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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.

  • The Interplay of Time-of-day and Chronotype Results in No General and Robust Cognitive Boost

    Authors: Alodie Rey-Mermet, Nicolas Rothen
    DOI: https://doi.org/10.1525/collabra.88337
    Submitted by areyme      

    Why should we attempt to reproduce this paper?

    In this paper, an R package was used to improve the reproducibility of the analyses. Therefore, it would be good to know to what extent this works. The R package includes the following analyses: (1) data trimming and preparation, (2) descriptive statistics, (3) reliability and correlations, (4) t-tests and Bayesian t-tests, (5) latent-change models (structural equation modeling approach), and (6) multiverse analyses. Furthermore, all deidentified data, experiment codes, research materials, and results are publicly accessible on the Open Science Framework (OSF) at https://osf.io/ngfxv. The study’s design and the analyses were pre-registered on OSF. The preregistration can be accessed at https://osf.io/ tywu7.

  • Droplet impact onto a spring-supported plate: analysis and simulations

    Authors: Michael J. Negus, Matthew R. Moore, James M. Oliver, Radu Cimpeanu
    DOI: https://doi.org/10.1007/s10665-021-10107-5
    Submitted by MNegus      
      Mean reproducibility score:   8.0/10   |   Number of reviews:   1
    Why should we attempt to reproduce this paper?

    The direct numerical simulations (DNS) for this paper were conducted using Basilisk (http://basilisk.fr/). As Basilisk is a free software program written in C, it can be readily installed on any Linux machine, and it should be straightforward to then run the driver code to re-produce the DNS from this paper. Given this, the numerical solutions presented in this paper are a result of many high-fidelity simulations, which each took approximately 24 CPU hours running between 4 to 8 cores. Hence the difficulty in reproducing the results should mainly be in the amount of computational resources it would take, so HPC resources will be required. The DNS in this paper were used to validate the presented analytical solutions, as well as extend the results to a longer timescale. Reproducing these numerical results will build confidence in these results, ensuring that they are independent of the system architecture they were produced on.

  • 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!

  • 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

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