{"id":32176265,"url":"https://github.com/brsynth/rp2biosensor","last_synced_at":"2026-02-18T21:02:55.617Z","repository":{"id":45323840,"uuid":"438315750","full_name":"brsynth/rp2biosensor","owner":"brsynth","description":"Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output","archived":false,"fork":false,"pushed_at":"2023-01-03T14:13:33.000Z","size":589,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-10-21T19:56:47.542Z","etag":null,"topics":["synbio","synthetic-biology"],"latest_commit_sha":null,"homepage":null,"language":"HTML","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/brsynth.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2021-12-14T16:03:16.000Z","updated_at":"2023-07-18T09:08:50.000Z","dependencies_parsed_at":"2023-02-01T06:31:27.066Z","dependency_job_id":null,"html_url":"https://github.com/brsynth/rp2biosensor","commit_stats":null,"previous_names":[],"tags_count":9,"template":false,"template_full_name":null,"purl":"pkg:github/brsynth/rp2biosensor","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frp2biosensor","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frp2biosensor/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frp2biosensor/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frp2biosensor/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/brsynth","download_url":"https://codeload.github.com/brsynth/rp2biosensor/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brsynth%2Frp2biosensor/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29596125,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-18T20:59:56.587Z","status":"ssl_error","status_checked_at":"2026-02-18T20:58:41.434Z","response_time":162,"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":["synbio","synthetic-biology"],"created_at":"2025-10-21T19:56:35.932Z","updated_at":"2026-02-18T21:02:55.611Z","avatar_url":"https://github.com/brsynth.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# rp2biosensor -- Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output\n\nrp2biosensor extracts metabolic paths linking undetectable compounds\ninto a detectable one using biochemical reactions. This concept is known\nas \"Sensing-Enabling Metabolic Pathways\". See [doi: 10.1021/acssynbio.5b00225](https://doi.org/10.1021/acssynbio.5b00225)\nfor more.\n\nIn short, rp2bionsensor converts the output of [RetroPath2.0](https://www.myexperiment.org/workflows/4987.html) into a HTML page showing the possible metabolic paths linking the compound to be detected to the detectable ones.\n\nNotice: only the shortest paths are kept. This mean that if there is a 1 step path, no 2 steps will be outputted.\n\n## Install\n\n```bash\nconda install -c conda-forge rp2biosensor\n```\n\n## Run\n\n```bash\npython -m rp2biosensor /path/to/rp2/results.csv --opath /path/to/output/file.html --otype file\n```\n\nBy default, all the needed dependancies are embedded into the HTML file. This includes CSS, JavaScript, and data files. Alternatively, the output could be outputted into a directory, using the `dir` output type:\n\n```bash\npython -m rp2biosensor /path/to/rp2/results.csv --opath /path/to/output --otype dir\n```\n\nThe embedded help:\n```bash\npython -m rp2biosensor -h\n\nusage: rp2biosensor [-h] [--opath OPATH] [--otype {dir,file}] [--ojson OJSON] [--cache-dir CACHE_DIR] rp2_results sink_file\n\nGenerate HTML outputs to explore Sensing Enabling Metabolic Pathway from RetroPath2 results.\n\npositional arguments:\n  rp2_results           RetroPath2.0 results\n  sink_file             Sink file used for RetroPath2.0\n\noptions:\n  -h, --help            show this help message and exit\n  --opath OPATH         Output path. Default: /Users/tduigou/code/rp2biosensor/biosensor.html.\n  --otype {dir,file}    Output type. This could be either (i) \"dir\" which means ouput files will outputted into this directory, or (ii) \"file\" which means that all files will be embedded into a single HTML page. Default: file\n  --ojson OJSON         Output the graph as json file if the path is not None. Default: None\n  --cache-dir CACHE_DIR\n                        Path to the cache directory. If not specified, None is passed to rrCache.\n```\n\n## Example\n\n```bash\npython -m rp2biosensor tests/data/input/rp2-results_lactate.csv --opath ./biosensor.html\n```\n\n## For developpers\n\n### Install\n```bash\nconda env create -f environment.yaml -n rp2biosensor-dev\nconda develop -n rp2biosensor-dev .\n```\n\n### Test\n```bash\npython -m pytest -vv\n```\n\n## Authors\n- Thomas Duigou ([tduigou](https://github.com/tduigou))\n\n## Licence\nrp2biosensor is released under the MIT licence. See the [LICENSE.md](LICENSE.md) file for details.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Frp2biosensor","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrsynth%2Frp2biosensor","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Frp2biosensor/lists"}