An improved TIGER2 implementation for NAMD suitable for the Blue Gene architecture

Here we present an improved implementation of the TIGER2 Replica Exchange Molecular Dynamics (REMD) method, using the replica exchange Application Programming Interface (API) found in contemporary versions of the NAMD Molecular Dynamics Package. The implementation takes the form of a TCL script which is used in conjunction with the standard configuration file. This implementation is validated against a previous TIGER2 implementation, as well as data reported for the original TIGER2 simulations. Our implementation is compatible with a range of architectures; crucially it enables the use of this wrapper with the BlueGene/Q architecture, in addition to the x86 architecture. Program summary: Program title: TIGER2-NAMD. Catalogue identifier: AEWC_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEWC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 34151. No. of bytes in distributed program, including test data, etc.: 424217. Distribution format: tar.gz. Programming language: Tcl 8.5. Computer: x86 Clusters, BlueGene/Q, Workstations. Operating system: Linux, IBM Compute Node Kernel. Has the code been vectorised or parallelised?: Yes. MPI Parallelism. Classification: 3. External routines: NAMD 2.9 (http://www.ks.uiuc.edu/Research/namd/). Nature of problem: Replica Exchange Molecular Dynamics. Solution method: Each replica runs through multiple cycles of heating and cooling with exchanges between them being attempted. Running time: Typically 30 mins, up to an hour.

The waterhole : using educational drama as a pedagogical tool in a foreign language class at a public primary school in Japan

This study investigates Japanese primary school students’ and teachers’ responses to educational drama as a pedagogical tool in their English language classes. Along with the participants’ responses, the applicability of educational drama as a teaching method for the Japanese teachers is also discussed. The study was conducted in Japan as ateacher-researcher using participatory action research methods. The participants of the study are three Year Six classes and their teachers in a public primary school in Japan. Educational drama is introduced as an alternative teaching and learning method to these participants who have had no experience of drama in education.

Assessment of online reflections : engaging English second language (ESL) students

Online discussion boards are being used increasingly by tertiary educators as a tool for encouraging greater student interaction and developing learning communities. In particular, educators who have adopted a learner centered, socio-constructivist approach to teaching have sought to facilitate collaborative learning in which students reflect upon and share their experiences and perspectives, and construct knowledge together through developing shared meanings. This paper presents the findings of an electronic survey of the perceptions of 70 distance education EFL and ESL students concerning a compulsory assessment item involving contribution to an online course discussion board. The study revealed that the majority of the students enjoyed the assessment item and agreed that posting to the online course discussion board had allowed them to achieve a range of cognitive and social learning outcomes, as well as to develop some important graduate skills. In particular, ESL students reported the benefits of posting to the discussion board in terms of sharing their experiences with others and reducing the feeling of isolation. Further, when considering social outcomes, ESL students perceive the discussion board provided them with an opportunity to meet and develop a closer relationship with other students in the course and encouraged them to keep up with their studies.

Introducing creative language learning in Japan through educational drama

Educational Drama as a teaching and learning methodology is already widely in use and well accepted by Australian teachers and students. This paper reports on a study in which the author investigated Japanese primary school students' and teachers' responses to educational drama as a pedagogical tool in their English language classes. The participants had no prior experience of drama in education. Along with the participants' responses, the applicability of educational drama as a teaching method for the Japanese teachers is also discussed. The author, as a teacher-researcher, used action research methods for this study. It became evident that educational drama tended to motivate the Japanese students' foreign language learning of English, by providing them with an opportunity for a higher level of engagement and participation in learning. In the study, the students showed enhancement of the skills necessary for learning, including social, communication, linguistic, non-linguistic and problem-solving skills.

Global English corner : using Elluminate to enhance international students' English language skills

Students at Victoria University (VU) in Melbourne, Australia, undertake their study in an English language context and they have a range of support options to assist with English language development. VU has partner universities in China (Sichuan University, Henan University and Liaoning University). VU’s programs in China often have fewer language support options than programs in Melbourne. The Australian Government’s Transnational Quality Strategy requires that educational programs on- and offshore provide students with a comparable learning experience. Given the relative lack of English speaking opportunities available to VU’s students in China, the university is exploring how technologies might achieve a greater comparability of the student experience. This paper reports on a pilot program that uses Elluminate to conduct English conversations between students in China and Australia. The perceived lack of English competence of international students has been an ongoing issue in Australian higher education while the ‘English corner’ is ‘a characteristically Chinese approach to informal practice’ (Jin & Cortazzi, 2002) that helps students learning English in a foreign context to develop their English language proficiency. How might the idea of ‘English corner’ be used with educational technologies to encourage international students to practise and develop their English? This paper discusses a pilot program at VU that combines the idea of the English Corner together with the online conferencing tool Elluminate and a blog developed in WordPress, to engage Chinese students offshore in English language conversations. Through Elluminate and the Global English Corner blog, a pair of student peers in Melbourne conducts semi-structured conversations with groups of students offshore. In Elluminate, students can both hear and see each other – and they can simultaneously txt chat, share documents, images and websites and use the collaborative whiteboard function of Elluminate – to have dynamic conversations in real time. Preliminary findings of this pilot that uses technology to emphasise the societal aspects of learning – including language learning – will be presented. The discussion will consider how a more widespread English Corner program could aid the transition of international students in Australia, encourage the interaction of local students and international students, increase opportunities for international students to practise English and achieve a greater comparability of language support options on- and offshore.

Development and evaluation of a screening tool to identify people with diabetes at increased risk of medication problems relating to hypoglycaemia and medication non-adherence

Abstract Aims: To develop and evaluate a screening tool to identify people with diabetes at increased risk of medication problems relating to hypoglycaemia and medication non-adherence. Methods: A retrospective audit of attendances at a diabetes outpatient clinic at a public, teaching hospital over a 16-month period was conducted. Logistic regression was undertaken to examine risk factors associated with medication problems relating to hypoglycaemia and medication non-adherence and the most predictive set of factors comprise the Diabetes Medication Risk Screening Tool. Evaluating the tool involved assessing sensitivity and specificity, positive and negative predictive values, cut-off scores, inter-rater reliability, and content validity. Results: The Diabetes Medication Risk Screening Tool comprises seven predictive factors: age, living alone, English language, mental and behavioural problems, comorbidity index score, number of medications prescribed, and number of high-risk medications prescribed. The tool has 76.5% sensitivity, 59.5% specificity, and has a 65.1% positive predictive value, and a 71.8% negative predictive value. A score of 27 or more out of 62 was associated with high-risk of a medication problem. The inter-rater reliability of the tool was high (κ = 0.79, 95% CI 0.75 - 0.84) and the content validity index was 99.4%. Conclusion: The Diabetes Medication Risk Screening Tool has good psychometric properties and can proactively identify people with diabetes at greatest risk of medication problems relating to hypoglycaemia and medication non-adherence.

A visual language and environment for enterprise system modelling and automation

Objective: We want to support enterprise service modelling and generation using a more end user-friendly metaphor than current approaches, which fail to scale to large organisations with key issues of "cobweb" and "labyrinth" problems and large numbers of hidden dependencies. Method: We present and evaluate an integrated visual approach for business process modelling using a novel tree-based overlay structure that effectively mitigate complexity problems. A tree-overlay based visual notation (EML) and its integrated support environment (MaramaEML) supplement and integrate with existing solutions. Complex business architectures are represented as service trees and business processes are modelled as process overlay sequences on the service trees. Results: MaramaEML integrates EML and BPMN to provide complementary, high-level business service modelling and supports automatic BPEL code generation from the graphical representations to realise web services implementing the specified processes. It facilitates generated service validation using an integrated LTSA checker and provides a distortion-based fisheye and zooming function to enhance complex diagram navigation. Evaluations of EML show its effectiveness. Conclusions: We have successfully developed and evaluated a novel tree-based metaphor for business process modelling and enterprise service generation. Practice implications: a more user-friendly modelling approach and support tool for business end users.

SecDSVL: a domain-specific visual language to support enterprise security modelling

Enterprise security management requires capturing different security and IT systems' details, analyzing and enforcing these security details, and improving employed security to meet new risks. Adopting structured models greatly helps in simplifying and organizing security specification and enforcement processes. However, existing security models are generally limited to specific security details and do not deliver a comprehensive security model. They also often do not have user-friendly notations, being complicated extensions of existing modeling languages (such as UML). In this paper, we introduce a comprehensive Security Domain Specific Visual Language (SecDSVL), which enables capturing of key security details to support enterprise systems security management process. We discuss our SecDSVL, tool support and the model-based enterprise security management approach it supports, give a usage example, and present evaluation experiments of SecDSVL.

Generating domain-specific visual language tools from abstract visual specifications

Domain-specific visual languages support high-level modeling for a wide range of application domains. However, building tools to support such languages is very challenging. We describe a set of key conceptual requirements for such tools and our approach to addressing these requirements, a set of visual language-based metatools. These support definition of metamodels, visual notations, views, modeling behaviors, design critics, and model transformations and provide a platform to realize target visual modeling tools. Extensions support collaborative work, human-centric tool interaction, and multiplatform deployment. We illustrate application of the metatoolset on tools developed with our approach. We describe tool developer and cognitive evaluations of our platform and our exemplar tools, and summarize key future research directions.

Enhancing English language learners’ text understanding through metaphor awareness

 The study examined awareness of metaphor as a tool to enhance English language learners’ understanding of texts with embedded metaphors. Findings revealed that an enhanced awareness of metaphor, as indicated by greater use of the metalanguage of metaphor, longer turns conversation and reflective journals, helped them get deeper text meaning.

MaramaAIC: tool support for consistency management and validation of requirements

Requirements captured by requirements engineers (REs) are commonly inconsistent with their client’s intended requirements and are often error prone. There is limited tool support providing end-to-end support between the REs and their client for the validation and improvement of these requirements. We have developed an automated tool called MaramaAIC (Automated Inconsistency Checker) to address these problems. MaramaAIC provides automated requirements traceability and visual support to identify and highlight inconsistency, incorrectness and incompleteness in captured requirements. MaramaAIC provides an end-to-end rapid prototyping approach together with a patterns library that helps to capture requirements and check the consistency of requirements that have been expressed in textual natural language requirements and then extracted to semi-formal abstract interactions, essential use cases (EUCs) and user interface prototype models. It helps engineers to validate the correctness and completeness of the EUCs modelled requirements by comparing them to “best-practice” templates and generates an abstract prototype in the form of essential user interface prototype models and concrete User Interface views in the form of HTML. We describe its design and implementation together with results of evaluating our tool’s efficacy and performance, and user perception of the tool’s usability and its strengths and weaknesses via a substantial usability study. We also present a qualitative study on the effectiveness of the tool’s end-to-end rapid prototyping approach in improving dialogue between the RE and the client as well as improving the quality of the requirements.

iPrevent®: a tailored, web-based, decision support tool for breast cancer risk assessment and management

We aimed to develop a user-centered, web-based, decision support tool for breast cancer risk assessment and personalized risk management. Using a novel model choice algorithm, iPrevent(®) selects one of two validated breast cancer risk estimation models (IBIS or BOADICEA), based on risk factor data entered by the user. Resulting risk estimates are presented in simple language and graphic formats for easy comprehension. iPrevent(®) then presents risk-adapted, evidence-based, guideline-endorsed management options. Development was an iterative process with regular feedback from multidisciplinary experts and consumers. To verify iPrevent(®), risk factor data for 127 cases derived from the Australian Breast Cancer Family Study were entered into iPrevent(®), IBIS (v7.02), and BOADICEA (v3.0). Consistency of the model chosen by iPrevent(®) (i.e., IBIS or BOADICEA) with the programmed iPrevent(®) model choice algorithm was assessed. Estimated breast cancer risks from iPrevent(®) were compared with those attained directly from the chosen risk assessment model (IBIS or BOADICEA). Risk management interventions displayed by iPrevent(®) were assessed for appropriateness. Risk estimation model choice was 100 % consistent with the programmed iPrevent(®) logic. Discrepant 10-year and residual lifetime risk estimates of >1 % were found for 1 and 4 cases, respectively, none was clinically significant (maximal variation 1.4 %). Risk management interventions suggested by iPrevent(®) were 100 % appropriate. iPrevent(®) successfully integrates the IBIS and BOADICEA risk assessment models into a decision support tool that provides evidence-based, risk-adapted risk management advice. This may help to facilitate precision breast cancer prevention discussions between women and their healthcare providers.

TeeVML : tool support for semi-automatic integration testing environment emulation

Software environment emulation provides a means for simulating an operational environment of a system. This process involves approximation of systems’ external behaviors and their communications with a system to be tested in the environment. Development of such an environment is a tedious task and involves complex low level coding. Model driven engineering is an avenue to raise the level of abstraction beyond programming by specifying solution directly using problem domain concepts. In this paper we propose a novel domain-specific modeling tool to generate complex testing environments. Our tool employs a suite of domain-specific visual modeling languages for modelling emulation environment at a high level of abstraction. These high level specifications are then automatically transformed to runtimeenvironment for application integration testing, boosting development productivity and ease of use.

Wayne McGregor's choreographic language agent

The paper notebook with its companion pencil or pen is a creative tool for many contemporary choreographers and their dancers. Using the notebook affords a relationship with a set of external objects inscribed “on the page” in the form of drawn sketches, notations, and diagrams combined with text (Blackwell et al.). This relationship can be described in cognitive terms, for example, where the page becomes a surrogate for working memory, or a way for seeing something new by modeling structures or processes. The notebook in this sense becomes a site for the encounter of cognition and creativity, providing a place for thinking generatively with external objects (sketches, notations, etc.), an idea this essay will revisit.