Orthrus: an AI-powered, cloud-ready, and open-source hybrid approach for metaproteomics

Quick start

For cloud execution:

Click orthrus_cloud_stable_v100 folder, open .ipynb notebooks in Colab, and just follow the notebook instructions from there!

• please note: a Github account will be needed for authorisation. Go to Github and get one if you haven't >_<

For local execution:

git clone https://github.com/yc386/orthrus_metaproteomics.git
cd orthrus_metaproteomics/orthrus_local_runner
mamba env create -f environment.yaml
conda activate orthrus_metaproteomics
python walking_orthrus_locally_stable_v100.py --help

basic usage

python walking_orthrus_locally_stable_v100.py --folder_path path_to_folder --file_type mgf --use_SwissProt \
--sage_path path_to_sage_binary --json_file_path path_to_sage_json \
--missed_cleavages 1 --max_variable_mods 2 \
--static_CAM --aas P N Q --mods 15.994915 0.984016 0.984016 \
--default_Percolator --joint_modelling

FAQs

1. Do I need a Google Colab subscription?
   Without any Colab+, general CPU runtime, T4 GPU, and TPU should still be accessible.
2. Do I need a Google account?
   May make life easier. Colab can also access files in your Google drive (with permission).
3. Help! Still unsure how to walk Orthrus.
   Open an issue or get in touch with me (preprint)