This is a seminal paper on reproducibility in cancer biology. It should be a gold standard for reproducible research work. Therefore, it should be attempted to reproduce it. Supposedly, this will be pretty easy to reproduce and can be used as a *positive control* in repro hacks!
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The current code is written in Torch, which is no longer actively maintained. Since deep learning in nanophotonics is an area of active interest (e.g. for the design of new metamaterials), it is important to update the code to use a more modern deep learning library such as tensorflow/keras