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  • A comprehensive comparison of tools for fitting mutational signatures

    Authors: Matúš Medo, Michaela Medová
    DOI: 10.48550/arXiv.2310.01562
    Submitted by 8medom    

    Why should we attempt to reproduce this paper?

    I hope that the evaluation framework introduced in the paper can become used by other researchers working on mutational signatures.

  • Machine learning a model for RNA structure prediction

    Authors: Nicola Calonaci, Alisha Jones, Francesca Cuturello, Michael Sattler, Giovanni Bussi
    DOI: 10.1093/nargab/lqaa090
    Submitted by giovannibussi      

    Why should we attempt to reproduce this paper?

    The method is trained on the data that were available, but it is meant to be re-trainable as soon as new data are published. It would be great to be really sure that even someone else will be able to do it. In case we receive any feedback, we would be really happy to improve our Github repository so as to make the reproduction easier!

  • Analytical solutions for the isobaric evaporation of pure cryogens in storage tanks

    Authors: Felipe Huerta, Velisa Vesovic,
    DOI: 10.1016/j.ijheatmasstransfer.2019.118536
    Submitted by hub-admin    

    Why should we attempt to reproduce this paper?

    1. Because it contains customized numerical methods to implement analytical solutions for an engineering problem relevant to cryogenic storage. This will become increasingly relevant in the future with the increase in the use of liquid hydrogen and LNG as fuel. 2. The storage tank is implemented as a Class and there is an opportunity to understand the object oriented programming mindset of the authors. 3. In the provided Jupyter Notebook, thermodynamic data for nitrogen and methane are provided which enable the users the quick implementation. 4. To reproduce some of the figures and results, the storage tanks need to be modified with inputs available in the paper.

    Tags: Python Matlab
  • Good Me Bad Me: Prioritization of the Good-Self During Perceptual Decision-Making

    Authors: Hu, C.-P., Lan, Y., Macrae, C. N., & Sui, J.
    DOI: 10.1525/collabra.301
    Submitted by hub-admin    
      Mean reproducibility score:   7.0/10   |   Number of reviews:   1
    Why should we attempt to reproduce this paper?

    It'll a great helpful to independently check the scientific record I've published, so that errors, if there are any, could be corrected. Also, I will learn how to share the data in a more accessible to other if you could give me feedback.

    Tags: Python R Matlab
  • Cell Contractility Facilitates Alignment of Cells and Tissues to Static Uniaxial Stretch

    Authors: Rens, E. G., & Merks, R. M. H.
    Submitted by hub-admin    
      Mean reproducibility score:   1.0/10   |   Number of reviews:   2
    Why should we attempt to reproduce this paper?

    This paper shows a fun and interesting simulation result. I find it (of course) very important that our results are reproducible. In this paper, however, we did not include the exact code for these specific simulations, but the results should be reproducible using the code of our previous paper in PLOS Computational Biology (Van Oers, Rens et al. https://doi.org/10.1371/journal.pcbi.1003774). I am genuinely curious to see if there is sufficient information for the Biophys J paper or if we should have done better. Other people have already successfully built upon the 2014 (PLOS) paper using our code; see e.g., https://journals.aps.org/pre/abstract/10.1103/PhysRevE.97.012408 and https://doi.org/10.1101/701037).

    Tags: C Matlab
  • Spatial modelling of rice yield losses in Tanzania due to bacterial leaf blight and leaf blast in a changing climate

    Authors: C. Duku, A. H. Sparks, S. J. Zwart.
    DOI: 10.1007/s10584-015-1580-2
    Submitted by hub-admin    
      Mean reproducibility score:   4.0/10   |   Number of reviews:   2
    Why should we attempt to reproduce this paper?

    This was my third attempt at making a paper fully reproducible. To date I it's the most reproducible that I have published. I'm interested to know what stumbling blocks exist that I'm not aware of (aside from needing software like ArcGIS to fully rerun the complete analysis).

    Tags: Python R ArcGIS

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