Ten Quick Tips for Using a Raspberry Pi

Much of biology (and, indeed, all of science) is becoming increasingly computational. We tend to think of this in regards to algorithmic approaches and software tools, as well as increased computing power. There has also been a shift towards slicker, packaged solutions--which mirrors everyday life, from smart phones to smart homes. As a result, it's all too easy to be detached from the fundamental elements that power these changes, and to see solutions as "black boxes". The major goal of this piece is to use the example of the Raspberry Pi--a small, general-purpose computer--as the central component in a highly developed ecosystem that brings together elements like external hardware, sensors and controllers, state-of-the-art programming practices, and basic electronics and physics, all in an approachable and useful way. External devices and inputs are easily connected to the Pi, and it can, in turn, control attached devices very simply. So whether you want to use it to manage laboratory equipment, sample the environment, teach bioinformatics, control your home security or make a model lunar lander, it's all built from the same basic principles. To quote Richard Feynman, "What I cannot create, I do not understand".Comment: 12 pages, 2 figure

Ten Simple Rules for organizing a non–real-time web conference

The present work describes the 100% virtual ATIDES (Avances en Tecnologı ´as, Innovacio ´n y Desafı ´os de la Educacio ´n Superior) conference that was held between October 15 and 31, 2018, sponsored by Universitat Jaume I (UJI), Spain. Online conferences like this have been the subject of some controversy in the field of education over the last decade. Indeed, we have found a few texts that are against them. One of these is [1], whose authors claim that “interaction is not enough” to ensure efficient simulation of face-to-face contact. However, the Canadian academic community (for instance, the Centre for Distance Education at Athabasca University) is a strong advocate of online conferences (see [2,3]). Among other advantages, this kind of conference is “family-friendly,” i.e., they break barriers for researchers with family obligations [4], in particular many women [5]. In addition, these conferences overcome the drawback of parallel sessions at face-to-face conferences, at which participants must choose certain talks and miss others. Anderson and Anderson [6] even put forward environmental and economic arguments: “Transportation is a major contributor of carbon dioxide (CO2) emissions.” On the other hand, Abdullah [7] and Kear, Chetwynd, and Jefferis [8] look at the matter from another point of view that is also important: Social presence at online conferences

GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training

In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy—paradoxically, many are actually closing “niche” bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all

GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training

In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy--paradoxically, many are actually closing "niche" bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all

A quick guide for building a successful bioinformatics community

“Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop “The ‘How To Guide’ for Establishing a Successful Bioinformatics Network” at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB)

The Cure: Making a game of gene selection for breast cancer survival prediction

Motivation: Molecular signatures for predicting breast cancer prognosis could greatly improve care through personalization of treatment. Computational analyses of genome-wide expression datasets have identified such signatures, but these signatures leave much to be desired in terms of accuracy, reproducibility and biological interpretability. Methods that take advantage of structured prior knowledge (e.g. protein interaction networks) show promise in helping to define better signatures but most knowledge remains unstructured. Crowdsourcing via scientific discovery games is an emerging methodology that has the potential to tap into human intelligence at scales and in modes previously unheard of. Here, we developed and evaluated a game called The Cure on the task of gene selection for breast cancer survival prediction. Our central hypothesis was that knowledge linking expression patterns of specific genes to breast cancer outcomes could be captured from game players. We envisioned capturing knowledge both from the players prior experience and from their ability to interpret text related to candidate genes presented to them in the context of the game. Results: Between its launch in Sept. 2012 and Sept. 2013, The Cure attracted more than 1,000 registered players who collectively played nearly 10,000 games. Gene sets assembled through aggregation of the collected data clearly demonstrated the accumulation of relevant expert knowledge. In terms of predictive accuracy, these gene sets provided comparable performance to gene sets generated using other methods including those used in commercial tests. The Cure is available at http://genegames.org/cure