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Journal of Open Research Software
141 Publications
OpenAIRE 3.0 (OA, funding)


  • Tethys – A Python Package for Spatial and Temporal Downscaling of Global Water Withdrawals

    Li, Xinya; Vernon, Chris R.; Hejazi, Mohamad I.; Link, Robert P.; Huang, Zhongwei; Liu, Lu; Feng, Leyang (2018)
    Downscaling of water withdrawals from regional/national to local scale is a fundamental step and also a common problem when integrating large scale economic and integrated assessment models with high-resolution detailed sectoral models. Tethys, an open-access software written in Python, is developed with statistical downscaling algorithms, to spatially and temporally downscale water withdrawal data to a finer scale. The spatial resolution will be downscaled from region/basin scale to grid (0....

    ConfBuster: Open-Source Tools for Macrocycle Conformational Search and Analysis

    Barbeau, Xavier; Vincent, Antony T.; Lagüe, Patrick (2018)
    Macrocycles are cyclic macromolecules that have gained an increased interest in drug development. To our knowledge, the current bioinformatics tools that are available to investigate and predict macrocycles 3D conformations are limited in their availability. In this paper, we introduce ConfBuster, a suite of tools written in Python with the goal of sampling the lower energy conformations of macrocycles. The suite also includes tools for the analysis and visualisation of the conformational sea...

    VIGoR: Variational Bayesian Inference for Genome-Wide Regression

    Onogi, Akio; Iwata, Hiroyoshi (2016)
    Genome-wide regression using a number of genome-wide markers as predictors is now widely used for genome-wide association mapping and genomic prediction. We developed novel software for genome-wide regression which we named VIGoR (variational Bayesian inference for genome-wide regression). Variational Bayesian inference is computationally much faster than widely used Markov chain Monte Carlo algorithms. VIGoR implements seven regression methods, and is provided as a command line program packa...

    Transitive Credit as a Means to Address Social and Technological Concerns Stemming from Citation and Attribution of Digital Products

    Katz, Daniel S. (2014)
    The pursuit of science and engineering research increasingly relies on activities that facilitate research but are not currently rewarded or recognized, such as development of products and infrastructure. In research publications, citations are used to credit previous works. This paper suggests that a modified citation system that includes the technological idea of transient credit could be used to recognize the developers of products other than research publications and that if this were don...

    Open Source Software for Mapping Human Impacts on Marine Ecosystems with an Additive Model

    Stock, Andy (2016)
    This paper describes an easy-to-use open source software tool implementing a commonly used additive model (Halpern et al., 'Science', 2008) for mapping human impacts on marine ecosystems. The tool has been used to map the potential for cumulative human impacts in Arctic marine waters and can support future human impact mapping projects by 1) making the model easier to use; 2) making updates of model results straightforward when better input data become available; 3) storing input data and inf...
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