EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data

Background: Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the Minimum Information About a Microarray Experiment (MIAME) recommendations, the MAGE-ML format for data interchange, and the use of controlled vocabularies or ontologies. The existing software systems for microarray data analysis implement the mentioned standards only partially and are often hard to use and extend. Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems. Results: The EMMA 2 software has been designed to resolve shortcomings with respect to full MAGE-ML and ontology support and makes use of modern data integration techniques. We present a software system that features comprehensive data analysis functions for spotted arrays, and for the most common synthesized oligo arrays such as Agilent, Affymetrix and NimbleGen. The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services. Conclusion: Our model-driven approach for automatically implementing a full MAGE object model provides high flexibility and compatibility. Data integration via SOAP-based web-services is advantageous in a distributed client-server environment as the collaborative analysis of microarray data is gaining more and more relevance in international research consortia. The adequacy of the EMMA 2 software design and implementation has been proven by its application in many distributed functional genomics projects. Its scalability makes the current architecture suited for extensions towards future transcriptomics methods based on high-throughput sequencing approaches which have much higher computational requirements than microarrays.

Um modelo para aferir o nível de maturidade na adoção de SOA

Tese (doutorado)—Universidade de Brasília, Faculdade de Tecnologia, Departamento de Engenharia Elétrica, 2015.

Assessing Decision Making Skill in Complex and Dynamic Environments Using Representative and Simulated Tasks

Traditional decision making research has often focused on one's ability to choose from a set of prefixed options, ignoring the process by which decision makers generate courses of action (i.e., options) in-situ (Klein, 1993). In complex and dynamic domains, this option generation process is particularly critical to understanding how successful decisions are made (Zsambok & Klein, 1997). When generating response options for oneself to pursue (i.e., during the intervention-phase of decision making) previous research has supported quick and intuitive heuristics, such as the Take-The-First heuristic (TTF; Johnson & Raab, 2003). When generating predictive options for others in the environment (i.e., during the assessment-phase of decision making), previous research has supported the situational-model-building process described by Long Term Working Memory theory (LTWM; see Ward, Ericsson, & Williams, 2013). In the first three experiments, the claims of TTF and LTWM are tested during assessment- and intervention-phase tasks in soccer. To test what other environmental constraints may dictate the use of these cognitive mechanisms, the claims of these models are also tested in the presence and absence of time pressure. In addition to understanding the option generation process, it is important that researchers in complex and dynamic domains also develop tools that can be used by `real-world' professionals. For this reason, three more experiments were conducted to evaluate the effectiveness of a new online assessment of perceptual-cognitive skill in soccer. This test differentiated between skill groups and predicted performance on a previously established test and predicted option generation behavior. The test also outperformed domain-general cognitive tests, but not a domain-specific knowledge test when predicting skill group membership. Implications for theory and training, and future directions for the development of applied tools are discussed.

Towards flexible parsing of structured textual model representations

Existing parsers for textual model representation formats such as XMI and HUTN are unforgiving and fail upon even the smallest inconsistency between the structure and naming of metamodel elements and the contents of serialised models. In this paper, we demonstrate how a fuzzy parsing approach can transparently and automatically resolve a number of these inconsistencies, and how it can eventually turn XML into a human-readable and editable textual model representation format for particular classes of models.

Integration of a graph-based model indexer in commercial modelling tools

Softeam has over 20 years of experience providing UML-based modelling solutions, such as its Modelio modelling tool, and its Constellation enterprise model management and collaboration environment. Due to the increasing number and size of the models used by Softeam’s clients, Softeam joined the MONDO FP7 EU research project, which worked on solutions for these scalability challenges and produced the Hawk model indexer among other results. This paper presents the technical details and several case studies on the integration of Hawk into Softeam’s toolset. The first case study measured the performance of Hawk’s Modelio support using varying amounts of memory for the Neo4j backend. In another case study, Hawk was integrated into Constellation to provide scalable global querying of model repositories. Finally, the combination of Hawk and the Epsilon Generation Language was compared against Modelio for document generation: for the largest model, Hawk was two orders of magnitude faster.

Stress-testing centralised model stores

One of the current challenges in model-driven engineering is enabling effective collaborative modelling. Two common approaches are either storing the models in a central repository, or keeping them under a traditional file-based version control system and build a centralized index for model-wide queries. Either way, special attention must be paid to the nature of these repositories and indexes as networked services: they should remain responsive even with an increasing number of concurrent clients. This paper presents an empirical study on the impact of certain key decisions on the scalability of concurrent model queries, using an Eclipse Connected Data Objects model repository and a Hawk model index. The study evaluates the impact of the network protocol, the API design and the internal caching mechanisms and analyzes the reasons for their varying performance.

Two case studies on generating administrative process applications with AdminDSL

Some organizations end up reimplementing the same class of business process over and over: an "administrative process", which consists of managing a form through several states and involving various roles in the organization. This results in wasted time that could be dedicated to better understanding the process or dealing with the fine details that are specific to the process. Existing virtual office solutions require specific training and infrastructure andmay result in vendor lock-in. In this paper, we propose using a high-level domain-specific language (AdminDSL) to describe the administrative process and a separate code generator targeting a standard web framework. We have implemented the approach using Xtext, EGL and the Django web framework, and we illustrate it through two case studies: a synthetic examination process which illustrates the architecture of the generated code, and a real-world workplace survey process that identified several future avenues for improvement.

A next application prediction service using the BaranC framework

Predicting user behaviour enables user assistant services provide personalized services to the users. This requires a comprehensive user model that can be created by monitoring user interactions and activities. BaranC is a framework that performs user interface (UI) monitoring (and collects all associated context data), builds a user model, and supports services that make use of the user model. A prediction service, Next-App, is built to demonstrate the use of the framework and to evaluate the usefulness of such a prediction service. Next-App analyses a user's data, learns patterns, makes a model for a user, and finally predicts, based on the user model and current context, what application(s) the user is likely to want to use. The prediction is pro-active and dynamic, reflecting the current context, and is also dynamic in that it responds to changes in the user model, as might occur over time as a user's habits change. Initial evaluation of Next-App indicates a high-level of satisfaction with the service.

Increasing the value of household appliances by adding a heat pump system

Historically, domestic tasks such as preparing food and washing and drying clothes and dishes were done by hand. In a modern home many of these chores are taken care of by machines such as washing machines, dishwashers and tumble dryers. When the first such machines came on the market customers were happy that they worked at all! Today, the costs of electricity and customers’ environmental awareness are high, so features such as low electricity, water and detergent use strongly influence which household machine the customer will buy. One way to achieve lower electricity usage for the tumble dryer and the dishwasher is to add a heat pump system. The function of a heat pump system is to extract heat from a lower temperature source (heat source) and reject it to a higher temperature sink (heat sink) at a higher temperature level. Heat pump systems have been used for a long time in refrigerators and freezers, and that industry has driven the development of small, high quality, low price heat pump components. The low price of good quality heat pump components, along with an increased willingness to pay extra for lower electricity usage and environmental impact, make it possible to introduce heat pump systems in other household products. However, there is a high risk of failure with new features. A number of household manufacturers no longer exist because they introduced poorly implemented new features, which resulted in low quality and product performance. A manufacturer must predict whether the future value of a feature is high enough for the customer chain to pay for it. The challenge for the manufacturer is to develop and produce a high-performance heat pump feature in a household product with high quality, predict future willingness to pay for it, and launch it at the right moment in order to succeed. Tumble dryers with heat pump systems have been on the market since 2000. Paper I reports on the development of a transient simulation model of a commercial heat pump tumble dryer. The measured and simulated results were compared with good similarity. The influence of the size of the compressor and the condenser was investigated using the validated simulation model. The results from the simulation model show that increasing the cylinder volume of the compressor by 50% decreases the drying time by 14% without using more electricity.  Paper II is a concept study of adding a heat pump system to a dishwasher in order to decrease the total electricity usage. The dishwasher, dishware and water are heated by the condenser, and the evaporator absorbs the heat from a water tank. The majority of the heat transfer to the evaporator occurs when ice is generated in the water tank. An experimental setup and a transient simulation model of a heat pump dishwasher were developed. The simulation results show a 24% reduction in electricity use compared to a conventional dishwasher heated with an electric element. The simulation model was based on an experimental setup that was not optimised. During the study it became apparent that it is possible to decrease electricity usage even more with the next experimental setup.

Searching for novel targets to control wheat Head Blight Disease-I-Protein identification, 3D modeling and virtual screening.

2016

Employing the five-factor mentoring instrument : analysing mentoring practices for teaching primary science.

Primary science education is a concern around the world and quality mentoring within schools can develop preservice teachers’ practices. A five-factor model for mentoring has been identified, namely, personal attributes, system requirements, pedagogical knowledge, modelling, and feedback. Final-year preservice teachers (mentees, n=211) from three Turkish universities were administered a previously validated instrument to gather perceptions of their mentoring in primary science teaching. ANOVA indicated that each of these five factors was statistically significant (p<.001) with mean scale scores ranging from 3.36 to 4.12. Although mentees perceived their mentors to provide evaluation feedback (95%), model classroom management (88%), guide their preparation (96%), and outline the science curriculum (92%), the majority of mentors were perceived not to assist their mentees in 10 of the 34 survey items. Professional development programmes that target the specific needs of these mentors may further enhance mentoring practices for advancing primary science teaching.

National guidelines for digital modelling

These National Guidelines and Case Studies for Digital Modelling are the outcomes from one of a number of Building Information Modelling (BIM)-related projects undertaken by the CRC for Construction Innovation. Since the CRC opened its doors in 2001, the industry has seen a rapid increase in interest in BIM, and widening adoption. These guidelines and case studies are thus very timely, as the industry moves to model-based working and starts to share models in a new context called integrated practice. Governments, both federal and state, and in New Zealand are starting to outline the role they might take, so that in contrast to the adoption of 2D CAD in the early 90s, we ensure that a national, industry-wide benefit results from this new paradigm of working. Section 1 of the guidelines give us an overview of BIM: how it affects our current mode of working, what we need to do to move to fully collaborative model-based facility development. The role of open standards such as IFC is described as a mechanism to support new processes, and make the extensive design and construction information available to asset operators and managers. Digital collaboration modes, types of models, levels of detail, object properties and model management complete this section. It will be relevant for owners, managers and project leaders as well as direct users of BIM. Section 2 provides recommendations and guides for key areas of model creation and development, and the move to simulation and performance measurement. These are the more practical parts of the guidelines developed for design professionals, BIM managers, technical staff and ‘in the field’ workers. The guidelines are supported by six case studies including a summary of lessons learnt about implementing BIM in Australian building projects. A key aspect of these publications is the identification of a number of important industry actions: the need for BIM-compatible product information and a national context for classifying product data; the need for an industry agreement and setting process-for-process definition; and finally, the need to ensure a national standard for sharing data between all of the participants in the facility-development process.

National guidelines for digital modelling : case studies

These National Guidelines and Case Studies for Digital Modelling are the outcomes from one of a number of Building Information Modelling (BIM)-related projects undertaken by the CRC for Construction Innovation. Since the CRC opened its doors in 2001, the industry has seen a rapid increase in interest in BIM, and widening adoption. These guidelines and case studies are thus very timely, as the industry moves to model-based working and starts to share models in a new context called integrated practice. Governments, both federal and state, and in New Zealand are starting to outline the role they might take, so that in contrast to the adoption of 2D CAD in the early 90s, we ensure that a national, industry-wide benefit results from this new paradigm of working. Section 1 of the guidelines give us an overview of BIM: how it affects our current mode of working, what we need to do to move to fully collaborative model-based facility development. The role of open standards such as IFC is described as a mechanism to support new processes, and make the extensive design and construction information available to asset operators and managers. Digital collaboration modes, types of models, levels of detail, object properties and model management complete this section. It will be relevant for owners, managers and project leaders as well as direct users of BIM. Section 2 provides recommendations and guides for key areas of model creation and development, and the move to simulation and performance measurement. These are the more practical parts of the guidelines developed for design professionals, BIM managers, technical staff and ‘in the field’ workers. The guidelines are supported by six case studies including a summary of lessons learnt about implementing BIM in Australian building projects. A key aspect of these publications is the identification of a number of important industry actions: the need for BIMcompatible product information and a national context for classifying product data; the need for an industry agreement and setting process-for-process definition; and finally, the need to ensure a national standard for sharing data between all of the participants in the facility-development process.

Resembling Florida : transpacific transfer of ideas from one Gold Coast to another

Despite different political structures and planning systems, striking physical similarities exist between the tourist destinations of the Gold Coasts of Queensland and Florida. Both have been fast developing sub-tropical coastal areas, subject to massive land booms, speculation, and entrepreneurs’ grand visions throughout their history. As a result, both have become tourist destinations of international renown. Drawing on historical sources, the present research seeks to investigate the extent to which these similarities result from taking American cities as a model for newer development in Australia; in this case from transferring planning and marketing ideas from one Gold Coast to another, with the development of the Florida Gold Coast setting precedent for the development of the Queensland Gold Coast.

Financial planning and well-being

The aim of this paper is to provide a review of the theoretical and research literature on the ways in which financial planning can enhance well-being. In reviewing the literature, the paper develops a conceptual framework for thinking about the extended value of financial planning, beyond financial outcomes, by examining the process of planning in the financial domain and its relationship to life satisfaction, living an intentional life, attainment of life goals, and the development of a sense of mastery. An essential element of psychological well-being is engagement in life tasks and roles. Planning can be considered a life management strategy that enables individuals to control and structure their lives. Having meaningful goals and the plans to achieve those goals enable individuals to experience higher levels of life engagement and well-being (MacLeod et al., 2008). Recent research on well-being suggests that domain-specific behaviours contribute to domain-specific satisfactions, which in turn contribute to an individual’s overall satisfaction with life (Easterlin, 2003; 2006). Thus changes in domain satisfaction, such as financial satisfaction, are likely to effect changes in life satisfaction.