The TPP_HMM_Analysis_Vignette.Rmd was run on RStudio version 1.3.1093 and R version 4.0.2. All other packages and requirements are listed in the Vigentte.
Open and follow the instruction in TPP_HMM_Analysis_Vignette.Rmd on the main branch. The Vignette will walk through a full analysis, including EM optimization, of the exosome protein complex. The initial input (as shown in the vignette) is data/becher_fullCycle_reformat.csv and the final output we recieved is data/exosome_hmm_result.csv
To view the code and output from our hmm training using the aphid package view the file HMM_finalcode.Rmd. All required packages are listed at the top of the file, the only package that may be new to a user is Aphid. This HMM model was trained using the data/Exosome_TPCA_Result_pvalues.csv, data is loaded and cleaned as needed throughout the R-file.
Since we did not use python environments like venv or conda, there are 2 requirements files in the simulator directory. requirements-full.txt lists all the python packages installed globally on my (Darvesh's) machine. requirements-min.txt lists only the packages imported in simulator.py and Development.ipynb. Please use requirements-min.txt if you're unsure. This code was tested on Python 3.9.7 and 3.7.9 but the code should work for Python 3.x.x. Please reach out if there are version-specific issues. The simulator is quite light and runs within seconds on a Intel dual-core Macbook Pro from 2017. Your mileage may vary. This has not been tested on Apple Silicon or Windows (10 or 11). The safest, most reliable way to test this would be inside a conda environment or virtual environment.
Although some data was used for debugging and exploratory purposes the simulator itself does not use sample data. All relevant data for exploratory purposes and debugging can be found in the protein-hmm/data directory. Debugging takes place in debugging.py and exploration takes place n Development.ipynb.
We use python for the simulator so no compilation is necessary unless you would like to install the requirements from source and potentially compile some C libraries on your own. This is not recommended, but not hindered.
To check and see if everything runs fine, you can run the test.py from within the simulator/ directory (i.e. cd into the directory). To run the tests simply run
python3 test.py
Running this should also highlight any missing dependencies or incompatible versions which may not have been captured during initial installation. You can also generate some figures from the paper by running (again from within the simulator/ directory).
python3 generate_figures.py