{"id":24231884,"url":"https://github.com/apdavison/bulbnet-reproduction","last_synced_at":"2026-01-28T20:02:50.018Z","repository":{"id":146354748,"uuid":"259920167","full_name":"apdavison/bulbnet-reproduction","owner":"apdavison","description":"Code associated with the article \"[Rp] Dendrodendritic inhibition and simulated odor responses in a detailed olfactory bulb network model\"","archived":false,"fork":false,"pushed_at":"2020-08-07T15:33:00.000Z","size":13882,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-09-04T18:56:04.905Z","etag":null,"topics":["computational-neuroscience","neuron-simulator","olfaction","reproducible-paper","rescience","simulation"],"latest_commit_sha":null,"homepage":null,"language":"TeX","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/apdavison.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":"AUTHORS","dei":null,"publiccode":null,"codemeta":"codemeta.json","zenodo":null}},"created_at":"2020-04-29T12:33:12.000Z","updated_at":"2020-08-07T15:33:03.000Z","dependencies_parsed_at":null,"dependency_job_id":"dd44ec92-3754-409e-9637-a9b35a42d2a3","html_url":"https://github.com/apdavison/bulbnet-reproduction","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/apdavison/bulbnet-reproduction","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/apdavison%2Fbulbnet-reproduction","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/apdavison%2Fbulbnet-reproduction/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/apdavison%2Fbulbnet-reproduction/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/apdavison%2Fbulbnet-reproduction/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/apdavison","download_url":"https://codeload.github.com/apdavison/bulbnet-reproduction/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/apdavison%2Fbulbnet-reproduction/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28850474,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-28T15:15:36.453Z","status":"ssl_error","status_checked_at":"2026-01-28T15:15:13.020Z","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":["computational-neuroscience","neuron-simulator","olfaction","reproducible-paper","rescience","simulation"],"created_at":"2025-01-14T14:36:13.511Z","updated_at":"2026-01-28T20:02:50.000Z","avatar_url":"https://github.com/apdavison.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"# bulbnet-reproduction\n\nThis is a model of the mammalian olfactory bulb for the\nNEURON simulator. The model contains only mitral and\ngranule cells.\n\nA full description may be found in:\nDavison A.P., Feng J. and Brown D. (2003) Dendrodendritic\ninhibition and simulated odor responses in a detailed\nolfactory bulb network model. J. Neurophysiol. 90:1921-35\n\nTo reproduce the figures from this paper, install NEURON, change to the code\ndirectory, run:\n\n```\n  $ nrnivmodl\n```\n\nthen for each figure run:\n\n```\n  $ python run.py figure_2\n```\n\nand similarly for the other figures.\n\n\n## Time required to run simulations\n\nThe following times are for running with 32 threads on a workstation with dual Intel Xeon E5-2640 processors (8 cores, 2.6 GHz, 20 MB cache), 128 GB 2400 MHz DDR4 ECC RAM, writing to a 400 GB SSD SAS 12 Gbit/s hard disk. The time to run with a single core was about 10 times as long.\n\n```\nfigure_2   1m 19s\nfigure_3   9m 10s\nfigure_4   3m 46s\nfigure_5   3m 56s\nfigure_7   2m 32s\nfigure_8   5m 25s\nfigure_9   14m 58s\nfigure_10  1h 46m\nfigure_11  15m 50s\nfigure_12  10m 42s\nfigure_13  1h 24m\nfigure_14  34m 19s\nfigure_15  8m 46s\nfigure_16  25m 32s\nfigure_17  6m 23s\n```\n\n## Dependencies\n\n- NEURON (https://neuron.yale.edu/neuron/)\n- Gnuplot (http://www.gnuplot.info/)\n- Python (v3.6 or more recent)\n- NumPy\n- PyYAML\n- Jinja2\n- epstopdf (optional - for converting figure to PDF)\n- ImageMagick (optional - for converting figures to PNG)\n\nFor more information, contact andrew.davison@cnrs.fr\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fapdavison%2Fbulbnet-reproduction","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fapdavison%2Fbulbnet-reproduction","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fapdavison%2Fbulbnet-reproduction/lists"}