Research and Education in Computational Science and Engineering

Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers of all persuasions with algorithmic inventions and software systems that transcend disciplines and scales. Carried on a wave of digital technology, CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments---including the architectural complexity of extreme-scale computing, the data revolution that engulfs the planet, and the specialization required to follow the applications to new frontiers---is redefining the scope and reach of the CSE endeavor. This report describes the rapid expansion of CSE and the challenges to sustaining its bold advances. The report also presents strategies and directions for CSE research and education for the next decade.Comment: Major revision, to appear in SIAM Revie

Establishment of computational biology in Greece and Cyprus: Past, present, and future.

We review the establishment of computational biology in Greece and Cyprus from its inception to date and issue recommendations for future development. We compare output to other countries of similar geography, economy, and size—based on publication counts recorded in the literature—and predict future growth based on those counts as well as national priority areas. Our analysis may be pertinent to wider national or regional communities with challenges and opportunities emerging from the rapid expansion of the field and related industries. Our recommendations suggest a 2-fold growth margin for the 2 countries, as a realistic expectation for further expansion of the field and the development of a credible roadmap of national priorities, both in terms of research and infrastructure funding

Mathematical models in physiology

Computational modelling of biological processes and systems has witnessed a remarkable development in recent years. The search-term (modelling OR modeling) yields over 58000 entries in PubMed, with more than 34000 since the year 2000: thus, almost two-thirds of papers appeared in the last 5–6 years, compared to only about one-third in the preceding 5–6 decades.\ud \ud The development is fuelled both by the continuously improving tools and techniques available for bio-mathematical modelling and by the increasing demand in quantitative assessment of element inter-relations in complex biological systems. This has given rise to a worldwide public domain effort to build a computational framework that provides a comprehensive theoretical representation of integrated biological function—the Physiome.\ud \ud The current and next issues of this journal are devoted to a small sub-set of this initiative and address biocomputation and modelling in physiology, illustrating the breadth and depth of experimental data-based model development in biological research from sub-cellular events to whole organ simulations

Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1)

Challenges related to development, deployment, and maintenance of reusable software for science are becoming a growing concern. Many scientists’ research increasingly depends on the quality and availability of software upon which their works are built. To highlight some of these issues and share experiences, the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1) was held in November 2013 in conjunction with the SC13 Conference. The workshop featured keynote presentations and a large number (54) of solicited extended abstracts that were grouped into three themes and presented via panels. A set of collaborative notes of the presentations and discussion was taken during the workshop. Unique perspectives were captured about issues such as comprehensive documentation, development and deployment practices, software licenses and career paths for developers. Attribution systems that account for evidence of software contribution and impact were also discussed. These include mechanisms such as Digital Object Identifiers, publication of “software papers”, and the use of online systems, for example source code repositories like GitHub. This paper summarizes the issues and shared experiences that were discussed, including cross-cutting issues and use cases. It joins a nascent literature seeking to understand what drives software work in science, and how it is impacted by the reward systems of science. These incentives can determine the extent to which developers are motivated to build software for the long-term, for the use of others, and whether to work collaboratively or separately. It also explores community building, leadership, and dynamics in relation to successful scientific software

Computational Sociolinguistics: A Survey

Language is a social phenomenon and variation is inherent to its social nature. Recently, there has been a surge of interest within the computational linguistics (CL) community in the social dimension of language. In this article we present a survey of the emerging field of "Computational Sociolinguistics" that reflects this increased interest. We aim to provide a comprehensive overview of CL research on sociolinguistic themes, featuring topics such as the relation between language and social identity, language use in social interaction and multilingual communication. Moreover, we demonstrate the potential for synergy between the research communities involved, by showing how the large-scale data-driven methods that are widely used in CL can complement existing sociolinguistic studies, and how sociolinguistics can inform and challenge the methods and assumptions employed in CL studies. We hope to convey the possible benefits of a closer collaboration between the two communities and conclude with a discussion of open challenges.Comment: To appear in Computational Linguistics. Accepted for publication: 18th February, 201

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