1,720,971 research outputs found
tmm4py: Global Ocean Biogeochemical Modeling in Python With the Transport Matrix Method
No full textAbstract Marine biogeochemical models are important tools in the quest to understand the cycling of chemical and biological tracers such as nutrients, carbon and oxygen, as well as key components of the Earth System Models used to project climate change. Historically, given the need for speed, global scale modeling has been performed in compiled languages like Fortran. However, as high level scripting languages such as Python and Julia gain popularity, the need for models and tools accessible from them has become imperative. This paper introduces tmm4py, a Python interface to a redesigned version of the Transport Matrix Method (TMM) software, a computationally efficient numerical scheme for “offline” simulation of marine geochemical and biogeochemical tracers. The TMM provides a convenient framework for developing and testing new biogeochemical parameterizations, as well as running existing complex models driven by circulations derived from state‐of‐the‐art physical models. tmm4py exposes all of the TMM library's functionality in Python, including transparent parallelization, allowing users to not only interactively use models written in compiled languages, but also develop complex models in pure Python with performance similar to compiled code. tmm4py enables users to exploit the large Python‐based scientific software ecosystem, including libraries for machine learning and deploying models on Graphics Processing Units. The various features of tmm4py are described and illustrated through practical examples, including a full‐fledged biogeochemical model written entirely in Python
Author Correction: Glacial deep ocean deoxygenation driven by biologically mediated air–sea disequilibrium
No full textGoing Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
A computational framework for simulation of biogeochemical tracers in the ocean
No full textA novel computational framework is introduced for the efficient simulation of chemical and biological tracers in ocean models. The framework is based on the "transport matrix" formulation, a scheme for capturing the complex three-dimensional transport of tracers in a general circulation model (GCM) as a sparse matrix, thus reducing the task of simulating tracers to a sequence of simple matrix-vector products. The principal advantages of this formulation are efficiency and convenience. It is many orders of magnitude more efficient than GCMs, allowing us to address problems that are currently either difficult or unaffordable with GCMs. The scheme also allows us to quickly "prototype" new biogeochemical parameterizations or "plug in" existing ones. This paper describes the key features and advantages of the transport matrix method, and illustrates its application to a series of realistic problems in chemical and biological oceanography. The examples range from simulation of a transient tracer (SF6) to adjoint sensitivity of a complex coupled biogeochemical model. Finally, the paper describes an efficient, portable, and freely available implementation of this computational scheme that provides the necessary framework for simulating any biogeochemical tracer. Copyright 2007 by the American Geophysical Union
Fast Spin‐Up of Geochemical Tracers in Ocean Circulation and Climate Models
Full text linkAbstract Ocean geochemical tracers such as radiocarbon, protactinium and thorium isotopes, and noble gases are widely used to constrain a range of physical and biogeochemical processes in the ocean. However, their routine simulation in global ocean circulation and climate models is hindered by the computational expense of integrating them to a steady state. Here, a new approach to this long‐standing “spin‐up” problem is introduced to efficiently compute equilibrium distributions of such tracers in seasonally‐forced models. Based on “Anderson Acceleration,” a sequence acceleration technique developed in the 1960s to solve nonlinear integral equations, the new method is entirely “black box” and offers significant speed‐up over conventional direct time integration. Moreover, it requires no preconditioning, ensures tracer conservation and is fully consistent with the numerical time‐stepping scheme of the underlying model. It thus circumvents some of the drawbacks of other schemes such as matrix‐free Newton Krylov that have been proposed to address this problem. An implementation specifically tailored for the batch HPC systems on which ocean and climate models are typically run is described, and the method illustrated by applying it to a variety of geochemical tracer problems. The new method, which provides speed‐ups by over an order of magnitude, should make simulations of such tracers more feasible and enable their inclusion in climate change assessments such as IPCC
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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