{"id":34656466,"url":"https://github.com/andim/paper-tcellexp","last_synced_at":"2026-05-25T18:02:31.287Z","repository":{"id":72334592,"uuid":"187282612","full_name":"andim/paper-tcellexp","owner":"andim","description":"Source code accompanying the paper \"Regulation of T cell expansion by antigen presentation dynamics \"","archived":false,"fork":false,"pushed_at":"2019-05-17T21:33:48.000Z","size":938,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-12-26T06:54:35.563Z","etag":null,"topics":["biophysics","openscience"],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/andim.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2019-05-17T21:17:49.000Z","updated_at":"2019-05-17T21:34:52.000Z","dependencies_parsed_at":null,"dependency_job_id":"5043b9da-80a8-45a2-8c08-e1aec6ea4218","html_url":"https://github.com/andim/paper-tcellexp","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/andim/paper-tcellexp","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andim%2Fpaper-tcellexp","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andim%2Fpaper-tcellexp/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andim%2Fpaper-tcellexp/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andim%2Fpaper-tcellexp/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/andim","download_url":"https://codeload.github.com/andim/paper-tcellexp/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andim%2Fpaper-tcellexp/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33486787,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-25T14:31:05.219Z","status":"ssl_error","status_checked_at":"2026-05-25T14:31:02.878Z","response_time":57,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["biophysics","openscience"],"created_at":"2025-12-24T18:04:22.361Z","updated_at":"2026-05-25T18:02:31.242Z","avatar_url":"https://github.com/andim.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Regulation of T cell expansion by antigen presentation dynamics\n\n\u003cimg src=\"https://raw.githubusercontent.com/andim/paper-tcellexp/master/fig1_S234/fig1final.png\" width=\"400\" alt='Figure 1' title=\"Limitation of T cell expansion by antigen decay can explain the power-law dependence of fold expansion on the initial number of cognate T cells\"\u003e\n\nThis repository contains the source code associated with the manuscript\n\nMayer, Zhang, Perelson, Wingreen: [Regulation of T cell expansion by antigen presentation dynamics](https://doi.org/10.1073/pnas.1812800116), PNAS 2019\n\nIt allows reproduction of all numerical results reported in the manuscript.\n\n## Installation requirements\n\nThe code uses Python 3.6+.\n\nA number of standard scientific python packages are needed for the numerical simulations and visualizations. An easy way to install all of these is to install a Python distribution such as [Anaconda](https://www.continuum.io/downloads). \n\n- [numpy](http://github.com/numpy/numpy/)\n- [scipy](https://github.com/scipy/scipy)\n- [pandas](http://github.com/pydata/pandas)\n- [matplotlib](http://github.com/matplotlib/matplotlib)\n\nAdditionally the code also relies on this package:\n\n- [projgrad](https://github.com/andim/projgrad)\n\n## Structure/running the code\n\nEvery folder contains a file `plot.py` which needs to be run to produce the figures. For a number of figures cosmetic changes were done in inkscape as a postprocessing step. In these cases the figures will not be reproduced precisely. To help reuse the final edited figures are provided in png/svg format.\n\n## Contact\n\nIf you run into any difficulties running the code, feel free to contact us at `andimscience@gmail.com`.\n\n## License\n\nThe source code is freely available under an MIT license. The plots are licensed under a Creative commons attributions license (CC-BY).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fandim%2Fpaper-tcellexp","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fandim%2Fpaper-tcellexp","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fandim%2Fpaper-tcellexp/lists"}