Papers



Submit a Paper!

Browse ReproHack papers

  • 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.

  • A multi-level analysis of data quality for formal software citation

    Authors: David Schindler, Tazin Hossain, Sascha Spors, Frank Krüger
    DOI: https://doi.org/10.48550/arXiv.2306.17535
    Submitted by frank.krueger    
      Mean reproducibility score:   9.0/10   |   Number of reviews:   2
    Why should we attempt to reproduce this paper?

    We spend a lot of time to make our analyses reproducible. A review would allow us to collect some information on whether we are successful with it.

  • Laser-assisted propagation of a relativistic electron bunch in air

    Authors: R M G M Trines, A P L Robinson, J R Wilkinson, J N Kirk, D S Hills, R M Deas, S Morris, T Goffrey, K Bennett, T D Arber
    DOI: 10.1088/1361-6587/ac0b9d
    Submitted by Stuart_Morris      

    Why should we attempt to reproduce this paper?

    Most electron beam physics is considered in the context of a vacuum, but there are applications to long-range electron beam transmission in air. As particle acceleration sources become more compact, we may have the chance to take particle beams out to the real world. The example provided in the paper describes that of x-ray backscatter detectors, where significantly stronger signals could be achieved by scanning objects with electron beams. This paper forms the basis for a potential new mode of particle-beam research, and it is important to ensure the reproducibility of this work for groups who wish to explore the applications of this new technology.

  • 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!

  • Thermodynamics of stacking disorder in ice nuclei

    Authors: David Quigley
    DOI: 10.1063/1.4896376
    Submitted by dquigley      
      Mean reproducibility score:   3.0/10   |   Number of reviews:   1
    Why should we attempt to reproduce this paper?

    The results of this paper have been used in multiple subsequent studies as a benchmark against which other methods of performing the same calculation have been tested. Other groups have challenged the results as suffering from finite size effects, in particular the calculations on mixtures of cubic and hexagonal ice. Should there be time during in the event, participants could check this by performing calculations on larger unit cells. Each individual calculation should converge adequately within 96 hours making it amenable to a HPC ReproHack. Given modern HPC hardware many such calculations could be run concurrently on a single HPC node.

  • Highly efficient conversion of laser energy to hard X-rays in high intensity laser-solid simulations

    Authors: S. Morris, A. Robinson, C. Ridgers
    DOI: 10.1063/5.0055398
    Submitted by Stuart_Morris      

    Why should we attempt to reproduce this paper?

    There are many applications to multi-MeV X-rays. Their penetrative properties make them good for scanning dense objects for industry, and their ionising properties can destroy tumours in radiotherapy. They are also around the energy of nuclear transitions, so they can trigger nuclear reactions to break down nuclear waste into medical isotopes, or to reveal smuggled nuclear-materials for port security. Laser-driven X-ray generation offers a compact and efficient way to create a bright source of X-rays, without having to construct a large synchrotron. To fully utilise this capability, work on optimising the target design and understanding the underlying X-ray mechanisms are essential. The hybrid-PIC code is in a unique position to model the full interaction, so its ease-of-use and reproducibility are crucial for this field to develop.

Search for papers

Filter by tags

Python R GDAL GEOS GIS Shiny PROJ Galaxies Astronomy HPC Databases Binder Social Science Stata make Computer Science Jupyter Notebook tidyverse emacs literate earth sciences clumped isotopes org-mode geology eyetracking LaTeX Git ArcGIS Docker Drake SVN knitr C Matlab Mathematica Meta-analysis swig miniconda tensorflow keras Pandas SQL neuroscience robotics deep learning planner reiforcement learning Plasma physics Hybrid-PIC EPOCH Laser Gamma-ray X-ray radiation Petawatt Fortran plasma PIC physics Monte Carlo Atomistic Simulation LAMMPS Electron Transport DFT descriptors interatomic potentials machine learning Molecular Dynamics Python scripting AIRSS structure prediction density functional theory high-throughput machine-learning RNA bioinformatics CFD Fluid Dynamics OpenFOAM C++ DNS Mathematics Droplets Basilisk Particle-In-Cell psychology Stan Finance SAS Replication crisis Economics Malaria consumer behavior number estimation mental arithmetic psychophysics Archaeology Precipitation Epidemiology Parkrun Health Health Economics HTA plumber science of science Zipf networks city size distribution urbanism literature review Preference Visual Questionnaire Mann-Whitney Correlation Conceptual replication Cognitive psychology Multinomial processing tree (MPT) modeling #urbanism #R k-means cluster analysis city-regions Urban Knowledge Systems Topic modelling Planning Support Systems Software Citation Quarto snakemake Numerical modelling Ocean climate physical oceanography apptainer oceanography R package structural equation modeling bayes factor Forest Simulations Models of forest dynamics multi-lab study mice mechanics growth Tissue Cells Clustering Expectation-Maximization bootstrapping R software Position Weight Matrices singularity neuroimaging effect size biology replicability cancer reproducibility csv osf preclinical research genomics All tags Clear tags

Key

  Associated with an event
  Available for general review
  Public reviews welcome