{"id":16763157,"url":"https://github.com/linas/biome-distribution","last_synced_at":"2026-01-03T10:10:18.507Z","repository":{"id":149559862,"uuid":"235888136","full_name":"linas/biome-distribution","owner":"linas","description":"Research into statistical distributions of genomes, proteomes and reactomes","archived":false,"fork":false,"pushed_at":"2022-02-14T20:19:41.000Z","size":14853,"stargazers_count":6,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-22T22:29:11.424Z","etag":null,"topics":["genomic-data-analysis","genomics-visualization","proteogenomics","proteomics","reactome","reactome-pathway"],"latest_commit_sha":null,"homepage":null,"language":"Scheme","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/linas.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","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}},"created_at":"2020-01-23T21:16:36.000Z","updated_at":"2024-12-06T08:09:58.000Z","dependencies_parsed_at":null,"dependency_job_id":"5f4da7db-20f8-4704-bfdd-fe42309a1c8b","html_url":"https://github.com/linas/biome-distribution","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linas%2Fbiome-distribution","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linas%2Fbiome-distribution/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linas%2Fbiome-distribution/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linas%2Fbiome-distribution/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/linas","download_url":"https://codeload.github.com/linas/biome-distribution/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243853947,"owners_count":20358502,"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":["genomic-data-analysis","genomics-visualization","proteogenomics","proteomics","reactome","reactome-pathway"],"created_at":"2024-10-13T05:05:45.306Z","updated_at":"2026-01-03T10:10:18.455Z","avatar_url":"https://github.com/linas.png","language":"Scheme","funding_links":[],"categories":[],"sub_categories":[],"readme":"\nBiome Distributions\n-------------------\nResearch concerning the statistical distribution of genetic\ninteractions, the proteins expressed by genes, and their\nparticipation in reaction pathways.\n\nThe primary result is a paper, being prepared for publication.\nIt is in the [paper](./paper) directory. The\n[PDF is here](./paper/biome-distributions.pdf).\n\nIt was naively hypothesized that genome/proteome reaction pathways\nform a scale-free network, and thus would have a Zipfian distribution.\nMuch to our surprise, this is not the case! It seems like *everything*\nfollows a square-root Zipfian distribution! I do not know of any\nnetwork theory or biology theory that would explain this, so it is\na surprise.\n\nAn exploration of the mutual information of interaction pathways is\nalso performed. It appears that these are easily fit with a bimodal\nGaussian distribution.\n\nThis is for human genome/reactome data. I don't doubt that the results\nare generic in biology.\n\n### Directory layout\nOther directories here:\n\n* [diary](./diary) A research diary of notes.\n* [graphs](./graphs) Graphs and the tools used to prepare them.\n* [src](./src) Source code for loading, processing and analyzing\n  the genomic and proteomic data, including reactome data, etc.\n\n### License\n\u003ca rel=\"license\" href=\"http://creativecommons.org/licenses/by-sa/4.0/\"\u003e\u003cimg alt=\"Creative Commons License\" style=\"border-width:0\" src=\"https://i.creativecommons.org/l/by-sa/4.0/88x31.png\" /\u003e\u003c/a\u003e\u003cbr /\u003eThis work is licensed under a \u003ca rel=\"license\" href=\"http://creativecommons.org/licenses/by-sa/4.0/\"\u003eCreative Commons Attribution-ShareAlike 4.0 International License\u003c/a\u003e.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinas%2Fbiome-distribution","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flinas%2Fbiome-distribution","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinas%2Fbiome-distribution/lists"}