On Patterns of Multi-domain Interaction for Scientific Software Development focused on Separation of Concerns

This year’s ICCS conference theme promotes the use of computational science as a means to foster multidisciplinarity and synergies with other fields. Our thesis is that this trend towards multidisciplinarity should be accompanied by the use of best practices issued from the software engineering community in order to avoid obtaining overly complex and tangled code, difficult to validate, to maintain and to port. In this paper we argue for the need of applying separation of concerns principles when the development involves scientists from various application fields. We overview several strategies that may be used to achieve this separation, focusing mainly on two approaches drawn from our previous experiences with multidisciplinary projects, addressing two distinct patterns of multi-domain interaction that may occur in scientific software development

Early aspects: aspect-oriented requirements engineering and architecture design

This paper reports on the third Early Aspects: Aspect-Oriented Requirements Engineering and Architecture Design Workshop, which has been held in Lancaster, UK, on March 21, 2004. The workshop included a presentation session and working sessions in which the particular topics on early aspects were discussed. The primary goal of the workshop was to focus on challenges to defining methodical software development processes for aspects from early on in the software life cycle and explore the potential of proposed methods and techniques to scale up to industrial applications

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

The Scalability-Efficiency/Maintainability-Portability Trade-off in Simulation Software Engineering: Examples and a Preliminary Systematic Literature Review

Large-scale simulations play a central role in science and the industry. Several challenges occur when building simulation software, because simulations require complex software developed in a dynamic construction process. That is why simulation software engineering (SSE) is emerging lately as a research focus. The dichotomous trade-off between scalability and efficiency (SE) on the one hand and maintainability and portability (MP) on the other hand is one of the core challenges. We report on the SE/MP trade-off in the context of an ongoing systematic literature review (SLR). After characterizing the issue of the SE/MP trade-off using two examples from our own research, we (1) review the 33 identified articles that assess the trade-off, (2) summarize the proposed solutions for the trade-off, and (3) discuss the findings for SSE and future work. Overall, we see evidence for the SE/MP trade-off and first solution approaches. However, a strong empirical foundation has yet to be established; general quantitative metrics and methods supporting software developers in addressing the trade-off have to be developed. We foresee considerable future work in SSE across scientific communities.Comment: 9 pages, 2 figures. Accepted for presentation at the Fourth International Workshop on Software Engineering for High Performance Computing in Computational Science and Engineering (SEHPCCSE 2016

Multi-Party Coordination in the Context of MOWS

Separation of concerns has been presented as a promising tool to tackle the design of complex systems in which cross-cutting properties that do not fit into the scope of a class must be satisfied. In this paper, we show that interactions amongst a number of objects can also be described separately from functionality, which enhances reusability of functional code and interaction patterns. We present our proposal in the context of Multi-Qrganisational Web-Based Systems (MOWS) and also present a framework that provides the infrastructure needed to implement multiparty coordination as an independent aspect

Multi-Sensor Context-Awareness in Mobile Devices and Smart Artefacts

The use of context in mobile devices is receiving increasing attention in mobile and ubiquitous computing research. In this article we consider how to augment mobile devices with awareness of their environment and situation as context. Most work to date has been based on integration of generic context sensors, in particular for location and visual context. We propose a different approach based on integration of multiple diverse sensors for awareness of situational context that can not be inferred from location, and targeted at mobile device platforms that typically do not permit processing of visual context. We have investigated multi-sensor context-awareness in a series of projects, and report experience from development of a number of device prototypes. These include development of an awareness module for augmentation of a mobile phone, of the Mediacup exemplifying context-enabled everyday artifacts, and of the Smart-Its platform for aware mobile devices. The prototypes have been explored in various applications to validate the multi-sensor approach to awareness, and to develop new perspectives of how embedded context-awareness can be applied in mobile and ubiquitous computing

SensorCloud: Towards the Interdisciplinary Development of a Trustworthy Platform for Globally Interconnected Sensors and Actuators

Although Cloud Computing promises to lower IT costs and increase users' productivity in everyday life, the unattractive aspect of this new technology is that the user no longer owns all the devices which process personal data. To lower scepticism, the project SensorCloud investigates techniques to understand and compensate these adoption barriers in a scenario consisting of cloud applications that utilize sensors and actuators placed in private places. This work provides an interdisciplinary overview of the social and technical core research challenges for the trustworthy integration of sensor and actuator devices with the Cloud Computing paradigm. Most importantly, these challenges include i) ease of development, ii) security and privacy, and iii) social dimensions of a cloud-based system which integrates into private life. When these challenges are tackled in the development of future cloud systems, the attractiveness of new use cases in a sensor-enabled world will considerably be increased for users who currently do not trust the Cloud.Comment: 14 pages, 3 figures, published as technical report of the Department of Computer Science of RWTH Aachen Universit

Report of the user requirements and web based access for eResearch workshops

The User Requirements and Web Based Access for eResearch Workshop, organized jointly by NeSC and NCeSS, was held on 19 May 2006. The aim was to identify lessons learned from e-Science projects that would contribute to our capacity to make Grid infrastructures and tools usable and accessible for diverse user communities. Its focus was on providing an opportunity for a pragmatic discussion between e-Science end users and tool builders in order to understand usability challenges, technological options, community-specific content and needs, and methodologies for design and development. We invited members of six UK e-Science projects and one US project, trying as far as possible to pair a user and developer from each project in order to discuss their contrasting perspectives and experiences. Three breakout group sessions covered the topics of user-developer relations, commodification, and functionality. There was also extensive post-meeting discussion, summarized here. Additional information on the workshop, including the agenda, participant list, and talk slides, can be found online at http://www.nesc.ac.uk/esi/events/685/ Reference: NeSC report UKeS-2006-07 available from http://www.nesc.ac.uk/technical_papers/UKeS-2006-07.pd

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: NL

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: N