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  1. Code for: Disruption of biological processes in the Anthropocene: the case of phenological mismatch

    Code for: Disruption of biological processes in the Anthropocene: the case of phenological mismatch


    CRAN R code to analyze disruption of plant-pollinator networks for the article: Disruption of biological processes in the Anthropocene: the case of phenological mismatch.

    Abstract

    CRAN R code to analyze disruption of plant-pollinator networks for the article: Disruption of biological processes in the Anthropocene: the case of phenological mismatch

  2. Analyses d’ouvrages : Franck Varenne, From models to simulations

    Analyses d’ouvrages : Franck Varenne, From models to simulations

    Revue d’histoire des sciences


    L’invention et le développement des ordinateurs a ouvert de nouvelles possibilités pour la modélisation. En physique, l’existence de théories mathématisées

    Abstract

    L’invention et le développement des ordinateurs a ouvert de nouvelles possibilités pour la modélisation. En physique, l’existence de théories mathématisées permet d’utiliser l’ordinateur pour calculer des solutions approchées à des problèmes déjà bien circonscrits théoriquement et épistémologiquement. En biologie, par contre, il n’existe pas de théorie jouant ce rôle épistémologique, et l’informatique a permis l’émergence de pratiques de modélisation combinant plusieurs cadres mathématiques. L’ouvrage de Franck Varenne porte sur ces pratiques novatrices, leur histoire et leur épistémologie, à travers le cas des simulations de morphogenèse d’arbres et plus généralement de plantes.

  3. A Few Pending Challenges from the Perspective of a Theory of Organisms

    A Few Pending Challenges from the Perspective of a Theory of Organisms

    Constructivist Foundations


    I discuss convergences between the approach of N. Palfreyman and J. Miller-Young and my work aiming for a theory of organisms, in particular on randomness.

    Abstract

    Open peer commentary on the article “What Is a Cognizing Subject? Construction, Autonomy and Original Causation” by Niall Palfreyman & Janice Miller-Young. http://constructivist.info/13/3/362.palfreyman Upshot: I discuss convergences between the approach of the authors and my work aiming for a theory of organisms. I also discuss some pitfalls and challenges pertaining to biological randomness, which, I argue, require original developments.

  4. NTP. CLARITY-BPA. Chemical Effects in Biological Systems (CEBS): Mammary Gland

    NTP. CLARITY-BPA. Chemical Effects in Biological Systems (CEBS): Mammary Gland


    Citation
    Montévil, Maël, Nicole Acevedo, Cheryl M. Schaeberle, Manushree Bharadwaj, Suzanne E. Fenton, and Ana M. Soto. 2018. “NTP. CLARITY-BPA. Chemical Effects in Biological Systems (CEBS): Mammary Gland.” Dataset. National Toxicology Program (NTP). https://doi.org/10.22427/NTP-DATA-018-00014-0001-000-5
    Citation Publisher Details
  5. Philosophical Accounts of Biological Functions

    Philosophical Accounts of Biological Functions

    Science & Education


    Review of "A critical overview of biological functions" by Justin Garson (2016). I focus on the etiological and the organizational accounts of functions.

  6. Documentation for SAMA: A Method for 3D Morphological Analysis

    Documentation for SAMA: A Method for 3D Morphological Analysis

    PLoS ONE


    Documentation for Software for Automated Morphological Analysis, a method by which epithelial structures grown in 3D cultures can be imaged, reconstructed and analyzed.

    Abstract

    Three-dimensional (3D) culture models are critical tools for understanding tissue morphogenesis. A key requirement for their analysis is the ability to reconstruct the tissue into computational models that allow quantitative evaluation of the formed structures. Here, we present Software for Automated Morphological Analysis (SAMA), a method by which epithelial structures grown in 3D cultures can be imaged, reconstructed and analyzed with minimum human intervention. SAMA allows quantitative analysis of key features of epithelial morphogenesis such as ductal elongation, branching and lumen formation that distinguish different hormonal treatments. SAMA is a user-friendly set of customized macros operated via FIJI (http://fiji.sc/Fiji), an open-source image analysis platform in combination with a set of functions in R (http://www.r-project.org/), an open-source program for statistical analysis. SAMA enables a rapid, exhaustive and quantitative 3D analysis of the shape of a population of structures in a 3D image. SAMA is cross-platform, licensed under the GPLv3 and available at http://montevil.theobio.org/content/sama.

    Keywords: Open source software, Image analysis, Ellipsoids, Morphogenesis, Computer software, Morphometry, Image processing, Branching morphogenesis

    Citation
    Paulose, Tessie, Maël Montévil, Lucia Speroni, Florent Cerruti, Carlos Sonnenschein, and Ana M. Soto. 2016. “SAMA: A Method for 3D Morphological Analysis.” Edited by Tiffany Seagroves. PLoS ONE 11 (4): 1–14. https://doi.org/10.1371/journal.pone.0153022
    Manuscript Citation Publisher Details