QueryOR: a comprehensive web platform for genetic variant analysis and prioritization

Background: Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to facilitate data analysis. Results: Here we describe QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. Instead of being designed on specific datasets, it works on a general XML schema specifying formats and criteria of each data source. Thanks to this flexibility, new criteria can be easily added for future expansion. Currently, up to 70 user-selectable criteria are available, including a wide range of gene and variant features. Moreover, rather than progressively discarding variants taking one criterion at a time, the prioritization is achieved by a global positive selection process that considers all transcript isoforms, thus producing reliable results. QueryOR is easy to use and its intuitive interface allows to handle different kinds of inheritance as well as features related to sharing variants in different patients. QueryOR is suitable for investigating single patients, families or cohorts. Conclusions: QueryOR is a comprehensive and flexible web platform eligible for an easy user-driven variant prioritization. It is freely available for academic institutions at http://queryor.cribi.unipd.it/

Non-Technical Individual Skills are Weakly Connected to the Maturity of Agile Practices

Context: Existing knowledge in agile software development suggests that individual competency (e.g. skills) is a critical success factor for agile projects. While assuming that technical skills are important for every kind of software development project, many researchers suggest that non-technical individual skills are especially important in agile software development. Objective: In this paper, we investigate whether non-technical individual skills can predict the use of agile practices. Method: Through creating a set of multiple linear regression models using a total of 113 participants from agile teams in six software development organizations from The Netherlands and Brazil, we analyzed the predictive power of non-technical individual skills in relation to agile practices. Results: The results show that there is surprisingly low power in using non-technical individual skills to predict (i.e. explain variance in) the mature use of agile practices in software development. Conclusions: Therefore, we conclude that looking at non-technical individual skills is not the optimal level of analysis when trying to understand, and explain, the mature use of agile practices in the software development context. We argue that it is more important to focus on the non-technical skills as a team-level capacity instead of assuring that all individuals possess such skills when understanding the use of the agile practices.Comment: 18 pages, 1 figur

Approach to attributed feature modeling for requirements elicitation in Scrum agile development

Requirements elicitation is a core activity of requirements engineering for the product to be developed. The knowledge that has been gained during requirements engineering about the product to be developed forms the basis for requirement elicitation. The agile approach is becoming known day by day as the most widely used innovative process in the domain of requirements engineering. Requirements elicitation in agile development faces several challenges. Requirements must be gathered sufficiently to reflect stakeholders' needs. Furthermore, because of the development process, requirements evolve, and they must be adequately treated to keep up with the changing demands of the market and the passage of time. Another challenge with agile implementation is handling non-functional requirements in software development. Addressing non- functional requirements is still a critical factor in the success of any product. Requirements prioritization is also one of the most challenging tasks, and it is uncommon for requirement engineers to be able to specify and document all the requirements at once. This paper presents an approach for requirements elicitation in scrum-based agile development. The approach operates with the feature modeling technique, which is originally used in the Software Product Line (SPL). One of the most important proposed extensions to Feature Models (FMs) is the introduction of feature attributes. Our method uses attributed FMs to consider both functional and non-functional requirements as well as requirement prioritization. For the evaluation purposes, we have demonstrated our approach through two case studies in different domains of software product development. The first case study is in the domain of education, and the second one is in the domain of health care. The results reveal that our approach fits the requirements elicitation process in scrum agile development.Bourns College of Engineering, University of California, Riverside(undefined

Interdependent policy instrument preferences: a two-mode network approach

In policymaking, actors are likely to take the preferences of others into account when strategically positioning themselves. However, there is a lack of research that conceives of policy preferences as an interdependent system. In order to analyse interdependencies, we link actors to their policy preferences in water protection, which results in an actor-instrument network. As actors exhibit multiple preferences, a complex two-mode network between actors and policies emerges. We analyse whether actors exhibit interdependent preference profiles given shared policy objectives or social interactions among them. By fitting an exponential random graph model to the actor-instrument network, we find considerable clustering, meaning that actors tend to exhibit preferences for multiple policy instruments in common. Actors tend to exhibit interdependent policy preferences when they are interconnected, that is, they collaborate with each other. By contrast, actors are less likely to share policy preferences when a conflict line divides them

An Empirical Study on the Role of Requirement Engineering in Agile Method and Its Impact on Quality

Agile Methods are characterized as flexible and easily adaptable. The need to keep up with multiple high-priority projects and shorter time-to-market demands could explain their increasing popularity. It also raises concerns of whether or not use of these methods jeopardizes quality. Since Agile methods allow for changes throughout the process, they also create probabilities to impact software quality at any time. This thesis examines the process of requirement engineering as performed with Agile method in terms of its similarities and differences to requirement engineering as performed with the more traditional Waterfall method. It compares both approaches from a software quality perspective using a case study of 16 software projects. The main contribution of this work is to bring empirical evidence from real life cases that illustrate how Agile methods significantly impacts software quality, including the potential for a larger number of defects due to poor non-functional requirements elicitation

What causes positive customer satisfaction in an ineffectual software development project? A mechanism from a process tracing case study

The customer role is crucial in agile information systems development (ISD). There is, however, a scarceness in research on how this role is enacted, and how its practice influences project outcome. In this longitudinal case study, an agile ISD project is followed with a particular focus on the customer organization’s participation, aiming to contribute to the understanding of how customers influence agile ISD projects. The data analysis follows a process tracing approach, a case study method where one aims to identify the causes and outcomes of any kind of process through the rigorous analysis of qualitative data. The analysis of the case shows that the low completion of the initial project requirements was caused by over-scoping and by an immature customer. Further, the customer’s acceptance of the outcome was caused by the agile practices introduced in the project. These helped to create a high customer’s sense of responsibility for the outcome, which worked as a mediator towards a positive acceptance of the delivery. The study contributes a mechanism for why agile projects may still be successful in light of low delivery. It is also a first case study in the information systems field explicitly using a process tracing approach