共查询到6条相似文献，搜索用时 15 毫秒
1.
2.
Data support knowledge development and theory advances in ecology and evolution. We are increasingly reusing data within our teams and projects and through the global, openly archived datasets of others. Metadata can be challenging to write and interpret, but it is always crucial for reuse. The value metadata cannot be overstated—even as a relatively independent research object because it describes the work that has been done in a structured format. We advance a new perspective and classify methods for metadata curation and development with tables. Tables with templates can be effectively used to capture all components of an experiment or project in a single, easy‐to‐read file familiar to most scientists. If coupled with the R programming language, metadata from tables can then be rapidly and reproducibly converted to publication formats including extensible markup language files suitable for data repositories. Tables can also be used to summarize existing metadata and store metadata across many datasets. A case study is provided and the added benefits of tables for metadata, a priori, are developed to ensure a more streamlined publishing process for many data repositories used in ecology, evolution, and the environmental sciences. In ecology and evolution, researchers are often highly tabular thinkers from experimental data collection in the lab and/or field, and representations of metadata as a table will provide novel research and reuse insights. 相似文献
3.
Althea A. Archmiller Andrew D. Johnson Jane Nolan Margaret Edwards Lisa H. Elliott Jake M. Ferguson Fabiola Iannarilli Juliana Vélez Kelsey Vitense Douglas H. Johnson John Fieberg 《The Journal of wildlife management》2020,84(5):1012-1017
Scientific progress depends upon the accumulation of empirical knowledge via reproducible methodology. Although reproducibility is a main tenet of the scientific method, recent studies have highlighted widespread failures in adherence to this ideal. The goal of this study was to gauge the level of computational reproducibility, or the ability to obtain the same results using the same data and analytic methods as in the original publication, in the field of wildlife science. We randomly selected 80 papers published in the Journal of Wildlife Management and Wildlife Society Bulletin between 1 June 2016 and 1 June 2018. Of those that were suitable for reproducibility review (n = 74), we attempted to obtain study data from online repositories or directly from authors. Forty-two authors did not respond to our requests, and we were further unable to obtain data from authors of 13 other studies. Of the 19 studies for which we were able to obtain data and complete our analysis, we judged that 13 were mostly or fully reproducible. We conclude that the studies with publicly available data or data shared upon request were largely reproducible, but we remain concerned about the difficulty in obtaining data from recently published papers. We recommend increased data-sharing, data organization and documentation, communication, and training to advance computational reproducibility in the wildlife sciences. © 2020 The Authors. The Journal of Wildlife Management published by Wiley Periodicals, Inc. on behalf of The Wildlife Society. 相似文献
4.
5.
The colony-forming ability of Escherichia coli genetically engineered to produce eicosapentaenoic acid (EPA) grown in 3mM hydrogen peroxide (H(2)O(2)) was similar to that of untreated cells. It was rapidly lost in the absence of EPA. H(2)O(2)-induced protein carbonylation was enhanced in cells lacking EPA. The fatty acid composition of the transformants was unaffected by H(2)O(2) treatment, but the amount of fatty acids decreased in cultures of cells lacking EPA and increased in cultures of cells producing EPA, suggesting that cellular EPA is stable in the presence of H(2)O(2) in vivo and may protect cells directly against oxidative damage. We discuss the possible role of EPA in partially blocking the penetration of H(2)O(2) into cells through membranes containing EPA. 相似文献
6.
Imaging mass spectrometry (IMS) has developed into a powerful tool allowing label-free detection of numerous biomolecules in situ. In contrast to shotgun proteomics, proteins/peptides can be detected directly from biological tissues and correlated to its morphology leading to a gain of crucial clinical information. However, direct identification of the detected molecules is currently challenging for MALDI–IMS, thereby compelling researchers to use complementary techniques and resource intensive experimental setups. Despite these strategies, sufficient information could not be extracted because of lack of an optimum data combination strategy/software. Here, we introduce a new open-source software ImShot that aims at identifying peptides obtained in MALDI–IMS. This is achieved by combining information from IMS and shotgun proteomics (LC–MS) measurements of serial sections of the same tissue. The software takes advantage of a two-group comparison to determine the search space of IMS masses after deisotoping the corresponding spectra. Ambiguity in annotations of IMS peptides is eliminated by introduction of a novel scoring system that identifies the most likely parent protein of a detected peptide in the corresponding IMS dataset. Thanks to its modular structure, the software can also handle LC–MS data separately and display interactive enrichment plots and enriched Gene Ontology terms or cellular pathways. The software has been built as a desktop application with a conveniently designed graphic user interface to provide users with a seamless experience in data analysis. ImShot can run on all the three major desktop operating systems and is freely available under Massachusetts Institute of Technology license. 相似文献