{"id":47423568,"url":"https://github.com/ProjectPyRhO/PyRhO","last_synced_at":"2026-04-05T01:01:00.051Z","repository":{"id":44094192,"uuid":"51864257","full_name":"ProjectPyRhO/PyRhO","owner":"ProjectPyRhO","description":"A virtual optogenetics laboratory","archived":false,"fork":false,"pushed_at":"2023-07-24T10:42:18.000Z","size":3980,"stargazers_count":40,"open_issues_count":1,"forks_count":9,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-03-08T07:16:41.293Z","etag":null,"topics":["brain","brainweb","brian2","computational-neuroscience","jupyter-widget","neuron","neuroscience","opsin","optogenetics","python"],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ProjectPyRhO.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2016-02-16T19:59:00.000Z","updated_at":"2026-01-30T19:27:41.000Z","dependencies_parsed_at":"2023-01-22T04:04:12.317Z","dependency_job_id":"8e7ef348-6423-422d-8a6a-d087a835b8a4","html_url":"https://github.com/ProjectPyRhO/PyRhO","commit_stats":{"total_commits":649,"total_committers":3,"mean_commits":"216.33333333333334","dds":"0.0030816640986132127","last_synced_commit":"78102f9ed2d82481a8e96a932487cedb78c16a3f"},"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/ProjectPyRhO/PyRhO","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ProjectPyRhO%2FPyRhO","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ProjectPyRhO%2FPyRhO/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ProjectPyRhO%2FPyRhO/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ProjectPyRhO%2FPyRhO/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ProjectPyRhO","download_url":"https://codeload.github.com/ProjectPyRhO/PyRhO/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ProjectPyRhO%2FPyRhO/sbom","scorecard":{"id":114559,"data":{"date":"2025-08-11","repo":{"name":"github.com/ProjectPyRhO/PyRhO","commit":"dade008ad2f9d18cf7c3b26782b7063e1a597e40"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":2.5,"checks":[{"name":"Packaging","score":-1,"reason":"packaging workflow not detected","details":["Warn: no GitHub/GitLab publishing workflow detected."],"documentation":{"short":"Determines if the project is published as a package that others can easily download, install, easily update, and uninstall.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#packaging"}},{"name":"Maintained","score":0,"reason":"0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"Binary-Artifacts","score":10,"reason":"no binaries found in the repo","details":null,"documentation":{"short":"Determines if the project has generated executable (binary) artifacts in the source repository.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#binary-artifacts"}},{"name":"Code-Review","score":0,"reason":"Found 0/30 approved changesets -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project requires human code review before pull requests (aka merge requests) are merged.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#code-review"}},{"name":"Token-Permissions","score":0,"reason":"detected GitHub workflow tokens with excessive permissions","details":["Warn: no topLevel permission defined: .github/workflows/python-package.yml:1","Info: no jobLevel write permissions found"],"documentation":{"short":"Determines if the project's workflows follow the principle of least privilege.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#token-permissions"}},{"name":"Dangerous-Workflow","score":10,"reason":"no dangerous workflow patterns detected","details":null,"documentation":{"short":"Determines if the project's GitHub Action workflows avoid dangerous patterns.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#dangerous-workflow"}},{"name":"SAST","score":0,"reason":"no SAST tool detected","details":["Warn: no pull requests merged into dev branch"],"documentation":{"short":"Determines if the project uses static code analysis.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#sast"}},{"name":"CII-Best-Practices","score":0,"reason":"no effort to earn an OpenSSF best practices badge detected","details":null,"documentation":{"short":"Determines if the project has an OpenSSF (formerly CII) Best Practices Badge.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#cii-best-practices"}},{"name":"Pinned-Dependencies","score":0,"reason":"dependency not pinned by hash detected -- score normalized to 0","details":["Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/python-package.yml:23: update your workflow using https://app.stepsecurity.io/secureworkflow/ProjectPyRhO/PyRhO/python-package.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/python-package.yml:25: update your workflow using https://app.stepsecurity.io/secureworkflow/ProjectPyRhO/PyRhO/python-package.yml/master?enable=pin","Warn: containerImage not pinned by hash: .devcontainer/Dockerfile:5","Warn: pipCommand not pinned by hash: .devcontainer/Dockerfile:25-27","Warn: pipCommand not pinned by hash: pyrho/NEURON/install_neuron.sh:123","Warn: pipCommand not pinned by hash: .github/workflows/python-package.yml:30","Warn: pipCommand not pinned by hash: .github/workflows/python-package.yml:31","Warn: pipCommand not pinned by hash: .github/workflows/python-package.yml:34","Info:   0 out of   2 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of   1 containerImage dependencies pinned","Info:   0 out of   5 pipCommand dependencies pinned"],"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"Security-Policy","score":0,"reason":"security policy file not detected","details":["Warn: no security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"Fuzzing","score":0,"reason":"project is not fuzzed","details":["Warn: no fuzzer integrations found"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"License","score":10,"reason":"license file detected","details":["Info: project has a license file: LICENSE:0","Info: FSF or OSI recognized license: BSD 3-Clause \"New\" or \"Revised\" License: LICENSE:0"],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Signed-Releases","score":-1,"reason":"no releases found","details":null,"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Branch-Protection","score":0,"reason":"branch protection not enabled on development/release branches","details":["Warn: branch protection not enabled for branch 'master'"],"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}},{"name":"Vulnerabilities","score":0,"reason":"27 existing vulnerabilities detected","details":["Warn: Project is vulnerable to: GHSA-44cc-43rp-5947","Warn: Project is vulnerable to: PYSEC-2021-130 / GHSA-4952-p58q-6crx","Warn: Project is vulnerable to: GHSA-9q39-rmj3-p4r2","Warn: Project is vulnerable to: PYSEC-2018-34 / GHSA-2fc2-6r4j-p65h","Warn: Project is vulnerable to: PYSEC-2021-856 / GHSA-5545-2q6w-2gh6","Warn: Project is vulnerable to: PYSEC-2019-108 / GHSA-9fq2-x9r6-wfmf","Warn: Project is vulnerable to: PYSEC-2018-33 / GHSA-cw6w-4rcx-xphc","Warn: Project is vulnerable to: PYSEC-2021-857 / GHSA-f7c7-j99h-c22f","Warn: Project is vulnerable to: GHSA-fpfv-jqm9-f5jm","Warn: Project is vulnerable to: PYSEC-2017-1 / GHSA-frgw-fgh6-9g52","Warn: Project is vulnerable to: PYSEC-2020-73","Warn: Project is vulnerable to: PYSEC-2019-156 / GHSA-xp76-357g-9wqq","Warn: Project is vulnerable to: PYSEC-2023-102","Warn: Project is vulnerable to: PYSEC-2023-114","Warn: Project is vulnerable to: GHSA-29gw-9793-fvw7","Warn: Project is vulnerable to: PYSEC-2022-12 / GHSA-pq7m-3gw7-gq5x","Warn: Project is vulnerable to: PYSEC-2018-18 / GHSA-3p4q-x8f3-p7vq","Warn: Project is vulnerable to: PYSEC-2018-17 / GHSA-49qr-xh3w-h436","Warn: Project is vulnerable to: PYSEC-2018-57 / GHSA-6cwv-x26c-w2q4","Warn: Project is vulnerable to: PYSEC-2020-215 / GHSA-c7vm-f5p4-8fqh","Warn: Project is vulnerable to: PYSEC-2019-159 / GHSA-hhx8-cr55-qcxx","Warn: Project is vulnerable to: GHSA-hwvq-6gjx-j797","Warn: Project is vulnerable to: PYSEC-2019-157 / GHSA-jqwc-jm56-wcwj","Warn: Project is vulnerable to: PYSEC-2022-180 / GHSA-m87f-39q9-6f55","Warn: Project is vulnerable to: PYSEC-2019-158 / GHSA-rcx2-m7jp-p9wj","Warn: Project is vulnerable to: GHSA-rv62-4pmj-xw6h","Warn: Project is vulnerable to: PYSEC-2022-212 / GHSA-v7vq-3x77-87vg"],"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}}]},"last_synced_at":"2025-08-16T00:48:21.277Z","repository_id":44094192,"created_at":"2025-08-16T00:48:21.277Z","updated_at":"2025-08-16T00:48:21.277Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31420789,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-05T00:25:07.052Z","status":"ssl_error","status_checked_at":"2026-04-05T00:25:05.923Z","response_time":60,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: 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":["brain","brainweb","brian2","computational-neuroscience","jupyter-widget","neuron","neuroscience","opsin","optogenetics","python"],"created_at":"2026-03-21T20:00:25.398Z","updated_at":"2026-04-05T01:01:00.016Z","avatar_url":"https://github.com/ProjectPyRhO.png","language":"Python","funding_links":[],"categories":["Open Code"],"sub_categories":["Simulation Software"],"readme":"![PyRhO](https://raw.githubusercontent.com/ProjectPyRhO/PyRhO/master/docs/figs/PyRhO_logo_H_300px.png)\n\n*A Virtual Optogenetics Laboratory*\n\n------------------------------------------------------------------------\n\nPyRhO is a Python module to fit, characterise and simulate (rhod)opsin\nphotocurrents.\n\n[![PyPI](https://img.shields.io/pypi/v/PyRhO)](https://pypi.org/project/PyRhO/) [![GitHub](https://img.shields.io/github/license/ProjectPyRhO/PyRhO)](https://github.com/ProjectPyRhO/PyRhO/blob/master/LICENSE) [![image](https://travis-ci.org/ProjectPyRhO/PyRhO.svg?branch=master)](https://travis-ci.org/ProjectPyRhO/PyRhO) [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/PyRhO)](https://pypi.org/project/PyRhO/) [![GitHub stars](https://img.shields.io/github/stars/ProjectPyRhO/PyRhO)](https://github.com/ProjectPyRhO/PyRhO/stargazers)\n\nBackground\n==========\n\nOptogenetics has become a key tool for understanding the function of\nneural circuits and controlling their behaviour. An array of directly\nlight driven opsins have been genetically isolated from several families\nof organisms, with a wide range of temporal and spectral properties. In\norder to characterize, understand and apply these rhodopsins, we present\nan integrated suite of open-source, multi-scale computational tools\ncalled PyRhO.\n\nPyRhO enables users to:\n\n1. Characterize new (and existing) rhodopsins by automatically fitting a minimal set of experimental data to three, four or six-state kinetic models,\n2. Simulate these models at the channel, neuron \u0026 network levels and\n3. Gain functional insights through model selection and virtual experiments *in silico*.\n\nThe module is written in Python with an additional IPython/[Jupyter](https://jupyter.org/)\nnotebook based GUI, allowing models to be fit, simulations to be run and\nresults to be shared through simply interacting with a webpage. The\nseamless integration of model fitting algorithms with simulation\nenvironments for these virtual opsins (including\n[NEURON](http://www.neuron.yale.edu/neuron/) and\n[Brian2](http://briansimulator.org/)) will enable (neuro)scientists to\ngain a comprehensive understanding of their behaviour and rapidly\nidentify the most suitable variant for application in a particular\nbiological system. This process may thereby guide not only experimental\ndesign and opsin choice but also alterations of the rhodopsin genetic\ncode in a neuro-engineering feed-back loop. In this way, we hope PyRhO\nwill help to significantly improve optogenetics as a tool for\ntransforming biological sciences.\n\nArchitecture\n============\n\n\u003cimg alt=\"PyRhO\narchitecture\" src=\"https://raw.githubusercontent.com/ProjectPyRhO/PyRhO/master/docs/figs/architecture.png\" width=\"50%\" align=\"right\"\u003e\n\nPyRhO is composed of several abstraction layers, including the Model\nlayer, Protocol layer and Simulator layer (shown in the architectural\nschematic below). Choices in each layer are independent or one another,\ngiving a large number of possible combinations to suit many needs for _in\nsilico_ experiments. Additionally, parameters may be fit to each type of\nkinetic model from experimental data or loaded from the default options\nof popular opsins.\n\nPrometheus\n==========\n\nIf you would like to try PyRhO before installing it, go to\n[try.projectpyrho.org](http://try.projectpyrho.org) to launch a fully\nconfigured Jupyter notebook in your browser.\n\nDocker\n======\n\nIf you wish to use PyRhO in a [Docker](https://www.docker.com/) container, a Dockerfile is provided\nin the accompanying Prometheus repository:\n\u003chttps://github.com/ProjectPyRhO/Prometheus\u003e\n\nThe Dockerfile will build a full installation including the NEURON and\nBrian2 simulators and the Jupyter notebook GUI. See the repository\\'s\nREADME file for instructions.\n\nInstallation\n============\n\nTo install PyRhO (including the GUI) from PyPI use the command: :\n\n    pip install pyrho[full]\n\nAlternatively, to install the latest code from GitHub (including the\nGUI) use the command: :\n\n    pip install git+https://github.com/ProjectPyRhO/PyRhO.git#egg=PyRhO[full]\n\nTo use PyRhO with the [NEURON\nsimulator](http://www.neuron.yale.edu/neuron/) in a Python 3\nenvironment, NEURON must be compiled from its source code. An\ninstallation script is provided for doing this on Mac OS X or Linux. The\nresultant installation will also work with Python 2. If you only wish to\nuse PyRhO/NEURON with Python 2 however, a standard NEURON installation\nshould be sufficient. The shell script may be called after importing\nPyRhO with the following function: :\n\n    from pyrho import *\n    setupNEURON('/installation/path/for/NEURON/')\n\nThis will attempt to compile NEURON from source, copy the supplied `mod`\nand `hoc` files into place (the current working directory by default)\nfinally compiling the `mod` files describing the opsin models ready for\ninclusion in simulations.\n\nThe [Brian simulator](http://briansimulator.org/) is included with the\nPyRhO installation for modelling networks of optogenetically transfected\nspiking neurons.\n\nFurther Information\n===================\n\nIf you use PyRhO please cite our paper:\n\nEvans, B. D., Jarvis, S., Schultz, S. R. \u0026 Nikolic K. (2016) \\\"PyRhO: A\nMultiscale Optogenetics Simulation Platform\\\", *Frontiers in\nNeuroinformatics, 10* (8).\n[doi:10.3389/fninf.2016.00008](https://dx.doi.org/10.3389/fninf.2016.00008)\n\n    @ARTICLE{pyrho,\n        AUTHOR={Evans, Benjamin D. and Jarvis, Sarah and Schultz, Simon R. and Nikolic, Konstantin},\n        TITLE={PyRhO: A Multiscale Optogenetics Simulation Platform},\n        JOURNAL={Frontiers in Neuroinformatics},\n        VOLUME={10},\n        YEAR={2016},\n        NUMBER={8},\n        URL={http://journal.frontiersin.org/article/10.3389/fninf.2016.00008/full},\n        DOI={10.3389/fninf.2016.00008}\n    }\n\nThe PyRhO project website with additional documentation may be found\nhere:\n[www.imperial.ac.uk/bio-modelling/pyrho](http://www.imperial.ac.uk/a-z-research/bio-modelling/pyrho)\n\nFinally, don\\'t forget to follow us on twitter for updates:\n[\\@ProjectPyRhO](https://twitter.com/ProjectPyRhO)!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FProjectPyRhO%2FPyRhO","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FProjectPyRhO%2FPyRhO","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FProjectPyRhO%2FPyRhO/lists"}