Biblio.bib

@article{Marina2018,
    author = {Marina, Tomás Ignacio AND Saravia, Leonardo A. AND Cordone, Georgina AND Salinas, Vanesa AND Doyle, Santiago R. AND Momo, Fernando R.},
    journal = {PLOS ONE},
    publisher = {Public Library of Science},
    title = {Architecture of marine food webs: To be or not be a ‘small-world’},
    year = {2018},
    month = {05},
    volume = {13},
    url = {https://doi.org/10.1371/journal.pone.0198217},
    pages = {1-13},
    abstract = {The search for general properties in network structure has been a central issue for food web studies in recent years. One such property is the small-world topology that combines a high clustering and a small distance between nodes of the network. This property may increase food web resilience but make them more sensitive to the extinction of connected species. Food web theory has been developed principally from freshwater and terrestrial ecosystems, largely omitting marine habitats. If theory needs to be modified to accommodate observations from marine ecosystems, based on major differences in several topological characteristics is still on debate. Here we investigated if the small-world topology is a common structural pattern in marine food webs. We developed a novel, simple and statistically rigorous method to examine the largest set of complex marine food webs to date. More than half of the analyzed marine networks exhibited a similar or lower characteristic path length than the random expectation, whereas 39% of the webs presented a significantly higher clustering than its random counterpart. Our method proved that 5 out of 28 networks fulfilled both features of the small-world topology: short path length and high clustering. This work represents the first rigorous analysis of the small-world topology and its associated features in high-quality marine networks. We conclude that such topology is a structural pattern that is not maximized in marine food webs; thus it is probably not an effective model to study robustness, stability and feasibility of marine ecosystems.},
    number = {5},
    doi = {10.1371/journal.pone.0198217}
}


@article{Wilson2017,
    author = {Wilson, Greg AND Bryan, Jennifer AND Cranston, Karen AND Kitzes, Justin AND Nederbragt, Lex AND Teal, Tracy K.},
    journal = {PLOS Computational Biology},
    publisher = {Public Library of Science},
    title = {Good enough practices in scientific computing},
    year = {2017},
    month = {06},
    volume = {13},
    url = {https://doi.org/10.1371/journal.pcbi.1005510},
    pages = {1-20},
    abstract = {Author summary Computers are now essential in all branches of science, but most researchers are never taught the equivalent of basic lab skills for research computing. As a result, data can get lost, analyses can take much longer than necessary, and researchers are limited in how effectively they can work with software and data. Computing workflows need to follow the same practices as lab projects and notebooks, with organized data, documented steps, and the project structured for reproducibility, but researchers new to computing often don't know where to start. This paper presents a set of good computing practices that every researcher can adopt, regardless of their current level of computational skill. These practices, which encompass data management, programming, collaborating with colleagues, organizing projects, tracking work, and writing manuscripts, are drawn from a wide variety of published sources from our daily lives and from our work with volunteer organizations that have delivered workshops to over 11,000 people since 2010.},
    number = {6},
    doi = {10.1371/journal.pcbi.1005510}
}


@article{Mislan2016,
abstract = {Code is increasingly central to ecological research but often remains unpublished and insufficiently recognized. Making code available allows analyses to be more easily reproduced and can facilitate research by other scientists. We evaluate journal handling of code, discuss barriers to its publication, and suggest approaches for promoting and archiving code., Code is frequently written for ecological studies., Most ecology journals do not address code or software., Journals can promote release of code by changing article formats and requirements., Code archives should provide a license and be long-term and citable.},
author = {Mislan, K a. S and Heer, Jeffrey M and White, Ethan P},
doi = {10.1016/j.tree.2015.11.006},
file = {:home/leonardo/Mendeley/Trends in Ecology {\&} Evolution/Mislan, Heer, White - 2016 - Elevating The Status of Code in Ecology.pdf:pdf},
issn = {0169-5347},
journal = {Trends in Ecology {\&} Evolution},
keywords = {data,publish,reproducibility,software},
language = {English},
mendeley-groups = {Nuevo/EcoInformatics},
month = {jan},
number = {1},
pages = {4--7},
title = {{Elevating The Status of Code in Ecology}},
url = {http://www.cell.com/article/S0169534715002906/abstract http://www.cell.com/article/S0169534715002906/pdf},
volume = {31},
year = {2016}
}