In the middle of the COVID-19 pandemic, this paper provided important evidence regarding the effect of misinformation on vaccination intent. Its analyses and conclusions were extremely important for decision makers. Therefore, it is also important that the analyses are reproducible.
Metadata annotation is key to reproducibility in sequencing experiments. Reproducing this research using the scripts provided will also show the current level of annotation in years since 2015 when the paper was published.
The paper describes pyKNEEr, a python package for open and reproducible research on femoral knee cartilage using Jupyter notebooks as a user interface. I created this paper with the specific intent to make both the workflows it describes and the paper itself open and reproducible, following guidelines from authorities in the field. Therefore, two things in the paper can be reproduced: 1) workflow results: Table 2 contains links to all the Jupyter notebooks used to calculate the results. Computations are long and might require a server, so if you want to run them locally, I recommend using only 2 or 3 images as inputs for the computations. Also, the paper should be sufficient, but if you need further introductory info, there are a documentation website: https://sbonaretti.github.io/pyKNEEr/ and a "how to" video: https://youtu.be/7WPf5KFtYi8 2) paper graphs: In the captions of figures 1, 4, and 5 you can find links to data repository, code (a Jupyter notebook), and the computational environment (binder) to fully reproduce the graph. These computations can be easily run locally and require a few seconds. All Jupyter notebooks automatically download data from Zenodo and provide dependencies, which should make reproducibility easier.
I tried hard to make this paper as reproducible as possible, but as techniques and dependencies become more complex, it is hard to make it 100% clear. Any form of feedback is more than welcome.