Data management for large‐scale scientific computations in high performance distributed systems

With the increasing number of scientific applications manipulating huge amounts of data, effective high-level data management is an increasingly important problem. Unfortunately, so far the solutions to the high‐level data management problem either require deep understanding of specific storage architectures and file layouts (as in high-performance file storage systems) or produce unsatisfactory I/O performance in exchange for ease-of-use and portability (as in relational DBMSs). In this paper we present a novel application development environment which is built around an active meta-data management system (MDMS) to handle high-level data in an effective manner. The key components of our three-tiered architecture are user application, the MDMS, and a hierarchical storage system (HSS). Our environment overcomes the performance problems of pure database-oriented solutions, while maintaining their advantages in terms of ease-of-use and portability. The high levels of performance are achieved by the MDMS, with the aid of user-specified, performance-oriented directives. Our environment supports a simple, easy-to-use yet powerful user interface, leaving the task of choosing appropriate I/O techniques for the application at hand to the MDMS. We discuss the importance of an active MDMS and show how the three components of our environment, namely the application, the MDMS, and the HSS, fit together. We also report performance numbers from our ongoing implementation and illustrate that significant improvements are made possible without undue programming effort. This revised version was published online in July 2006 with corrections to the Cover Date.     

Environmental impacts of end-of-life vehicles’ management: recovery versus elimination

Purpose

In Portugal, the management of end-of-life vehicles (ELV) is set out in targets of the European Union policy for the year 2015, including 85 % recycling, 95 % recovery, and maximum of 5 % landfilling. These goals will be attained only through more efficient technologies for waste separation and recycling of shredder residues or higher rates of dismantling components. Focusing on this last alternative, a field experiment was carried out. There is potential for additional recycling/recovery of 10 %.

Methods

Three scenarios were proposed for the management of ELV wastes: (1) scenario 1 corresponds to the baseline and refers to the current management, i.e., the 10 % of ELV wastes are shredded whereby some ferrous and non-ferrous metals are recovered and the remaining fraction, called automotive shredder residues (ASR), is landfilled, (2) scenario 2 wherein the ASR fraction is incinerated with energy recovery, and (3) scenario 3 includes the additional dismantling of components for recycling and for energy recovery through solid recovered fuel, to be used as a fuel substitute in the cement industry. The environmental performance of these scenarios was quantified by using the life cycle assessment methodology. Five impact categories were assessed: abiotic resource depletion, climate change, photochemical oxidant creation, acidification, and eutrophication.

Results and discussion

Compared to the other scenarios, in scenario 1 no benefits for the impact categories of climate change and eutrophication were observed. Scenario 2 has environmental credits due to the recycling of ferrous and non-ferrous metals and benefits from energy recovery. However, this scenario has a significant impact on climate change due to emissions from thermal oxidation of polymeric materials present in the ASR fraction. A net environmental performance upgrading seems to be ensured by scenario 3, mainly due to replacing fossil fuel by solid recovered fuel.

Conclusions

The proposed additional dismantling of ELV (scenario 3) not only brings environmental benefits but also meets the European recovery and recycling targets. The associated increase of dismantling costs can be compensated by the additional recycling material revenues as well as social benefits by a rise in employment.     

Immobilised enzymes: science or art?

Enzyme immobilisation is experiencing an important transition. Combinatorial approaches are increasingly applied in the design of robust immobilised enzymes by rational combination of fundamental immobilisation techniques (i.e. non-covalent adsorption, covalent binding, entrapment and encapsulation) or with other relevant technologies. The objective is to solve specific problems that cannot be solved by one of these basic immobilisation techniques.     

Railway ecology: Underrepresented in science?

Over the past two decades, the effects of roads on wildlife have been extensively studied. Theoretically, railways cause similar effects as well, yet ecologists do not understand the magnitude of these effects. Despite the field of road ecology rapidly expanding and the large footprint created by railways, there is a prominent lack of research related to railways and their effects on wildlife. To emphasize gaps between road and railway wildlife studies, we performed a thorough systematic review of twelve peer-reviewed journals in which ecologists and conservation biologists commonly publish. We found a clear underrepresentation of railway studies despite the potential negative ecological effects associated with this important anthropogenic feature. We found 259 road-wildlife articles and only 17 railway-wildlife articles in the journals we assessed with the majority of road studies focused in North America and the majority of railway studies in Europe. Although road-wildlife studies have increased through time, railway-wildlife studies have remained stagnant. In our opinion, the development of research pertaining to ‘Railway Ecology’ is long overdue.     

Linking science and practice in ecological research and management: How can we do it better?

Summary In conservation management, ensuring that the most appropriate research is conducted and results are actually put into practice is a complex and challenging process. While there are success stories, many hurdles can reduce the likelihood of appropriate research being initiated and its findings communicated and implemented. This article describes the ideal research–management cycle, summarizes the major factors that impede it and draws on the experiences of the authors to provide a series of examples of successful approaches to help keep the cycle going. We consider that the major impediments to a functioning research–management cycle relate to a lack of collaboration, poor communication, inappropriate funding and political timelines, change inertia and a lack of capacity. Although addressing structural difficulties such as matching funding timelines to those required for ecological research is a fundamental challenge, we can make incremental improvements to the way in which we operate that will improve the chances that research is both useful and used. The principles underpinning our success stories are (i) strategic development of capacity, (ii) increased breadth and depth of collaborations between researchers and managers and (iii) improved communications. Participants in the research–management cycle must seek to involve stakeholders through all project stages from project conception, to implementation, evaluation and knowledge updating. Finally, we should only see the first iteration of the research process as complete when new knowledge is applied operationally with monitoring and ongoing evaluation in place.     

Pluripotent versus totipotent plant stem cells: dependence versus autonomy?

Little is known of the mechanisms that induce the dedifferentiation of a single somatic cell into a totipotent embryogenic cell that can either be regenerated or develop into an embryo and subsequently an entire plant. In this Opinion article, we examine the cellular, physiological and molecular similarities and differences between different plant stem cell types. We propose to extend the plant stem cell concept to include single embryogenic cells as a totipotent stem cell based on their capacity to regenerate or develop into an embryo under certain conditions. Our survey suggests that differences in chromatin structure might ensure that meristem-localized stem cells have supervised freedom and are pluripotent, and that embryogenic stem cells are unsupervised, autonomous and, hence, freely totipotent.     

Big Data: Astronomical or Genomical?

Genomics is a Big Data science and is going to get much bigger, very soon, but it is not known whether the needs of genomics will exceed other Big Data domains. Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. Our estimates show that genomics is a “four-headed beast”—it is either on par with or the most demanding of the domains analyzed here in terms of data acquisition, storage, distribution, and analysis. We discuss aspects of new technologies that will need to be developed to rise up and meet the computational challenges that genomics poses for the near future. Now is the time for concerted, community-wide planning for the “genomical” challenges of the next decade.We compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. Astronomy has faced the challenges of Big Data for over 20 years and continues with ever-more ambitious studies of the universe. YouTube burst on the scene in 2005 and has sparked extraordinary worldwide interest in creating and sharing huge numbers of videos. Twitter, created in 2006, has become the poster child of the burgeoning movement in computational social science [6], with unprecedented opportunities for new insights by mining the enormous and ever-growing amount of textual data [7]. Particle physics also produces massive quantities of raw data, although the footprint is surprisingly limited since the vast majority of data are discarded soon after acquisition using the processing power that is coupled to the sensors [8]. Consequently, we do not include the domain in full detail here, although that model of rapid filtering and analysis will surely play an increasingly important role in genomics as the field matures.To compare these four disparate domains, we considered the four components that comprise the “life cycle” of a dataset: acquisition, storage, distribution, and analysis (

Brazilian alcohol: Food versus fuel?

The creation of the ProAlcool (National Alcohol Programme) late in 1975 for the production of fuel alcohol has raised varied criticisms as to the possible consequences for food production in Brazil. This food ‘problem’ in Brazil is embedded in its socio-economic and political system. Agricultural production has kept ahead of population growth, but the main beneficiaries have been commodity export crops; the issue can be identified as ‘commodity export crop production versus crop production for the domestic market’ rather than ‘food versus fuel’. The possible effects of the ProAlcool on food production have been exaggerated and the real implications largely overlooked. The sugar and alcohol sector is today among Brazil's largest industries and, with all its faults, the ProAlcool remains the world's most successful biomass energy programme and as such its importance extends beyond Brazil's national boundaries. Biomass has been demonstrated by a Third World country to be a viable alternative or complement to oil on a national scale. Despite the current (1986) low oil prices an interministerial commission has recently recommended that the ProAlcool programme should be maintained.     

Can a tablet device alter undergraduate science students' study behavior and use of technology?

This article reports findings from a study investigating undergraduate biological sciences students' use of technology and computer devices for learning and the effect of providing students with a tablet device. A controlled study was conducted to collect quantitative and qualitative data on the impact of a tablet device on students' use of devices and technology for learning. Overall, we found that students made extensive use of the tablet device for learning, using it in preference to laptop computers to retrieve information, record lectures, and access learning resources. In line with other studies, we found that undergraduate students only use familiar Web 2.0 technologies and that the tablet device did not alter this behavior for the majority of tools. We conclude that undergraduate science students can make extensive use of a tablet device to enhance their learning opportunities without institutions changing their teaching methods or computer systems, but that institutional intervention may be needed to drive changes in student behavior toward the use of novel Web 2.0 technologies.     

The GM debate: science or scaremongering?

Many conversations on genetic modification over the past few years have begun with the words 'I'm not a scientist, but...' They usually go on to say they do not follow the scientific detail, but it doesn't seem right to tamper with genes. The media and pressure groups have fuelled the fire with emotive terms like 'Frankenstein food', 'genetic pollution' and 'mutant crops'. There are important lessons here, which are as much about people and society as they are about science.     

XML: a lingua franca for science?

XML is a new language designed to solve one of the biggest problems of the World Wide Web: its main language, HTML, is not extensible. In this article, the authors discuss the current successes and limitations of the World Wide Web, briefly explain the basics of XML and present the benefits of using XML as a data-exchange language. Finally, they discuss real-life applications that have been developed using XML, with a focus on biology.     

Sensory systems: auditory action streams?

The visual system is suggested to have two main processing streams, dorsal and ventral, the former being an 'action stream' concerned with motor responses, as opposed to perception. Two recent studies suggest the existence of a comparable mechanism in the auditory system.     

Bioethics for technology?

Ethical concerns about biotechnology continue to be debated in the scientific and popular press. Ethical considerations have led to the development of frameworks within which biotechnology can be developed in socially acceptable and desirable ways: through legislation, the development of public-private collaborations, and regimes that safeguard consumer choice.