diverse sources through their incorporation into a knowledge graph. We validate our proposal by presenting four case studies.Funding for open Access charge: Universidad de Málaga / CBUA. This work has been partially funded by the Spanish Ministry of Science and Innovation via Grant PID2020-112540RB-C41 (AEI/FEDER, UE) and the Andalusian PAIDI program with grant P18-RT-2799. José F. Aldana-Martín is supported by Grant PRE2021-098594 (Spanish Ministry of Science, Innovation and Universities)

Assisted evolution enables HIV-1 to overcome a high trim5α-imposed genetic barrier to rhesus macaque tropism

Diversification of antiretroviral factors during host evolution has erected formidable barriers to cross-species retrovirus transmission. This phenomenon likely protects humans from infection by many modern retroviruses, but it has also impaired the development of primate models of HIV-1 infection. Indeed, rhesus macaques are resistant to HIV-1, in part due to restriction imposed by the TRIM5α protein (rhTRIM5α). Initially, we attempted to derive rhTRIM5α-resistant HIV-1 strains using two strategies. First, HIV-1 was passaged in engineered human cells expressing rhTRIM5α. Second, a library of randomly mutagenized capsid protein (CA) sequences was screened for mutations that reduced rhTRIM5α sensitivity. Both approaches identified several individual mutations in CA that reduced rhTRIM5α sensitivity. However, neither approach yielded mutants that were fully resistant, perhaps because the locations of the mutations suggested that TRIM5α recognizes multiple determinants on the capsid surface. Moreover, even though additive effects of various CA mutations on HIV-1 resistance to rhTRIM5α were observed, combinations that gave full resistance were highly detrimental to fitness. Therefore, we employed an 'assisted evolution' approach in which individual CA mutations that reduced rhTRIM5α sensitivity without fitness penalties were randomly assorted in a library of viral clones containing synthetic CA sequences. Subsequent passage of the viral library in rhTRIM5α-expressing cells resulted in the selection of individual viral species that were fully fit and resistant to rhTRIM5α. These viruses encoded combinations of five mutations in CA that conferred complete or near complete resistance to the disruptive effects of rhTRIM5α on incoming viral cores, by abolishing recognition of the viral capsid. Importantly, HIV-1 variants encoding these CA substitutions and SIVmac239 Vif replicated efficiently in primary rhesus macaque lymphocytes. These findings demonstrate that rhTRIM5α is difficult to but not impossible to evade, and doing so should facilitate the development of primate models of HIV-1 infection