{"id":16530664,"url":"https://github.com/LoLab-MSM/pyvipr","last_synced_at":"2025-10-28T11:30:41.120Z","repository":{"id":33445956,"uuid":"158030295","full_name":"LoLab-MSM/pyvipr","owner":"LoLab-MSM","description":"Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML","archived":false,"fork":false,"pushed_at":"2023-03-13T23:02:17.000Z","size":24617,"stargazers_count":27,"open_issues_count":23,"forks_count":4,"subscribers_count":7,"default_branch":"master","last_synced_at":"2024-05-22T08:44:38.577Z","etag":null,"topics":["bionetgen","cytoscapejs","jupyter-widget","jupyterlab-extension","network-visualization","networkx","pysb","sbgn","sbml","systems-biology","tellurium","visualization"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","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/LoLab-MSM.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}},"created_at":"2018-11-17T22:29:54.000Z","updated_at":"2023-10-18T17:52:39.000Z","dependencies_parsed_at":"2023-01-15T01:00:15.375Z","dependency_job_id":"45e7bc04-3b83-48d9-913b-9e8014f78688","html_url":"https://github.com/LoLab-MSM/pyvipr","commit_stats":null,"previous_names":["lolab-vu/pyvipr"],"tags_count":36,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LoLab-MSM%2Fpyvipr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LoLab-MSM%2Fpyvipr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LoLab-MSM%2Fpyvipr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LoLab-MSM%2Fpyvipr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LoLab-MSM","download_url":"https://codeload.github.com/LoLab-MSM/pyvipr/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":236905703,"owners_count":19223298,"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":["bionetgen","cytoscapejs","jupyter-widget","jupyterlab-extension","network-visualization","networkx","pysb","sbgn","sbml","systems-biology","tellurium","visualization"],"created_at":"2024-10-11T18:06:51.029Z","updated_at":"2025-10-28T11:30:38.920Z","avatar_url":"https://github.com/LoLab-MSM.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# \u003cimg alt=\"pyViPR\" src=\"https://github.com/LoLab-VU/pyvipr/blob/master/pyvipr_logo.png\" height=\"100\"\u003e\n\n\n[![Documentation Status](https://readthedocs.org/projects/pyvipr/badge/?version=latest)](https://pyvipr.readthedocs.io/en/latest/?badge=latest)\n![](https://github.com/Lolab-VU/pyvipr/workflows/build/badge.svg)\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/LoLab-VU/pyvipr/master?filepath=binder) \n\n[![Gitter](https://badges.gitter.im/LoLab-VU/pyvipr.svg)](https://gitter.im/LoLab-VU/pyvipr?utm_source=badge\u0026utm_medium=badge\u0026utm_campaign=pr-badge)\n\n# PyViPR\nPyViPR is a Jupyter widget that generates network dynamic and static visualizations of [PySB](http://pysb.org/), [Tellurium](http://tellurium.analogmachine.org/),\n[BNGL](https://www.csb.pitt.edu/Faculty/Faeder/?page_id=409), [SBML](http://sbml.org/Main_Page), and [Ecell4](https://github.com/ecell/ecell4) \n models using [Cytoscape.js](http://js.cytoscape.org/). Additionally, it can be used to visualize networks encoded in the graphml, \n sif, sbgn xml, cytoscape json, gexf, gml and yaml formats.\n \n ## Trying it online\n\nTo try out PyViPR interactively in your web browser, just click on the binder\nlink below:\n\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/LoLab-VU/pyvipr/master?filepath=binder)\n\n## Installation\n\n### From conda\n\n#### To use with Jupyter Notebooks:\n\n```bash\n\u003e conda install pyvipr -c ortegas\n```\n\n#### To use with JupyterLab:\n\n```bash\n\u003e conda install pyvipr -c ortegas\n\u003e jupyter labextension install @jupyter-widgets/jupyterlab-manager\n\u003e jupyter labextension install pyvipr\n```\n\n### From PyPI\n\n#### To use with Jupyter Notebooks:\n\n```bash\n\u003e pip install pyvipr\n```\n\n#### To use with JupyterLab:\n\n```bash\n\u003e pip install pyvipr\n\u003e jupyter labextension install @jupyter-widgets/jupyterlab-manager\n\u003e jupyter labextension install pyvipr\n```\n\n### From git (requires npm)\n```bash\n$ git clone https://github.com/LoLab-VU/pyvipr.git\n$ cd pyvipr\n$ pip install .\n```\n\n## How to use the widget\nAfter installing the widget, it can be used by importing it in the Jupyter notebook. The widget is simple to use with PySB \nmodels, [SimulationResult](https://pysb.readthedocs.io/en/stable/modules/simulator.html#pysb.simulator.SimulationResult) \nobjects, [Tellurium](http://tellurium.analogmachine.org/) models and BNGL \u0026 SBML files. \n\nPyViPR has three main interfaces: Graph formats, PySB, and a Tellurium.\n\n### Graph formats interface\nThis interface leverages NetworkX and Cytoscape.js to generate network visualizations of graphs encoded in different \nfile formats.\n\n#### Graphml example:\n```python\nimport pyvipr.network_viz as nviz\n\nnviz.graphml_view('path_to_file/mygraph.graphml', layout_name='fcose')\n```\n![graphml_view](graphml.png)\n\n### PySB interface\n\nPySB is needed to visualize PySB models and it is needed if you want to use the pyvipr.pysb_viz module:\n\nInstalling PySB from pip:\n```bash\n\u003e pip install pysb\n```\n\nWhen using pip the [installation of PySB](https://pysb.readthedocs.io/en/stable/installation.html#option-1-install-pysb-natively-on-your-computer)\nrequires to manually install BioNetGen into the default path for your platform \n(/usr/local/share/BioNetGen on Mac and Linux, c:\\Program Files\\BioNetGen on Windows), \nor set the BNGPATH environment variable to the BioNetGen path on your machine.\n\nInstalling PySB from conda:\n```bash\n\u003e conda install pysb -c alubbock\n```\n\n#### PySB static example:\n```python\nimport pyvipr.pysb_viz as pviz\nfrom pyvipr.examples_models.lopez_embedded import model\n\npviz.sp_comm_louvain_view(model, random_state=1, layout_name='klay')\n```\n![species_view_pysb](earm_communities.png)\n\n#### PySB Dynamic Example:\n```python\nimport pyvipr.pysb_viz as pviz\nfrom pyvipr.examples_models.mm_two_paths_model import model\nfrom pysb.simulator import ScipyOdeSimulator\nimport numpy as np\n\ntspan = np.linspace(0, 1000, 100)\nsim = ScipyOdeSimulator(model, tspan).run()\npviz.sp_dyn_view(sim)\n```\n\n![enzymatic_reaction](pyvipr_dynamic.gif)\n\n\n### Tellurium interface\n\nTellurium is needed to visualize Tellurium models and it is needed if you want to use the pyvipr.tellurium_viz module:\n\nInstalling Tellurium from pip:\n```bash\n\u003e pip install tellurium\n```\n\n```python\nimport tellurium as te\nimport pyvipr.tellurium_viz as tviz\n\nmodel = te.loadSBMLModel(\"https://www.ebi.ac.uk/biomodels-main/download?mid=BIOMD0000000001\")\n\ntviz.sp_view(model)\n```\n![species_view_tellurium](tellurium_example.png)\n\n## Documentation\n\nTo get started with using `PyViPR`, check out the full documentation\n\nhttps://pyvipr.readthedocs.io/\n\n## Citation\nTo cite PyViPR, please cite the iScience paper:\n\n[Interactive Multiresolution Visualization of Cellular Network Processes](https://www.cell.com/iscience/fulltext/S2589-0042(19)30493-6)\n\nOrtega O and Lopez C\n\n\n\n## License\n\n[MIT](https://opensource.org/licenses/MIT)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FLoLab-MSM%2Fpyvipr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FLoLab-MSM%2Fpyvipr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FLoLab-MSM%2Fpyvipr/lists"}