Drosophila, like other invertebrates and plants, relies mainly on RNA interference for its defense against viruses. In flies, viral infection also triggers the expression of many genes. One of the genes induced, Vago, encodes a 18-kilodalton cysteine-rich polypeptide. Here we provide genetic evidence that the Vago gene product controlled viral load in the fat body after infection with drosophila C virus. Induction of Vago was dependent on the helicase Dicer-2. Dicer-2 belongs to the same DExD/H-box helicase family as do the RIG-I-like receptors, which sense viral infection and mediate interferon induction in mammals. We propose that this family represents an evolutionary conserved set of sensors that detect viral nucleic acids and direct antiviral responses.

Organisms display astonishing levels of cell and molecular diversity, including genome size, shape, and architecture. In this chapter, we review how the genome can be viewed as both a structural and an informational unit of biological diversity and explicitly define our intended meaning of genetic information. A brief overview of the characteristic features of bacterial, archaeal, and eukaryotic cell types and viruses sets the stage for a review of the differences in organization, size, and packaging strategies of their genomes. We include a detailed review of genetic elements found outside the primary chromosomal structures, as these provide insights into how genomes are sometimes viewed as incomplete informational entities. Lastly, we reassess the definition of the genome in light of recent advancements in our understanding of the diversity of genomic structures and the mechanisms by which genetic information is expressed within the cell. Collectively, these topics comprise a good introduction to genome biology for the newcomer to the field and provide a valuable reference for those developing new statistical or computation methods in genomics. This review also prepares the reader for anticipated transformations in thinking as the field of genome biology progresses.

Biological networks are graphs used to represent the inner workings of a biological system. Networks describe the relationships of the elements of biological systems using edges and nodes. However, the resulting representation of the system can sometimes be too simplistic to usefully model reality. By combining several different interaction types within one larger multilayered biological network, tools such as SignaLink provide a more nuanced view than those relying on single-layer networks (where edges only describe one kind of interaction). Multilayered networks display connections between multiple networks (i.e., protein-protein interactions and their transcriptional and posttranscriptional regulators), each one of them describing a specific set of connections. Multilayered networks also allow us to depict cross talk between cellular systems, which is a more realistic way of describing molecular interactions. They can be used to collate networks from different sources into one multilayered structure, which makes them useful as an analytic tool as well.

In recent years, there has been an explosion in the popularity of hackathons — creative, participant-driven meetings at which software developers gather for an intensive bout of programming, often organized in teams. Hackathons have tangible and intangible outcomes, such as code, excitement, learning, networking, and so on, whose relative merits are unclear. For example, a frequent complaint is that code is abandoned when the hackathon ends, and questions like, “which outcomes are produced most reliably?” and, “how valuable are they for participants, organizers, and sponsors?” remain open. As a first step in giving “hackology” a more rigorous footing, this paper describes the NESCent hackathon model, developed over the course of a decade to serve the academic discipline of evolutionary biology, with the dual goals of augmenting the community’s shared software infrastructure, and fostering a diverse community of practice in open scientific software development. The paper presents a detailed guide to staging a NESCent-style hackathon, along with a structured information set on nine events involving 54 team projects. NESCent hackathons have produced tangible products with downstream impacts, including prototypes that were leveraged for major funding, incremental additions to production code bases, and creative drafts (designs, standards, and proofs-of-concept) that contributed to further work. The impacts of intangible outcomes could not be assessed objectively, but the subjective experience suggests that hackathons have a positive impact by (1) providing individuals with valuable experiences, networking, and training, and (2) fostering a more cohesive community of practice by enhancing awareness of challenges and best practices and by building links of familiarity between and among resources and people. Future research that recognizes the diverse outcomes of hackathons might enable evidence-based decisions about how to design hackathons for effectiveness.

An academic conference is a traditional platform for researchers and professionals to network and learn about recent developments and trends in a particular academic field [1–4]. Typically, the organizing committees and sponsors decide the main theme and sub-topics of the conference and select the presenters based on peer-reviewed papers [5]. The selected speakers usually share their research with a large audience by means of presentations and posters. However, the most stimulating discussions generally take place over coffee breaks when attendees can interact with each other and discuss various topics, including their own research interests, in a more informal manner [1, 6, 7], while expanding their own professional networks. An emphasis on facilitating such informal/networking interactions is a central focus of “unconventional conferences”—or “unconferences.” While many people may not yet have taken part in an unconference, the concept has been around for more than two decades. Events with unconference formats, beginning as early as 1985, include Open Space Technology, Foo Camp, BarCamp, Birds of a Feather, EdCamp, ScienceOnline, and many others. The success of these events has made the unconference format increasingly popular and widely known [8–11]. Unlike traditional conferences, an unconference is a participant-oriented meeting where the attendees decide on the agenda, discussion topics, workshops, and, often, even the time and venues. The informal and flexible program allows participants to suggest topics of their own interest and choose sessions accordingly. The format provides an excellent opportunity for researchers from diverse disciplines to work collaboratively on topics of common interest. The overarching goal for most unconferences is to prioritize conversation over presentation. In other words, the content for a session does not come from a select number of individuals at the front of the room, but is generated by all the attendees within the room, and, as such, every participant has an important role. Advantages of the unconference format include: a focus on topics that are relevant to the attendees (because they suggested them), an opportunity for teamwork development, flexibility of schedule, and an emphasis on contributions from every participant. The relationships built during an unconference often continue well past the event. The interactions can lead to productive collaborations, professional development opportunities, and a network of resources and are very effective at building a community amongst participants. The unconference format, therefore, gives participants experience in working together, and this can change how they think about their day-to-day work. A range of articles offer tips and advice for organizing and delivering aspects of scientific conferences and meetings or observations on features of successful meetings [5, 12, 13], including several from the PLOS Computational Biology “Ten Simple Rules” collection [14–16]. While the rules presented in this article are of particular relevance to the organization of unconferences, several of these points are also useful and complementary guidelines for organizing other kinds of events.

"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).

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTShort Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell RegulationKim Van Roey†, Bora Uyar†, Robert J. Weatheritt‡, Holger Dinkel†, Markus Seiler†, Aidan Budd†, Toby J. Gibson†, and Norman E. Davey*†§View Author Information† Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany‡ MRC Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom§ Department of Physiology, University of California, San Francisco, San Francisco, California 94143, United States*E-mail: [email protected]Cite this: Chem. Rev. 2014, 114, 13, 6733–6778Publication Date (Web):June 13, 2014Publication History Received17 October 2013Published online13 June 2014Published inissue 9 July 2014https://pubs.acs.org/doi/10.1021/cr400585qhttps://doi.org/10.1021/cr400585qreview-articleACS PublicationsCopyright © 2014 American Chemical SocietyRequest reuse permissionsArticle Views7806Altmetric-Citations326LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Cell and molecular biology,Modification,Peptides and proteins,Post-translational modification,Receptors Get e-Alerts

The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, classifying and curating information about short linear motifs (SLiMs). For >10 years, this resource has provided the scientific community with a freely accessible guide to the biology and function of linear motifs. The current version of ELM contains ∼200 different motif classes with over 2400 experimentally validated instances manually curated from >2000 scientific publications. Furthermore, detailed information about motif-mediated interactions has been annotated and made available in standard exchange formats. Where appropriate, links are provided to resources such as switches.elm.eu.org and KEGG pathways.

Summary: Rapid technological advances have led to an explosion of biomedical data in recent years. The pace of change has inspired new collaborative approaches for sharing materials and resources to help train life scientists both in the use of cutting-edge bioinformatics tools and databases and in how to analyse and interpret large datasets. A prototype platform for sharing such training resources was recently created by the Bioinformatics Training Network (BTN). Building on this work, we have created a centralized portal for sharing training materials and courses, including a catalogue of trainers and course organizers, and an announcement service for training events. For course organizers, the portal provides opportunities to promote their training events; for trainers, the portal offers an environment for sharing materials, for gaining visibility for their work and promoting their skills; for trainees, it offers a convenient one-stop shop for finding suitable training resources and identifying relevant training events and activities locally and worldwide. Availability and implementation: http://mygoblet.org/training-portal Contact: manuel.corpas@tgac.ac.uk