The reaming of life: Based on the 2010 Jim Gray eScience Award Lecture

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SUMMARY We are well into the era of data intensive-digital scientific discovery, an era defined by Jim Gray as the Fourth Paradigm. From my own perspective of the life sciences, much has been accomplished, but there is much to do if we are to maximize our understanding of biological systems given the data we have today, let alone what is coming. In my 2010 Jim Gray eScience Award Lecture, I gave my own thoughts on what needs to be accomplished, and with an additional year of hindsight, I expand on that here. Copyright © 2012 John Wiley & Sons, Ltd.

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... Further TCM research is therefore warranted, particularly with respect to IRR as it relates to grounding modern research, both clinical and technical, with classical theory. In the style of Jim Gray's vision of scientific discovery, driven by the collection, analysis, and comprehension of digital data by an ever-increasing interdisciplinary community of both professional and citizen-like scientists alike [69], perhaps the future of TCM lies in a big data design and deployment methodology with a new medical IRR at its core that is translational in nature, reducing health care costs and improving medical outcomes worldwide. ...
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Computer-based medical diagnostic systems have seen tremendous growth since the 1950s, particularly with the arrival of personal computers, the Internet, portable devices, and big data analytical environments. Such technologies utilize the fundamental principles of information representation and retrieval (IRR) to solve complex questions pertaining to health and disease. However, since inception, such systems have virtually ignored traditional Chinese medicine (TCM) techniques, oftentimes due to their lack of success in randomized controlled trials. To this day, little is known about how TCM works scientifically and, yet, it remains an essential part of the world’s healthcare system, particularly in several Asian countries. As disease remains widespread across society, the diagnostic and treatment methods of TCM should be compared alongside Western medical models, in light of modern IRR techniques, to determine if a new, futuristic form of translational medicine can be developed that improves medical outcomes and reduces health care costs worldwide. This study analyzes all published research in SCOPUS relating to TCM and IRR for the period 1985-2020 and employs bibliometric techniques, multiple correspondence analysis, and data visualizations to investigate author productivity, collaborations, and research trends. Opportunities and challenges were discovered that will help identify future directions within the field as we enter a new era of data-intensive scientific discovery in medicine.
Scientific discovery is increasingly driven by the collection, analysis, and comprehension of digital data. Collaborations between domain scientists and computer scientists can accelerate both the investigation and applications processes. The Microsoft eScience Workshop is a recognized venue for showcasing such collaborations and serves as a forum for exchanging both domain and computational researches. This editorial provides an overview of the papers that resulted from selected research collaboration presented at the 2010 Microsoft eScience workshop. Copyright (C) 2012 John Wiley & Sons, Ltd.
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science publishing, online communities, science policy, new forms of publishing, bioinformatics, digital repositories, semantic publishing, citation
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Getting a promotion or a new position are important parts of the scientific career process. Ironically, a committee whose membership has limited ability to truly judge your scholarly standing is often charged with making these decisions. Here are ten simple rules from my own experiences , in both getting promoted and serving on such committees, for how you might maximize your chances of getting ahead under such circumstances. The rules focus on what might be added to a CV, research statement, personal statement, or cover letter, depending on the format of the requested promotion materials. In part, the rules suggest that you educate the committee members, who have a range of expertise, on what they should find important in the promotion application provided by a computational biologist. Further, while some rules are generally applicable, the focus here is on promotion in an academic setting. Having said that, in such a setting teaching and community service are obviously important, but barely touched upon here. Rather, the focus is on how to maximize the appreciation of your research-related activities. As a final thought before we get started on the rules, this is not just about you, but an opportunity to educate a broad committee on what is important in our field. Use that opportunity well, for it will serve future generations of computational biologists.
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Scientific articles are tailored to present information in human-readable aliquots. Although the Internet has revolutionized the way our society thinks about information, the traditional text-based framework of the scientific article remains largely unchanged. This format imposes sharp constraints upon the type and quantity of biological information published today. Academic journals alone cannot capture the findings of modern genome-scale inquiry. Like many other disciplines, molecular biology is a science of facts: information inherently suited to database storage. In the past decade, a proliferation of public and private databases has emerged to house genome sequence, protein structure information, functional genomics data and more; these digital repositories are now a vital component of scientific communication. The next challenge is to integrate this vast and ever-growing body of information with academic journals and other media. To truly integrate scientific information we must modernize academic publishing to exploit the power of the Internet. This means more than online access to articles, hyperlinked references and web-based supplemental data; it means making articles fully computer-readable with intelligent markup and Structured Digital Abstracts. Here, we examine the changing roles of scholarly journals and databases. We present our vision of the optimal information architecture for the biosciences, and close with tangible steps to improve our handling of scientific information today while paving the way for an expansive central index in the future.
In this paper we suggest that the full scientific potential of workflows will be achieved through mechanisms for sharing and collaboration, empowering scientists to spread their experimental protocols and to benefit from those of others. To facilitate this process we have designed and built the Virtual Research Environment for collaboration and sharing of workflows and experiments. In contrast to systems which simply make workflows available, provides mechanisms to support the sharing of workflows within and across multiple communities. It achieves this by adopting a social web approach which is tailored to the particular needs of the scientist. We present the motivation, design and realisation of .
Library-run institutional repositories face a crossroads: adapt or die. The “build it and they will come” proposition has been decisively proven wrong. Citation advantages and preservation have not attracted faculty participants, though current-generation software and services offer faculty little else. Academic librarianship has not supported repositories or their managers. Most libraries consistently under-resource and understaff repositories, further worsening the participation gap. Software and services have been wildly out of touch with faculty needs and the realities of repository management. These problems are not insoluble, especially in light of Harvard University arts and science faculty’s recent permissions mandate, but they demand serious reconsideration of repository missions, goals, and means if we are to be ready for Harvard imitators, and especially to be ready should those imitators not surface. published or submitted for publication
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