{"id":15694206,"url":"https://github.com/avaamini/protease_activity_analysis","last_synced_at":"2025-06-15T15:07:03.859Z","repository":{"id":99515444,"uuid":"263712609","full_name":"avaamini/protease_activity_analysis","owner":"avaamini","description":"Python toolkit and package for analyzing enzyme activity data","archived":false,"fork":false,"pushed_at":"2022-06-17T20:58:59.000Z","size":32308,"stargazers_count":10,"open_issues_count":1,"forks_count":4,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-12T04:24:42.383Z","etag":null,"topics":["biochemistry","chemical-biology","database","enzyme","enzyme-kinetics","peptide-data","peptides","protease"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/avaamini.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2020-05-13T18:31:41.000Z","updated_at":"2025-03-20T20:49:30.000Z","dependencies_parsed_at":null,"dependency_job_id":"e8bbe025-5152-4de9-9261-c0b787e703b1","html_url":"https://github.com/avaamini/protease_activity_analysis","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/avaamini%2Fprotease_activity_analysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/avaamini%2Fprotease_activity_analysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/avaamini%2Fprotease_activity_analysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/avaamini%2Fprotease_activity_analysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/avaamini","download_url":"https://codeload.github.com/avaamini/protease_activity_analysis/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253020527,"owners_count":21841583,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["biochemistry","chemical-biology","database","enzyme","enzyme-kinetics","peptide-data","peptides","protease"],"created_at":"2024-10-03T18:54:22.891Z","updated_at":"2025-05-08T07:30:04.004Z","avatar_url":"https://github.com/avaamini.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cp align=\"center\" \u003e\n  \u003cimg src=\"img/PAA_logo.png\" alt=\"logo\" width=\"400\" /\u003e\n\u003c/p\u003e\n\u003c!-- \n\u003ch1 align=\"center\"\u003eProtease Activity Analysis\u003c/h1\u003e\n\u003ch4 align=\"center\"\u003eDeveloped and maintained by: Ava Soleimany, Carmen Martin Alonso, Melodi Anahtar, Cathy Wang, Sangeeta Bhatia\u003c/h4\u003e --\u003e\n\n\u003cp align=\"center\"\u003e [\u003cb\u003e\u003ca href=\"https://www.biorxiv.org/content/10.1101/2022.03.07.483375v1\"\u003ePaper\u003c/a\u003e\u003c/b\u003e] \u0026emsp; [\u003cb\u003e\u003ca href=\"#citation\"\u003eCitation\u003c/a\u003e\u003c/b\u003e] \u003c/p\u003e\n\u003cp align=\"center\"\u003e [\u003cb\u003e\u003ca href=\"https://lmrt.mit.edu\"\u003eLaboratory for Multiscale Regenerative Technologies\u003c/a\u003e\u003c/b\u003e] \u003c/p\u003e\n\n# Protease Activity Analysis (PAA)\nAnalyzing the activity of proteases and their substrates is critical to defining the\nbiological functions of these enzymes and to designing new diagnostics and therapeutics\nthat target protease dysregulation in disease.\n\nTo facilitate protease research, we present Protease Activity Analysis (PAA). PAA is a Python software package with a collection of tools for analyzing protease activity data. PAA provides a modular framework for streamlined analysis across three major components: \n\n1. _**Database**_: query and input datasets of synthetic peptide substrates and their cleavage susceptibilities across a diverse set of proteases. \n2. _**Cleavage analysis**_: analyze and visualize enzyme-substrate activity measurements generated through in vitro screens against synthetic peptide substrates. \n3. _**In vivo sensors**_: deploy a set of modular machine learning functions to analyze in vivo protease activity signatures that are generated by activity-based sensors.\n\nThe repository accompanies the paper, **Protease Activity Analysis: A Toolkit for Analyzing Enzyme Activity Data in Python**, and is developed and maintained by the paper's authors. If you use code from the repository, please cite the follwoing paper: _coming soon!_.\n\n## Setup\n1. Install the following dependencies: [conda 3.x](https://docs.conda.io/en/latest/miniconda.html)\n2. [Generate Github SSH keys](https://help.github.com/en/github/authenticating-to-github/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent). If you already have SSH keys you can first [check to make sure](https://help.github.com/en/github/authenticating-to-github/checking-for-existing-ssh-keys).\n3. [Add your SSH key to your Github account](https://help.github.com/en/github/authenticating-to-github/adding-a-new-ssh-key-to-your-github-account).\n4. Download this repository: \n```\ngit clone git@github.com:apsoleimany/protease_activity_analysis.git\n```\n\n## Installation\nTo use the protease activity analysis (paa) toolbox, first create the environment and then install the package:\n```\ncd protease_activity_analysis\nconda env create -f environment.yml\nconda activate paa\npip install -e .\n```\n\n## Usage\nTo enter the protease environment: `conda activate paa`\n\nOnce inside the environment, the package can be directly imported and used in a Python shell/script: \n```\n\u003e\u003e\u003e import protease_activity_analysis as paa\n\u003e\u003e\u003e paa.tests.test_installation()\n```\n\nTo deactivate after you are done: `conda deactivate`\n\n## Getting started\nTo get started using PAA, we recommend you select a tutorial in the `tutorials` folder that is most aligned with your application of interest. We also provide three template analysis scripts in the root directory:\n- `analyze_kinetic.py`: analysis of _in vitro_ screening data;\n- `analyze_ms_data.py`: analaysis and visualization of _in vivo_ activity sensor data;\n- `classify_ms_data.py`: machine learning classification of _in vivo_ activity sensor data. \n\n## Citation\n\nIf you use the code from the repository, please cite the accompanying [paper](https://www.biorxiv.org/content/10.1101/2022.03.07.483375v1):\n```\n@article{Soleimany2022,\n\ttitle = {Protease Activity Analysis: A Toolkit for Analyzing Enzyme Activity Data},\n\tauthor = {Soleimany, Ava P and Martin Alonso, Carmen and Anahtar, Melodi N and Wang, Cathy S and Bhatia, Sangeeta N},\n\tjournal = {bioRxiv},\n\tyear = {2022}\n}\n```\n\n## Contributing\nCode should be written in compliance with the [Google Python style guide](http://google.github.io/styleguide/pyguide.html) with [Google style docstrings](http://queirozf.com/entries/python-docstrings-reference-examples#google-style).\n\n## Contact\nPlease direct correspondence to Ava Soleimany (\u003cavasoleimany@microsoft.com\u003e).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Favaamini%2Fprotease_activity_analysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Favaamini%2Fprotease_activity_analysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Favaamini%2Fprotease_activity_analysis/lists"}