Design and Implementation of the UniProt Website

The UniProt consortium is the main provider of protein sequence and annotation data for much of the life sciences community. The "www.uniprot.org":http://www.uniprot.org website is the primary access point to this data and to documentation and basic tools for the data. This paper discusses the design and implementation of the new website, which was released in July 2008, and shows how it improves data access for users with different levels of experience, as well as to machines for programmatic access

Towards a Tool-based Development Methodology for Pervasive Computing Applications

Despite much progress, developing a pervasive computing application remains a challenge because of a lack of conceptual frameworks and supporting tools. This challenge involves coping with heterogeneous devices, overcoming the intricacies of distributed systems technologies, working out an architecture for the application, encoding it in a program, writing specific code to test the application, and finally deploying it. This paper presents a design language and a tool suite covering the development life-cycle of a pervasive computing application. The design language allows to define a taxonomy of area-specific building-blocks, abstracting over their heterogeneity. This language also includes a layer to define the architecture of an application, following an architectural pattern commonly used in the pervasive computing domain. Our underlying methodology assigns roles to the stakeholders, providing separation of concerns. Our tool suite includes a compiler that takes design artifacts written in our language as input and generates a programming framework that supports the subsequent development stages, namely implementation, testing, and deployment. Our methodology has been applied on a wide spectrum of areas. Based on these experiments, we assess our approach through three criteria: expressiveness, usability, and productivity

Cloud computing services: taxonomy and comparison

Cloud computing is a highly discussed topic in the technical and economic world, and many of the big players of the software industry have entered the development of cloud services. Several companies what to explore the possibilities and benefits of incorporating such cloud computing services in their business, as well as the possibilities to offer own cloud services. However, with the amount of cloud computing services increasing quickly, the need for a taxonomy framework rises. This paper examines the available cloud computing services and identifies and explains their main characteristics. Next, this paper organizes these characteristics and proposes a tree-structured taxonomy. This taxonomy allows quick classifications of the different cloud computing services and makes it easier to compare them. Based on existing taxonomies, this taxonomy provides more detailed characteristics and hierarchies. Additionally, the taxonomy offers a common terminology and baseline information for easy communication. Finally, the taxonomy is explained and verified using existing cloud services as examples

Structured Review of the Evidence for Effects of Code Duplication on Software Quality

This report presents the detailed steps and results of a structured review of code clone literature. The aim of the review is to investigate the evidence for the claim that code duplication has a negative effect on code changeability. This report contains only the details of the review for which there is not enough place to include them in the companion paper published at a conference (Hordijk, Ponisio et al. 2009 - Harmfulness of Code Duplication - A Structured Review of the Evidence)

Scala Server Faces

Progress in the Java language has been slow over the last few years. Scala is emerging as one of the probable successors for Java with features such as type inference, higher order functions, closure support and sequence comprehensions. This allows object-oriented yet concise code to be written using Scala. While Java based MVC frameworks are still prevalent, Scala based frameworks along with Ruby on Rails, Django and PHP are emerging as competitors. Scala has a web framework called Lift which has made an attempt to borrow the advantages of other frameworks while keeping code concise. Since Sun’s MVC framework, Java Server Faces 2.0 and its future versions seem to be heading in a reasonably progressive direction; I have developed a framework which attempts to overcome its limitations. I call such a framework ―Scala Server Faces‖. This framework provides a way of writing Java EE applications in Scala yet borrow from the concept of ―convention over configuration‖ followed by rival web frameworks. Again, an Eclipse tool is provided to make the programmer\u27s task of writing code on the popular Eclipse platform. Scala Server Faces, the framework and the tool allows the programmer to write enterprise web applications in Scala by providing features such as templating support, CRUD screen generation for database model objects, an Ant script to help deployment and integration with the Glassfish Application Server

A Semantic-Agent Framework for PaaS Interoperability

Suchismita Hoare, Na Helian, and Nathan Baddoo, 'A Semantic-Agent Framework for PaaS Interoperability', in Proceedings of the The IEEE International Conference on Cloud and Big Data Computing, Toulouse, France, 18-21, July 2016. DOI: 10.1109/UIC-ATC-ScalCom-CBDCom-IoP-SmartWorld.2016.0126 © 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.Cloud Platform as a Service (PaaS) is poised for a wider adoption by its relevant stakeholders, especially Cloud application developers. Despite this, the service model is still plagued with several adoption inhibitors, one of which is lack of interoperability between proprietary application infrastructure services of public PaaS solutions. Although there is some progress in addressing the general PaaS interoperability issue through various devised solutions focused primarily on API compatibility and platform-agnostic application design models, interoperability specific to differentiated services provided by the existing public PaaS providers and the resultant disparity owing to the offered services’ semantics has not been addressed effectively, yet. The literature indicates that this dimension of PaaS interoperability is awaiting evolution in the state-of-the-art. This paper proposes the initial system design of a PaaS interoperability (IntPaaS) framework to be developed through the integration of semantic and agent technologies to enable transparent interoperability between incompatible PaaS services. This will involve uniform description through semantic annotation of PaaS provider services utilizing the OWL-S ontology, creating a knowledgebase that enables software agents to automatically search for suitable services to support Cloud-based Greenfield application development. The rest of the paper discusses the identified research problem along with the proposed solution to address the issue.Submitted Versio