miRPlant : an integrated tool for identification of plant miRNA from RNA sequencing data

Background Small RNA sequencing is commonly used to identify novel miRNAs and to determine their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep*. miRDeep-P was developed to identify plant miRNA using miRDeep’s probabilistic model of miRNA biogenesis, but it depends on several third party tools and lacks a user-friendly interface. The objective of our miRPlant program is to predict novel plant miRNA, while providing a user-friendly interface with improved accuracy of prediction. Result We have developed a user-friendly plant miRNA prediction tool called miRPlant. We show using 16 plant miRNA datasets from four different plant species that miRPlant has at least a 10% improvement in accuracy compared to miRDeep-P, which is the most popular plant miRNA prediction tool. Furthermore, miRPlant uses a Graphical User Interface for data input and output, and identified miRNA are shown with all RNAseq reads in a hairpin diagram. Conclusions We have developed miRPlant which extends miRDeep* to various plant species by adopting suitable strategies to identify hairpin excision regions and hairpin structure filtering for plants. miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. miRPlant is also the first plant miRNA prediction tool that dynamically plots miRNA hairpin structure with small reads for identified novel miRNAs. This feature will enable biologists to visualize novel pre-miRNA structure and the location of small RNA reads relative to the hairpin. Moreover, miRPlant can be easily used by biologists with limited bioinformatics skills.

Z-source converter based grid-interface for variable-speed permanent magnet wind turbine generators

A Z-source inverter based grid-interface for a variable-speed wind turbine connected to a permanent magnet synchronous generator is proposed. A control system is designed to harvest maximum wind energy under varied wind conditions with the use of the permanent magnet synchronous generator, diode-rectifier and Z-source inverter. Control systems for speed regulation of the generator and for DC- and AC- sides of the Z-source inverter are investigated using computer simulations and laboratory experiments. Simulation and experimental results verify the efficacy of the proposed approach.

Web mediated market interactions and enterprise software

With increased consolidation and a few large vendors dominating the market, how can software vendors distinguish themselves in order to maintain profitability and gain market share? Increasingly customers are becoming more proactive in selecting a vendor and a product, drawing upon various publications, market surveys, mailing lists, and, of course, other users. In particular, though, a company's Web site is the obvious place to begin information gathering. In sum, it may seem that the days of the uninformed customer prepared to be "sold to" are potentially all but gone.

Reflections on issues of power in packaged software selection

The adoption of packaged software is becoming increasingly common in a variety of organizations and much of the packaged software literature presents this as a straightforward, linear process based on rationalistic evaluation. This paper applies the framework of power relations developed by Markus and Bjørn-­‐Anderson (1987) to a longitudinal study concerning the adoption of a customer relationship management package in a small organization. This is used to highlight both overt and covert power issues within the selection and procurement of the product and illustrate the interplay of power between senior management, IT managers, IT vendors and consultants, and end-­‐users. The paper contributes to the growing body of literature on packaged software and also to our understanding of how power is deeply embedded within the surrounding processes.

IT consultants, salesmanship and the challenges of packaged software selection in SMEs

Purpose – This paper seeks to analyse the process of packaged software selection in a small organization, focussing particularly on the role of IT consultants as intermediaries in the process. Design/methodology/approach – This is based upon a longitudinal, qualitative field study concerning the adoption of a customer relationship management package in an SME management consultancy. Findings – The authors illustrate how the process of “salesmanship”, an activity directed by the vendor/consultant and focussed on the interests of senior management, marginalises user needs and ultimately secures the procurement of the software package. Research limitations/implications – Despite the best intentions the authors lose something of the rich detail of the lived experience of technology in presenting the case study as a linear narrative. Specifically, the authors have been unable to do justice to the complexity of the multifarious ways in which individual perceptions of the project were influenced and shaped by the opinions of others. Practical implications – Practitioners, particularly those from within SMEs, should be made aware of the ways in which external parties may have a vested interest in steering projects in a particular direction, which may not necessarily align with their own interests. Originality/value – This study highlights in detail the role of consultants and vendors in software selection processes, an area which has received minimal attention to date. Prior work in this area emphasises the necessary conditions for, and positive outcomes of, appointing external parties in an SME context, with only limited attention being paid to the potential problems such engagements may bring.

The social shaping of packaged software selection

As organisations increasingly engage in the selection, purchase, and adoption of packaged software products, how these activities are carried out in practice becomes increasingly relevant for researchers and practitioners. Our focus in this paper is to propose a framework for understanding the packaged software selection process. The functionalist literature on this area of study suggests a number of generic recommendations, which are based on rational assumptions about the process and view the decision making that takes place as producing the “best technology solution.’” To explore this, we conducted a longitudinal, in-depth study of packaged software selection in a small organisation. For interpretation of the case, we draw upon the Social Construction of Technology, a theoretical framework arguing that technology is socially constituted and regarding the process of development as contradictory and uncertain. We offer a number of contributions. First, we further our understanding of packaged software selection with the critique that we offer of the functionalist literature, drawing insights from the emerging critical/constructivist literature and expanding our domain of interest to encompass the wider environment. Second, we weave this together with our experiences in the field, drawing on social constructivism for theoretical support, to develop a framework of packaged software selection that shows how various actors shape the process.

CRM packaged software : a study of organisational experiences

Customer Relationship Management (CRM) packaged software has become a key contributor to attempts at aligning business and IT strategies in recent years. Throughout the 1990s there was, in many organisations strategies, a shift from the need to manage transactions and toward relationship management. Where Enterprise Resource Planning packages dominated the management of transactions era, CRM packages lead in regard to relationships. At present, balanced views of CRM packages are scantly presented instead relying on vendor rhetoric. This paper uses case study research to analyse some of the issues associated with CRM packages. These issues include the limitations of CRM packages, the need for a relationship orientation and the problems of a dominant management perspective of CRM. It is suggested that these issues could be more readily accommodated by organisational detachment from beliefs in IT as utopia, consideration of prior IS theory and practice and a more informed approach to CRM package selection.

Potential pitfalls in packaged software adoption

The common reasons for those in organizations adopting large config- urable packaged software products are compelling. Problems with the existing software situation, the supposed predictability and perceived business benefits of packaged software, and various social influences, can lead to packages being preferred to custom approaches. Yet, for every reason, there is a potential associated problem that must be understood before an informed adoption decision can be made...

Achieving enterprise integration through software customization : part I-evidence from the field

Achieving business and IT integration is strategic goal for many organisations – it has almost become the ‘Holy Grail’ of organisational success. In this environment Enterprise Resource Planning (ERP) packages have become the defacto option for addressing this issue. Integration has come to mean adopting ERP, through configuration and without customization, but this all or nothing approach has proved difficult for many organisations. In part 1 of a 2 part update we provide evidence from the field that suggests that whilst costly, if managed appropriately, customization can have value in aiding organisational integration efforts. In part 2, we discuss in more detail the benefits and pitfalls involved in enacting a non-standard based integration strategy.

Achieving enterprise integration through software customization : part II-enacting the strategy

In part 1 of this update, we put forward the argument that integration in ERP based environments can be achieved in ways other than adopting a software configuration only approach. We drew on evidence from two large ERP implementations to show how, despite the cost implications, some customization, if carefully managed, could prove helpful. In this, the final part of the update, we discuss the benefits, and potential pitfalls, involved in enacting a non-standard based integration strategy. This requires attention to a) broadening the integration definition; b) bringing legacy practices forward and c) developing a customization based integration strategy.

Vagueness and software engineering

We do not commonly associate software engineering with philosophical debate. Indeed, software engineers ought to be concerned with building software systems and not settling philosophical questions. I attempt to show that software engineers do, in fact, take philosophical sides when designing software applications. In particular, I look at how the problem of vagueness arises in software engineering and argue that when software engineers solve it, they commit to philosophical views that they are seldom aware of. In the second part of the paper, I suggest a way of dealing with vague predicates without having to confront the problem of vagueness itself. The purpose of my paper is to highlight the currently prevalent disconnect between philosophy and software engineering. I claim that a better knowledge of the philosophical debate is important as it can have ramifications for crucial software design decisions. Better awareness of philosophical issues not only produces better software engineers, it also produces better engineered products.

A non-linear interface element model for thin layer high adhesive mortared masonry

A nonlinear interface element modelling method is formulated for the prediction of deformation and failure of high adhesive thin layer polymer mortared masonry exhibiting failure of units and mortar. Plastic flow vectors are explicitly integrated within the implicit finite element framework instead of relying on predictor–corrector like approaches. The method is calibrated using experimental data from uniaxial compression, shear triplet and flexural beam tests. The model is validated using a thin layer mortared masonry shear wall, whose experimental datasets are reported in the literature and is used to examine the behaviour of thin layer mortared masonry under biaxial loading.