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š What is restez? R packages for interacting with the National Center for Biotechnology Information (NCBI) have, to-date, depended on API query calls via NCBIās Entrez. For computational analyses that require the automated look-up of reams of biological sequence data, piecemeal querying via bandwith-limited requests is evidently not ideal. These queries are not only slow, but they depend on network connections and the remote serverās consistent behaviour. Additionally, users who make very large requests over extended periods of time run the risk of being blocked....
Although there are increasing incentives and pressures for researchers to share code (even for projects that are not essentially computational), practices vary widely and standards are mostly non-existent. The practice of reviewing code then falls to researchers and research groups before publication. With that in mind, rOpenSci hosted a discussion thread and a community call to bring together different researchers for a conversation about current practices, and challenges in reviewing code in the lab....
A few months ago, I wasnāt sure what to expect when looking at fluorescence microscopy images in published papers. I looked at the accompanying graph to understand the data or the point the authors were trying to make. Often, the graph represents one or more measures of the so-called co-localization, but I couldnāt figure out how to interpret them. It turned out; reading the images is simple. Cells are simultaneously stained by two dyes (say, red and green) for two different proteins....
Imagine you are a fish ecologist who compiled a list of fish species for your country. š Your list could be useful to others, so you publish it as a supplementary file to an article or in a research repository. That is fantastic, but it might be difficult for others to discover your list or combine it with other lists of species. Luckily thereās a better way to publish species lists: as a standardized checklist that can be harvested and processed by the Global Biodiversity Information Facility (GBIF)....
š Antarctic/Southern Ocean science and rOpenSci Collaboration and reproducibility are fundamental to Antarctic and Southern Ocean science, and the value of data to Antarctic science has long been promoted. The Antarctic Treaty (which came into force in 1961) included the provision that scientific observations and results from Antarctica should be openly shared. The high cost and difficulty of acquisition means that data tend to be re-used for different studies once collected....
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