Education and data-intensive science in the beginning of the 21st century

Data-intensive science will open up new avenues to explore, new questions to ask, and new ways to answer. Yet, this potential cannot be unlocked without new emphasis on education of the researchers gathering data, the analysts analyzing data and the cross-disciplinary participants working together to make it happen. This article is a summary of the education issues and challenges of data-intensive sciences and cloud computing as discussed in the Data-Intensive Science (DIS) workshop in Seattle, September 19-20, 2010.     

Opportunities and challenges for the life sciences community

Twenty-first century life sciences have transformed into data-enabled (also called data-intensive, data-driven, or big data) sciences. They principally depend on data-, computation-, and instrumentation-intensive approaches to seek comprehensive understanding of complex biological processes and systems (e.g., ecosystems, complex diseases, environmental, and health challenges). Federal agencies including the National Science Foundation (NSF) have played and continue to play an exceptional leadership role by innovatively addressing the challenges of data-enabled life sciences. Yet even more is required not only to keep up with the current developments, but also to pro-actively enable future research needs. Straightforward access to data, computing, and analysis resources will enable true democratization of research competitions; thus investigators will compete based on the merits and broader impact of their ideas and approaches rather than on the scale of their institutional resources. This is the Final Report for Data-Intensive Science Workshops DISW1 and DISW2. The first NSF-funded Data Intensive Science Workshop (DISW1, Seattle, WA, September 19-20, 2010) overviewed the status of the data-enabled life sciences and identified their challenges and opportunities. This served as a baseline for the second NSF-funded DIS workshop (DISW2, Washington, DC, May 16-17, 2011). Based on the findings of DISW2 the following overarching recommendation to the NSF was proposed: establish a community alliance to be the voice and framework of the data-enabled life sciences. After this Final Report was finished, Data-Enabled Life Sciences Alliance (DELSA, www.delsall.org ) was formed to become a Digital Commons for the life sciences community.     

Biosecurity in the age of Big Data: a conversation with the FBI

New scientific frontiers and emerging technologies within the life sciences pose many global challenges to society. Big Data is a premier example, especially with respect to individual, national, and international security. Here a Special Agent of the Federal Bureau of Investigation discusses the security implications of Big Data and the need for security in the life sciences.     

Policy and data-intensive scientific discovery in the beginning of the 21st century

Recent developments in our ability to capture, curate, and analyze data, the field of data-intensive science (DIS), have indeed made these interesting and challenging times for scientific practice as well as policy making in real time. We are confronted with immense datasets that challenge our ability to pool, transfer, analyze, or interpret scientific observations. We have more data available than ever before, yet more questions to be answered as well, and no clear path to answer them. We are excited by the potential for science-based solutions to humankind's problems, yet stymied by the limitations of our current cyberinfrastructure and existing public policies. Importantly, DIS signals a transformation of the hypothesis-driven tradition of science ("first hypothesize, then experiment") to one that is typified by "first experiment, then hypothesize" mode of discovery. Another hallmark of DIS is that it amasses data that are public goods (i.e., creates a "commons") that can further be creatively mined for various applications in different sectors. As such, this calls for a science policy vision that is long term. We herein reflect on how best to approach to policy making at this critical inflection point when DIS applications are being diversified in agriculture, ecology, marine biology, and environmental research internationally. This article outlines the key policy issues and gaps that emerged from the multidisciplinary discussions at the NSF-funded DIS workshop held at the Seattle Children's Research Institute in Seattle, on September 19-20, 2010.     

Millennium bugs

Microbiology has a long way to go. Microbes are ubiquitous, and all other life forms in the biosphere exist solely because of them, but, as less than 1% of microorganisms can be grown in the laboratory, more than a century of research has revealed only the tip of the iceberg concerning this most crucial of life sciences. There are many intellectual challenges remaining. The flow of complete sequences of bacterial genomes is likely to spawn renewed research in answering many questions of concern to academic, medical and industrial interests. Elucidating the roles of microbes, the oldest and most vital inhabitants of the biosphere, in the evolutionary process and in the maintenance of other life forms will be the major thrust in the years to come.     

Millennium bugs

Microbiology has a long way to go. Microbes are ubiquitous, and all other life forms in the biosphere exist solely because of them, but, as less than 1% of microorganisms can be grown in the laboratory, more than a century of research has revealed only the tip of the iceberg concerning this most crucial of life sciences. There are many intellectual challenges remaining. The flow of complete sequences of bacterial genomes is likely to spawn renewed research in answering many questions of concern to academic, medical and industrial interests. Elucidating the roles of microbes, the oldest and most vital inhabitants of the biosphere, in the evolutionary process and in the maintenance of other life forms will be the major thrust in the years to come.     

Millennium bugs

Microbiology has a long way to go. Microbes are ubiquitous, and all other life forms in the biosphere exist solely because of them, but, as less than 1% of microorganisms can be grown in the laboratory, more than a century of research has revealed only the tip of the iceberg concerning this most crucial of life sciences. There are many intellectual challenges remaining. The flow of complete sequences of bacterial genomes is likely to spawn renewed research in answering many questions of concern to academic, medical and industrial interests. Elucidating the roles of microbes, the oldest and most vital inhabitants of the biosphere, in the evolutionary process and in the maintenance of other life forms will be the major thrust in the years to come.     

From maturity to value-added innovation: lessons from the pharmaceutical and agro-biotechnology industries

The pharmaceutical and agro-biotechnology industries have been confronted by dwindling product pipelines and rapid developments in life sciences, thus demanding a strategic rethink of conventional research and development. Despite offering both industries a solution to the pipeline problem, the life sciences have also brought complex regulatory challenges for firms. In this paper, we comment on the response of these industries to the life science trajectory, in the context of maturing conventional small-molecule product pipelines and routes to market. The challenges of managing transition from maturity to new high-value-added innovation models are addressed. Furthermore, we argue that regulation plays a crucial role in shaping the innovation systems of both industries, and as such, we suggest potentially useful changes to the current regulatory system.     

Information engineering infrastructure for life sciences and its implementation in China

Biological data,represented by the data from omics platforms,are accumulating exponentially.As some other data-intensive scientific disciplines such as high-energy physics,climatology,meteorology,geology,geography and environmental sciences,modern life sciences have entered the information-rich era,the era of the 4th paradigm.The creation of Chinese information engineering infrastructure for pan-omics studies(CIEIPOS) has been long overdue as part of national scientific infrastructure,in accelerating the further development of Chinese life sciences,and translating rich data into knowledge and medical applications.By gathering facts of current status of international and Chinese bioinformatics communities in collecting,managing and utilizing biological data,the essay stresses the significance and urgency to create a ’data hub’ in CIEIPOS,discusses challenges and possible solutions to integrate,query and visualize these data.Another important component of CIEIPOS,which is not part of traditional biological data centers such as NCBI and EBI,is omics informatics.Mass spectroscopy platform was taken as an example to illustrate the complexity of omics informatics.Its heavy dependency on computational power is highlighted.The demand for such power in omics studies is argued as the fundamental function to meet for CIEIPOS.Implementation outlook of CIEIPOS in hardware and network is discussed.     

PubMed, the New York Times and the Chicago Tribune as tools for teaching genetics

An elementary course in human heredity for students not planning to major in the sciences can be based on current scientific literature and on the popular media. Examinations are constructed from questions on recent abstracts obtained from PubMed. The course is designed to promote writing skills in the sciences, and students write two papers in the course of a quarter. In the first paper, students trace the primary source of media reports on genetics and attempt to evaluate the reporter's translation. In a second paper, students write popular articles on the basis of current primary sources.     

The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors

The function of proteins can often be inferred from their three-dimensional structures. Experimental structural biologists spent decades studying these structures, but the accelerated pace of protein sequencing continuously increases the gaps between sequences and structures. The early 2020s saw the advent of a new generation of deep learning-based protein structure prediction tools that offer the potential to predict structures based on any number of protein sequences.In this review, we give an overview of the impact of this new generation of structure prediction tools, with examples of the impacted field in the life sciences. We discuss the novel opportunities and new scientific and technical challenges these tools present to the broader scientific community. Finally, we highlight some potential directions for the future of computational protein structure prediction.     

Nanoinformatics: an emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology

After the progress made during the genomics era, bioinformatics was tasked with supporting the flow of information generated by nanobiotechnology efforts. This challenge requires adapting classical bioinformatic and computational chemistry tools to store, standardize, analyze, and visualize nanobiotechnological information. Thus, old and new bioinformatic and computational chemistry tools have been merged into a new sub-discipline: nanoinformatics. This review takes a second look at the development of this new and exciting area as seen from the perspective of the evolution of nanobiotechnology applied to the life sciences. The knowledge obtained at the nano-scale level implies answers to new questions and the development of new concepts in different fields. The rapid convergence of technologies around nanobiotechnologies has spun off collaborative networks and web platforms created for sharing and discussing the knowledge generated in nanobiotechnology. The implementation of new database schemes suitable for storage, processing and integrating physical, chemical, and biological properties of nanoparticles will be a key element in achieving the promises in this convergent field. In this work, we will review some applications of nanobiotechnology to life sciences in generating new requirements for diverse scientific fields, such as bioinformatics and computational chemistry.     

“Positive” Results Increase Down the Hierarchy of the Sciences

The hypothesis of a Hierarchy of the Sciences with physical sciences at the top, social sciences at the bottom, and biological sciences in-between is nearly 200 years old. This order is intuitive and reflected in many features of academic life, but whether it reflects the “hardness” of scientific research—i.e., the extent to which research questions and results are determined by data and theories as opposed to non-cognitive factors—is controversial. This study analysed 2434 papers published in all disciplines and that declared to have tested a hypothesis. It was determined how many papers reported a “positive” (full or partial) or “negative” support for the tested hypothesis. If the hierarchy hypothesis is correct, then researchers in “softer” sciences should have fewer constraints to their conscious and unconscious biases, and therefore report more positive outcomes. Results confirmed the predictions at all levels considered: discipline, domain and methodology broadly defined. Controlling for observed differences between pure and applied disciplines, and between papers testing one or several hypotheses, the odds of reporting a positive result were around 5 times higher among papers in the disciplines of Psychology and Psychiatry and Economics and Business compared to Space Science, 2.3 times higher in the domain of social sciences compared to the physical sciences, and 3.4 times higher in studies applying behavioural and social methodologies on people compared to physical and chemical studies on non-biological material. In all comparisons, biological studies had intermediate values. These results suggest that the nature of hypotheses tested and the logical and methodological rigour employed to test them vary systematically across disciplines and fields, depending on the complexity of the subject matter and possibly other factors (e.g., a field''s level of historical and/or intellectual development). On the other hand, these results support the scientific status of the social sciences against claims that they are completely subjective, by showing that, when they adopt a scientific approach to discovery, they differ from the natural sciences only by a matter of degree.     

蛋白质结构预测进展

蛋白质的序列决定结构,结构决定功能。新一代准确的蛋白质结构预测工具为结构生物学、结构生物信息学、药物研发和生命科学等许多领域带来了全新的机遇与挑战,单链蛋白质结构预测的准确率达到与试验方法相媲美的水平。本综述概述了蛋白质结构预测领域的理论基础、发展历程与最新进展,讨论了大量预测的蛋白质结构和基于人工智能的方法如何影响实验结构生物学,最后,分析了当前蛋白质结构预测领域仍未解决的问题以及未来的研究方向。     

Bioinformatics and data-intensive scientific discovery in the beginning of the 21st century

This article is a summary of the bioinformatics issues and challenges of data-intensive science as discussed in the NSF-funded Data-Intensive Science (DIS) workshop in Seattle, September 19-20, 2010.     

Technology and data-intensive science in the beginning of the 21st century

This article is a summary of the technology issues and challenges of data-intensive science and cloud computing as discussed in the Data-Intensive Science (DIS) workshop in Seattle, September 19-20, 2010.     

The biological sciences in India: Aiming high for the future

India is gearing up to become an international player in the life sciences, powered by its recent economic growth and a desire to add biotechnology to its portfolio. In this article, we present the history, current state, and projected future growth of biological research in India. To fulfill its aspirations, India''s greatest challenge will be in educating, recruiting, and supporting its next generation of scientists. Such challenges are faced by the US/Europe, but are particularly acute in developing countries that are racing to achieve scientific excellence, perhaps faster than their present educational and faculty support systems will allow.India, like China, has been riding a rising economic wave. At the time of writing this article, four Indians rank among the ten wealthiest individuals in the world, and the middle class is projected to rise to 40% of the population by 2025 (Farrell and Beinhocker, 2007). Even with the present global economic setbacks, India''s economy is expected to grow to become the third largest in the world. India''s recent economic boom has been driven largely by its service and information technology industries, fueled to a large extent by jobs provided by multinational companies. However, this “outsourcing” model is unlikely to persist indefinitely. India''s future must rely upon its own capacity for innovation, which will require considerable investment in education and research.Biotechnology represents a potential sector of economic growth and an important component in India''s national health agenda. Appreciating the important role that biology will play in this century, the Indian government is expanding as well as starting several new biological research institutes, which will open up many new positions for life science researchers. Funds also are becoming available for state-of-the-art equipment, thus decreasing the earlier large disparity in support facilities between the top research institutes in India and the US/Europe. India is becoming an increasingly viable location to conduct biological research and a fertile ground for new biotechnology companies. However, success need not rise in proportion to money invested, unless India attracts and supports its best young people to do research.Many academic centers and industries in the US/Europe are beginning to have an eye on India, the world''s largest democratic country, for possible collaborations. Western institutions have long benefited from having Indian scientists on their faculty or postdoctoral fellows/graduate students in their laboratories (perhaps benefitting more than India itself). However, Western scientists, by and large, know very little about the scientific and educational systems in India. (As was true of authors of this article before we began our 8-month sabbatical at the National Center for Biological Sciences in Bangalore). The goal of this article is to provide a brief historical and contemporary view of the biological sciences in India. We also provide an editorial perspective on the upcoming challenges for the Indian life sciences, with a particular emphasis on how India will grow and support its next generation of scientific leaders.     

Scientific Wealth in Middle East and North Africa: Productivity,Indigeneity, and Specialty in 1981–2013

Several developing countries seek to build knowledge-based economies by attempting to expand scientific research capabilities. Characterizing the state and direction of progress in this arena is challenging but important. Here, we employ three metrics: a classical metric of productivity (publications per person), an adapted metric which we denote as Revealed Scientific Advantage (developed from work used to compare publications in scientific fields among countries) to characterize disciplinary specialty, and a new metric, scientific indigeneity (defined as the ratio of publications with domestic corresponding authors) to characterize the locus of scientific activity that also serves as a partial proxy for local absorptive capacity. These metrics—using population and publications data that are available for most countries–allow the characterization of some key features of national scientific enterprise. The trends in productivity and indigeneity when compared across other countries and regions can serve as indicators of strength or fragility in the national research ecosystems, and the trends in specialty can allow regional policy makers to assess the extent to which the areas of focus of research align (or not align) with regional priorities. We apply the metrics to study the Middle East and North Africa (MENA)—a region where science and technology capacity will play a key role in national economic diversification. We analyze 9.8 million publication records between 1981–2013 in 17 countries of MENA from Morocco to Iraq and compare it to selected countries throughout the world. The results show that international collaborators increasingly drove the scientific activity in MENA. The median indigeneity reached 52% in 2013 (indicating that almost half of the corresponding authors were located in foreign countries). Additionally, the regional disciplinary focus in chemical and petroleum engineering is waning with modest growth in the life sciences. We find repeated patterns of stagnation and contraction of scientific activity for several MENA countries contributing to a widening productivity gap on an international comparative yardstick. The results prompt questions about the strength of the developing scientific enterprise and highlight the need for consistent long-term policy for effectively addressing regional challenges with domestic research.