CompaGB: An open framework for genome browsers comparison

<p>Abstract</p> <p>Background</p> <p>Tools to visualize and explore genomes hold a central place in genomics and the diversity of genome browsers has increased dramatically over the last few years. It often turns out to be a daunting task to compare and choose a well-adapted genome browser, as multidisciplinary knowledge is required to carry out this task and the number of tools, functionalities and features are overwhelming.</p> <p>Findings</p> <p>To assist in this task, we propose a community-based framework based on two cornerstones: (i) the implementation of industry promoted software qualification method (QSOS) adapted for genome browser evaluations, and (ii) a web resource providing numerous facilities either for visualizing comparisons or performing new evaluations. We formulated 60 criteria specifically for genome browsers, and incorporated another 65 directly from QSOS's generic section. Those criteria aim to answer versatile needs, ranging from a biologist whose interest primarily lies into user-friendly and informative functionalities, a bioinformatician who wants to integrate the genome browser into a wider framework, or a computer scientist who might choose a software according to more technical features. We developed a dedicated web application to enrich the existing QSOS functionalities (weighting of criteria, user profile) with features of interest to a community-based framework: easy management of evolving data, user comments...</p> <p>Conclusions</p> <p>The framework is available at <url>http://genome.jouy.inra.fr/CompaGB</url>. It is open to anyone who wishes to participate in the evaluations. It helps the scientific community to (1) choose a genome browser that would better fit their particular project, (2) visualize features comparatively with easily accessible formats, such as tables or radar plots and (3) perform their own evaluation against the defined criteria. To illustrate the CompaGB functionalities, we have evaluated seven genome browsers according to the implemented methodology. A summary of the features of the compared genome browsers is presented and discussed.</p

CompaGB: An open framework for genome browsers comparison

<p>Abstract</p> <p>Background</p> <p>Tools to visualize and explore genomes hold a central place in genomics and the diversity of genome browsers has increased dramatically over the last few years. It often turns out to be a daunting task to compare and choose a well-adapted genome browser, as multidisciplinary knowledge is required to carry out this task and the number of tools, functionalities and features are overwhelming.</p> <p>Findings</p> <p>To assist in this task, we propose a community-based framework based on two cornerstones: (i) the implementation of industry promoted software qualification method (QSOS) adapted for genome browser evaluations, and (ii) a web resource providing numerous facilities either for visualizing comparisons or performing new evaluations. We formulated 60 criteria specifically for genome browsers, and incorporated another 65 directly from QSOS's generic section. Those criteria aim to answer versatile needs, ranging from a biologist whose interest primarily lies into user-friendly and informative functionalities, a bioinformatician who wants to integrate the genome browser into a wider framework, or a computer scientist who might choose a software according to more technical features. We developed a dedicated web application to enrich the existing QSOS functionalities (weighting of criteria, user profile) with features of interest to a community-based framework: easy management of evolving data, user comments...</p> <p>Conclusions</p> <p>The framework is available at <url>http://genome.jouy.inra.fr/CompaGB</url>. It is open to anyone who wishes to participate in the evaluations. It helps the scientific community to (1) choose a genome browser that would better fit their particular project, (2) visualize features comparatively with easily accessible formats, such as tables or radar plots and (3) perform their own evaluation against the defined criteria. To illustrate the CompaGB functionalities, we have evaluated seven genome browsers according to the implemented methodology. A summary of the features of the compared genome browsers is presented and discussed.</p

Assessing the Open Source Development Processes Using OMM

The assessment of development practices in Free Libre Open Source Software (FLOSS) projects can contribute to the improvement of the development process by identifying poor practices and providing a list of necessary practices. Available assessment methods (e.g., Capability Maturity Model Integration (CMMI)) do not address sufficiently FLOSS-specific aspects (e.g., geographically distributed development, importance of the contributions, reputation of the project, etc.). We present a FLOSS-focused, CMMI-like assessment/improvement model: the QualiPSo Open Source Maturity Model (OMM). OMM focuses on the development process. This makes it different from existing assessment models that are focused on the assessment of the product. We have assessed six FLOSS projects using OMM. Three projects were started and led by a software company, and three are developed by three different FLOSS communities. We identified poorly addressed development activities as the number of commit/bug reports, the external contributions, and the risk management. The results showed that FLOSS projects led by companies adopt standard project management approaches as product planning, design definition, and testing, that are less often addressed by community led FLOSS projects. The OMM is valuable for both the FLOSS community, by identifying critical development activities necessary to be improved, and for potential users that can better decide which product to adopt

Open Source Platforms for Big Data Analytics

O conceito de Big Data tem tido um grande impacto no campo da tecnologia, em particular na gestão e análise de enormes volumes de informação. Atualmente, as organizações consideram o Big Data como uma oportunidade para gerir e explorar os seus dados o máximo possível, com o objetivo de apoiar as suas decisões dentro das diferentes áreas operacionais. Assim, é necessário analisar vários conceitos sobre o Big Data e o Big Data Analytics, incluindo definições, características, vantagens e desafios. As ferramentas de Business Intelligence (BI), juntamente com a geração de conhecimento, são conceitos fundamentais para o processo de tomada de decisão e transformação da informação. Ao investigar as plataformas de Big Data, as práticas industriais atuais e as tendências relacionadas com o mundo da investigação, é possível entender o impacto do Big Data Analytics nas pequenas organizações. Este trabalho pretende propor soluções para as micro, pequenas ou médias empresas (PME) que têm um grande impacto na economia portuguesa, dado que representam a maioria do tecido empresarial. As plataformas de código aberto para o Big Data Analytics oferecem uma grande oportunidade de inovação nas PMEs. Este trabalho de pesquisa apresenta uma análise comparativa das funcionalidades e características das plataformas e os passos a serem tomados para uma análise mais profunda e comparativa. Após a análise comparativa, apresentamos uma avaliação e seleção de plataformas Big Data Analytics (BDA) usando e adaptando a metodologia QSOS (Qualification and Selection of software Open Source) para qualificação e seleção de software open-source. O resultado desta avaliação e seleção traduziu-se na eleição de duas plataformas para os testes experimentais. Nas plataformas de software livre de BDA foi usado o mesmo conjunto de dados assim como a mesma configuração de hardware e software. Na comparação das duas plataformas, demonstrou que a HPCC Systems Platform é mais eficiente e confiável que a Hortonworks Data Platform. Em particular, as PME portuguesas devem considerar as plataformas BDA como uma oportunidade de obter vantagem competitiva e melhorar os seus processos e, consequentemente, definir uma estratégia de TI e de negócio. Por fim, este é um trabalho sobre Big Data, que se espera que sirva como um convite e motivação para novos trabalhos de investigação.The concept of Big Data has been having a great impact in the field of technology, particularly in the management and analysis of huge volumes of information. Nowadays organizations look for Big Data as an opportunity to manage and explore their data the maximum they can, with the objective of support decisions within its different operational areas. Thus, it is necessary to analyse several concepts about Big Data and Big Data Analytics, including definitions, features, advantages and disadvantages. Business intelligence along with the generation of knowledge are fundamental concepts for the process of decision-making and transformation of information. By investigate today's big data platforms, current industrial practices and related trends in the research world, it is possible to understand the impact of Big Data Analytics on small organizations. This research intends to propose solutions for micro, small or médium enterprises (SMEs) that have a great impact on the Portuguese economy since they represente approximately 90% of the companies in Portugal. The open source platforms for Big Data Analytics offers a great opportunity for SMEs. This research work presents a comparative analysis of those platforms features and functionalities and the steps that will be taken for a more profound and comparative analysis. After the comparative analysis, we present an evaluation and selection of Big Data Analytics (BDA) platforms using and adapting the Qualification and Selection of software Open Source (QSOS) method. The result of this evaluation and selection was the selection of two platforms for the empirical experiment and tests. The same testbed and dataset was used in the two Open Source Big Data Analytics platforms. When comparing two BDA platforms, HPCC Systems Platform is found to be more efficient and reliable than Hortonworks Data Platform. In particular, Portuguese SMEs should consider for BDA platforms an opportunity to obtain competitive advantage and improve their processes and consequently define an IT and business strategy. Finally, this is a research work on Big Data; it is hoped that this will serve as an invitation and motivation for new research

A systematic literature review of open source software quality assessment models

Background: Many open source software (OSS) quality assessment models are proposed and available in the litera- ture. However, there is little or no adoption of these models in practice. In order to guide the formulation of newer models so they can be acceptable by practitioners, there is need for clear discrimination of the existing models based on their speci c properties. Based on this, the aim of this study is to perform a systematic literature review to inves- tigate the properties of the existing OSS quality assessment models by classifying them with respect to their quality characteristics, the methodology they use for assessment, and their domain of application so as to guide the formula- tion and development of newer models. Searches in IEEE Xplore, ACM, Science Direct, Springer and Google Search is performed so as to retrieve all relevant primary studies in this regard. Journal and conference papers between the year 2003 and 2015 were considered since the rst known OSS quality model emerged in 2003. Results: A total of 19 OSS quality assessment model papers were selected. To select these models we have devel- oped assessment criteria to evaluate the quality of the existing studies. Quality assessment models are classi ed into ve categories based on the quality characteristics they possess namely: single-attribute, rounded category, community-only attribute, non-community attribute as well as the non-quality in use models. Our study re ects that software selection based on hierarchical structures is found to be the most popular selection method in the existing OSS quality assessment models. Furthermore, we found that majority (47%) of the existing models do not specify any domain of application. Conclusions: In conclusion, our study will be a valuable contribution to the community and helps the quality assess- ment model developers in formulating newer models and also to the practitioners (software evaluators) in selecting suitable OSS in the midst of alternatives

Identifying and Scoping Context-Specific Use Cases For Blockchain-Enabled Systems in the Wild.

Advances in technology often provide a catalyst for digital innovation. Arising from the global banking crisis at the end of the first decade of the 21st Century, decentralised and distributed systems have seen a surge in growth and interest. Blockchain technology, the foundation of the decentralised virtual currency Bitcoin, is one such catalyst. The main component of a blockchain, is its public record of verified, timestamped transactions maintained in an append-only, chain-like, data structure. This record is replicated across n-nodes in a network of co-operating participants. This distribution offers a public proof of transactions verified in the past. Beyond tokens and virtual currency, real-world use cases for blockchain technology are in need of research and development. The challenge in this proof-of-concept research is to identify an orchestration model of innovation that leads to the successful development of software artefacts that utilise blockchain technology. These artefacts must maximise the potential of the technology and enhance the real-world business application. An original two phase orchestration model is defined. The model includes both a discovery and implementation phase and implements state-of-the-art process innovation frameworks: Capability Maturity Modelling, Business Process Redesign, Open Innovation and Distributed Digital Innovation. The model succeeds in its aim to generate feasible problem-solution design pairings to be implemented as blockchain enabled software systems. Three systems are developed: an internal supply-chain management system, a crowd-source sponsorship model for individual players on a team and a proof-of-origin smart tag system. The contribution is to have defined an innovation model through which context-specific blockchain usecases can be identified and scoped in the wild

A new model for the selection of web development frameworks: application to PHP frameworks

The use of a framework is often essential for medium and large scale developments, but is also of interest for small developments. PHP has evolved as the scripting language the most chosen by developers, which has generated an explosion of PHP frameworks. There is a big debate about what the best PHP frameworks are, because the simple fact is that not all frameworks are built for everyone. Indeed, not all frameworks meet the same needs, and several frameworks can be used together in certain situations. Choosing the right framework, however, can sometimes be difficult. In order to make the selection process easier, we propose a pragmatic and complete model to compare and evaluate the main PHP frameworks. This model is based on a set of comparison criteria based on the Intrinsic durability, industrialized solution, technical adaptability, strategy, technical architecture and Speed criteria. Results show that the values of these criteria allow developers to easily and properly choose the framwork that best meets their need

Supporting the Selection of Open Innovation Software Tools

International audienceIn this paper, we present a Web Mining exploratory approach to establish a comparative selection of current Open Innovation (OI) software tools. The starting point of this study is related to " ELLIOT " European project (FP7 ICT) that aims to develop an Internet of Things (IoT) experiential platform involving citizens and users from the early stage of idea creation to the further implementation of innovative IoT applications and services. In this project, one of the objectives is to help the citizens exchanging ideas and co-creating new green services based on environmental data. For this purpose, we develop an exploratory assessment approach based on the QSOS method to elaborate a feature grid in order to support the selection of OI Tools. We find that most of the related works focus on theories about innovation process or product life cycle to classify OI Tools. Our approach combines web mining techniques to finally instantiate the first QSOS reference criteria template dedicated to OI Tools