Robin Hood: A cost-efficient two-stage approach to large-scale simultaneous inference with non-homogeneous sparse effects.

A classical approach to experimental design in many scientific fields is to first gather all of the data and then analyze it in a single analysis. It has been recognized that in many areas such practice leaves substantial room for improvement in terms of the researcher's ability to identify relevant effects, in terms of cost efficiency, or both. Considerable attention has been paid in recent years to multi-stage designs, in which the user alternates between data collection and analysis and thereby sequentially reduces the size of the problem. However, the focus has generally been towards designs that require a hypothesis be tested in every single stage before it can be declared as rejected by the procedure. Such procedures are well-suited for homogeneous effects, i.e. effects of (almost) equal sizes, however, with effects of varying size a procedure that permits rejection at interim stages is much more suitable. Here we present precisely such multi-stage testing procedure called Robin Hood. We show that with heterogeneous effects our method substantially improves on the existing multi-stage procedures with an essentially zero efficiency trade-off in the homogeneous effect realm, which makes it especially useful in areas such as genetics, where heterogeneous effects are common. Our method improves on existing approaches in a number of ways including a novel way of performing two-sided testing in a multi-stage procedure with increased power for detecting small effects.

Breaking Out of the Academic Pipeline.

For many graduate students, the academic path may not be the best fit, and with limited faculty positions available, many students are now looking to other career possibilities. University programs are helping students to explore and pursue alternative careers.

The faculty costs to educate a biomedical sciences graduate student.

Academic medical centers nationwide face numerous fiscal challenges resulting from implementation of restructured healthcare delivery models, contracting state support for higher education, and increased competition for federal and other sources of biomedical research funding. In pursuing greater accountability and transparency in its fiscal operations, the Medical University of South Carolina (MUSC) has implemented a responsibility centers management budgetary model, which requires all MUSC colleges to be eventually self-sustaining financially. Graduate schools in the biomedical sciences are particularly vulnerable in the face of these challenges, depending traditionally as they do on financial support from training grant tuition, occasional medical school tuition and medical practice plan revenues, graduate college-based revenue-generating programs, and faculty payment of PhD tuition. The revenue streams are often insufficient to support PhD training programs, and supplemental financial support is required from the institution. In the context of a college of graduate studies, estimates of the cost of educating a graduate student become a significant necessity. This study presents a readily applicable model of empirically estimating the faculty salary costs that may provide a basis for budgetary planning that will help to sustain a biomedical sciences graduate school's commitment to its teaching, research, and service mission goals.

Conscience dilemma: to become a bioengineer or to survive as a biologist.

Bioengineering is the consideration of biological problems from modern engineering, therefore money-oriented, perspective. Today, grant-giving bodies always favor bioengineering projects rather than pure biology projects (like those in ecology, entomology, etc.). Therefore, today's biologist is forced to be on the horns of a dilemma. They have to either submit a very powerful and valid reason for the proposal of their project, or change the project to one having a potential of money-based outcome. On the other hand, because of dealing with the living components of nature, conducting a research in pure biology is like a kind of worship. For this reason, from a believer scientist's view, a deviation (in terms of research) from biology to bioengineering can be considered like committing a sin. Unfortunately, today's wild capitalism has been bringing new sinners day by day, and this system will continue for the foreseeable future unless grant-giving bodies comprehend the real importance of pure biology.

4273π: bioinformatics education on low cost ARM hardware.

BACKGROUND: Teaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. For a future career in biology or bioinformatics, the installation of software is a useful skill. We propose that this may be taught by running the course on GNU/Linux running on inexpensive Raspberry Pi computer hardware, for which students may be granted full administrator access. RESULTS: We release 4273π, an operating system image for Raspberry Pi based on Raspbian Linux. This includes minor customisations for classroom use and includes our Open Access bioinformatics course, 4273π Bioinformatics for Biologists. This is based on the final-year undergraduate module BL4273, run on Raspberry Pi computers at the University of St Andrews, Semester 1, academic year 2012-2013. CONCLUSIONS: 4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost.

Integration of physics and biology: synergistic undergraduate education for the 21st century.

This is an exciting time to be a biologist. The advances in our field and the many opportunities to expand our horizons through interaction with other disciplines are intellectually stimulating. This is as true for people tasked with helping the field move forward through support of research and education projects that serve the nation's needs as for those carrying out that research and educating the next generation of biologists. So, it is a pleasure to contribute to this edition of CBE-Life Sciences Education. This column will cover three aspects of the interactions of physics and biology as seen from the viewpoint of four members of the Division of Undergraduate Education of the National Science Foundation. The first section places the material to follow in context. The second reviews some of the many interdisciplinary physics-biology projects we support. The third highlights mechanisms available for supporting new physics-biology undergraduate education projects based on ideas that arise, focusing on those needing and warranting outside support to come to fruition.

Accelerators for America's Future Workshop: Medicine and Biology.

"Medicine and Biology" was one of five working groups of the "Accelerators for America's Future" Workshop held October 2009. The recently-released workshop report stresses that the leadership position of the United States in fields where accelerators play an important part is being seriously eroded because of lack of coordinated agency support for accelerator research and development. This is particularly true for biology and medicine. Radiation therapy with beams of protons and light ions was pioneered in the United States and has proven successful in the treatment of several different tumor sites in the body. Proton therapy is available in the United States in a number of centers; however, all but one contain accelerator and beam-delivery components manufactured abroad. Light-ion therapy is only available overseas. Why has the United States lost its lead in this field? The Working Group noted that in other countries, central governments are subsidizing construction and technology development by their industries, whereas in the United States funding for purchasing and building clinical facilities must be raised from private sources. As a result, most proton facilities in the United States, by virtue of having to recover investment costs, favor reimbursable treatments, detracting from the development of research protocols. The financial hurdle for starting a light-ion facility in the United States has been totally prohibitive for the private-equity market. While technological advances are being made that will provide some reduction in capital costs, the field will not flourish in the United States until effective funding means are developed that do not put the full burden on the private sector.

Vision and change in biology undergraduate education: Vision and change from the funding front.

The purpose of this short article is to (a) briefly summarize the findings of two important recent resources concerning the future of biology in the 21(st) century; one, Vision and Change, A Call to Action [AAAS, 2009. AAAS, Washington, DC], concerned with undergraduate education in biology, the other, A New Biology for the 21st Century [National Research Council, 2009. National Academies Press, Washington, DC], concerned with advances within the discipline itself; (b) urge you, the reader of BAMBED, to review the material on the Vision and Change website [AAAS, 2009. AAAS: Washington, DC] and then to think how you might change things at your own institution and within your courses, and; (c) make readers aware of the programs at the National Science Foundation (NSF) that might support change efforts, as well as refer you to efforts other funding agencies are making to help biology undergraduate education respond to the challenges and opportunities chronicled in these two reports. Although NSF funding opportunities are specifically available to US investigators, the recommendations of the two reports should be of interest to a wide spectrum of international researchers.

[Academician V.E. Sokolov is the head of the General Biology Department].

This paper considers the activity of Academician V.E. Sokolov as head of the General Biology Department of the Russian Academy of Sciences, which he headed from 1985 to 1998. The history of the struggle for the preservation of biological science, carried out by Sokolov and the Department headed by him over more than ten years, is shown based on archival and little-known published materials. Examples are given of the activity of the General Biology Department that had great scientific, public, and nature-conservation significance.