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      GENETICS and G3: Community-Driven Science, Community-Driven Journals

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          Abstract

          Most scholarly societies publish journals for the betterment of the community, among myriad reasons. Yet in this era of rapidly proliferating publications, societies and their journals offer many benefits for constituents, including affordable meetings, travel awards, public outreach, support for educators, science advocacy, dissemination of scientific discoveries via journals, the fostering of community, boards of directors elected by their peers, and a long-term view. At GENETICS and G3: Genes | Genomes | Genetics, we believe that society journals offer special value not found elsewhere: a voice and vehicle for practicing scientists to move science forward. The GSA journals have done this in several ways. As peer scientists and editors, we recognize that science advances faster when the development of new methods is accompanied by clear descriptions of how to implement these methods, along with the data that benchmarks the new approaches against existing ones (de Koning and McIntyre 2012). In 2010, the GSA journals created a revised data policy that requires public accessibility of all the data used to support the conclusions described in a paper (McIntyre 2010). The Editors felt a policy was necessary to ensure that analyses based on genomic data could be repeated just as easily, for example, as those based on polymerase chain reaction experiments; although no one today would publish the results of a polymerase chain reaction experiment without providing the sequences of the primers, this was not always the case. Even as shrinking methods sections plague many journals, we have expanded requirements for methodological details. As editors, we encourage our authors to make their findings as reproducible as possible, in part because we heard the community pleading for more information. As reviewers, we appreciate having the information needed to verify and reproduce and extend results. And, as authors, we sometimes struggle to conform to our own high standard. During this past year, although an increasing number of scientific journals have, with much fanfare, increased their demands for open access to data, the GSA journals have in fact quietly led the way as early proponents of open-data policies. Soon after we released our revised policy, we realized that requiring raw data were not enough. Deeper thought and discussion revealed that analysis programs, detailed bioinformatics methods, and full result files also were needed to create robust publications. How though to ensure that the data would be available in perpetuity? Unfortunately, local websites, although well-intentioned, often suffer from lack of maintenance over time, with broken links impeding readers’ ability to access data in the long-term (Vines et al. 2014). To accommodate the increasing volume of data, GENETICS and G3 encourage deposits with third-party data repositories like Dryad, FigShare, GEO, and others. We also encourage the provision of such data as supplemental information. In the spirit of serving the community, we started collections of articles on contemporary topics of interest organized across the two journals, offering a wider platform and greater visibility to each individual article (http://www.genetics.org/site/misc/GenomicSelection.xhtml; http://g3journal.org/site/misc/MouseGeneticResources.xhtml). The value of such efforts is most apparent when a single topic quickly captures the interest of our community. In these cases, having common datasets to work with becomes critical. In February 2012, the GSA journals featured a focus on the mouse Collaborative Cross, which underscored the role of society journals in promoting such community endeavors (McIntyre and de Koning 2012). GENETICS and G3 have gone on to encourage discussion in genomic selection (de Koning and McIntyre 2012), sex determination (http://www.genetics.org/site/misc/GeneticsOfsex.xhtml), and immunity (http://www.genetics.org/site/misc/GeneticsOfImmunity.xhtml), and we continue to promote and present literature on these topics. Please let us know if there are challenges and central questions in your community that need a venue for marshalling discussion. GENETICS and G3 Today: Multiparental Populations Collection In the continued spirit of hosting such scholarly resources, the current issues of GENETICS and G3 highlight articles on the study of multiparental populations (#MPP). As the limitations of two-parent cross designs have become obvious, we are struggling with analysis of experimental populations that have more than two segregating alleles. The papers in the MPP collection, along with their data and transparent methods, should stimulate discussion and, we hope, move the field forward. The realization of this first group of MPP papers exemplifies the ability of community-driven journals to support community-driven research. The idea for this initiative originated during a workshop on Multiparent Advanced Generation Inter-Cross (MAGIC) populations (http://mus.well.ox.ac.uk/19genomes/MAGIC-WORKSHOP/) in 2013 that was co-organized by one of our Associate Editors, B. Emma Huang. With the help of Associate Editors Fred van Eeuwijk and Alain Charcosset, the journals issued a call for papers (http://www.genetics.org/site/misc/CallForPapersMultiParental.xhtml). The submissions were managed by additional editors (the authors of this editorial, as well as Jim Birchler, Steve Chenoweth, Rebecca W. Doerge, Jim Holland, B. Emma Huang, Brian Yandell, and senior editor Krista Nichols), and nearly 70 referees. Such an effort—indeed, the very existence of society journals themselves—would be hard to envisage without the support and leadership of an engaged community of practicing scientists, who themselves understand what is necessary to “do science” and to thrive in today’s current climate. When we commit to publishing reproducible science, the synergy creates a body of long-standing work that is greater than the sum of its parts. We invite you to submit your own manuscripts for consideration in the rolling MPP collection as well as others, have your own voice heard, and advance discovery and discussion in your community.

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          The availability of research data declines rapidly with article age.

          Policies ensuring that research data are available on public archives are increasingly being implemented at the government [1], funding agency [2-4], and journal [5, 6] level. These policies are predicated on the idea that authors are poor stewards of their data, particularly over the long term [7], and indeed many studies have found that authors are often unable or unwilling to share their data [8-11]. However, there are no systematic estimates of how the availability of research data changes with time since publication. We therefore requested data sets from a relatively homogenous set of 516 articles published between 2 and 22 years ago, and found that availability of the data was strongly affected by article age. For papers where the authors gave the status of their data, the odds of a data set being extant fell by 17% per year. In addition, the odds that we could find a working e-mail address for the first, last, or corresponding author fell by 7% per year. Our results reinforce the notion that, in the long term, research data cannot be reliably preserved by individual researchers, and further demonstrate the urgent need for policies mandating data sharing via public archives. Copyright © 2014 Elsevier Ltd. All rights reserved.
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            Data: the foundation of science.

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              Facilitating Discovery: The Role of Society Journals in Collaborative Science

              SCIENTIFIC progress requires hypotheses and ideas, but it is enabled by resources. Genetic resource panels (GRPs) like the “Collaborative Cross” are a unique resource for the scientific community. Because this resource allows repeated generation of particular genetic combinations, the impact of DNA sequence variation on a wide range of phenotypes can be readily studied. Renewable resource populations have been created for flies, maize, Arabidopsis, yeast, worms, and mice (e.g., Giaever et al. 2002; Kamath et al. 2003; Complex Trait Consortium 2004; Macdonald and Long 2007; Ayroles et al. 2009; Kover et al. 2009; McMullen et al. 2009). With them phenotypic data for transcription, metabolites, proteins and whole organism can be linked to underlying genetic polymorphisms. These resources give scientists insight into how genetic variation percolates through the biological layers, from cells to the whole organism, from molecules to networks. One critical requirement for realizing the potential of these accumulating resources is that all data be publicly available, preferably accompanied with a set of online tools for mining them. The February 2012 issues of GENETICS and G3: Genes | Genomes | Genetics highlight the launch of the Collaborative Cross for mice and present the first exciting results, both data- and methods-driven, issuing from this cross. The most notable predecessor of the Collaborative Cross is the BXD panel of recombinant inbred lines for which a mass of phenotypic, transcriptomic, and genetic data are publically available online. Emerging technologies that allow measurements on single cells to complex behaviors mean that geneticists have the opportunity not only to revel in biological complexity but to deconstruct and understand it. How can society-sponsored, peer-edited journals like ours help the community in making the most of these exciting resources? GENETICS and G3 are sister journals committed to the highest level of scientific rigor. Both journals are committed to open access of all data used in their articles, and require that all the data are submitted to a public repository, or available as a supplement, thereby enabling others to connect the dots in their own experiments and analysis. We pay more than just lip service to our data policy. We believe it serves scientists and science well. Data sharing is particularly crucial for GRPs like the Collaborative Cross. If some of the pieces of the puzzle have been taken off the board and are only available only through a complex compact, then the puzzle is unlikely to be completed, and the community resource is compromised. Peer editors are invested in ensuring that these resources live up to their potential. The 15 articles on GRPs for the mouse in this month's issues of GENETICS and G3 illustrate The Editors’ vision for one way in which society-sponsored peer editing adds value for the scientific community. All the data associated with these papers is publicly available, and the authors are committed to its widest possible distribution. We are proud to provide a venue for the publication of such important work, and we will continue to facilitate publication of high-quality studies focused on this unique resource. The Editors of GENETICS and G3 are working together to maximize the full impact of such large scale endeavors. The scientific community needs new tools for analysis, as well as creative experiments that unlock the promise of GRPs. We welcome submissions of manuscripts that answer these broad challenges. We also invite submission of manuscripts that describe the use of the resources presented in this month's issues of Genetics and G3. The Editors of GENETICS and G3 are committed to publishing high-quality science and to supporting the scientific community. To that end, we seek to collaborate with scientific communities engaged in projects to develop genetic resources. We are developing ways to tag papers using specific metadata identifiers so all papers involving a particular GRP can be quickly located and collated. Look for our tags for mouse-GRP, mouse-CC, and mouse-DO. Tell us more about ways you think the journals of the Genetics Society of America can collaborate with and support our community.
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                Author and article information

                Journal
                G3 (Bethesda)
                Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes|Genomes|Genetics
                Genetics Society of America
                2160-1836
                01 September 2014
                September 2014
                : 4
                : 9
                : 1567-1568
                Affiliations
                [* ]Deputy Editor, G3: Genes|Genomes|Genetics, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
                []Senior Editor, GENETICS, University of Florida, Gainesville, Florida 32610
                Article
                GGG_013680
                10.1534/g3.114.013680
                4169148
                25237108
                Copyright © 2014 de Koning and McIntyre
                Page count
                Pages: 2
                Product
                Categories
                Editorial

                Genetics

                multiparent advanced generation inter-cross (magic), mpp, multiparental populations

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