{"id":27351932,"url":"https://github.com/genometric/tvq","last_synced_at":"2025-04-12T20:54:10.327Z","repository":{"id":40853485,"uuid":"206883234","full_name":"Genometric/TVQ","owner":"Genometric","description":"Contains scripts to study the impact of publishing software to package management systems on their scholarly recognition.","archived":false,"fork":false,"pushed_at":"2022-12-08T12:07:48.000Z","size":4037,"stargazers_count":1,"open_issues_count":4,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-12T20:54:06.789Z","etag":null,"topics":["bioconda","bioconductor","biotools","citation","scholarly-references","toolshed"],"latest_commit_sha":null,"homepage":"https://genometric.github.io/TVQ/","language":"C#","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/Genometric.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-09-06T22:30:35.000Z","updated_at":"2022-08-20T20:24:53.000Z","dependencies_parsed_at":"2023-01-25T13:01:03.454Z","dependency_job_id":null,"html_url":"https://github.com/Genometric/TVQ","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genometric%2FTVQ","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genometric%2FTVQ/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genometric%2FTVQ/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genometric%2FTVQ/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Genometric","download_url":"https://codeload.github.com/Genometric/TVQ/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248631717,"owners_count":21136560,"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":["bioconda","bioconductor","biotools","citation","scholarly-references","toolshed"],"created_at":"2025-04-12T20:54:09.659Z","updated_at":"2025-04-12T20:54:10.322Z","avatar_url":"https://github.com/Genometric.png","language":"C#","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://genometric.github.io/TVQ/docs/\"\u003e\n    \u003cimg src=\"https://raw.githubusercontent.com/Genometric/TVQ/docs/static/logo/logo_w_txt.png?raw=true\" alt=\"TVQ\" width=\"300\" /\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://doi.org/10.5281/zenodo.4276272\"\u003e\u003cimg src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.4276272.svg\" alt=\"DOI\"\u003e\u003c/a\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://genometric.github.io/TVQ/\"\u003eDocumentation\u003c/a\u003e |\n  \u003ca href=\"https://genometric.github.io/TVQ/docs/getting_started/quickstart\"\u003eQuick Start\u003c/a\u003e |\n  \u003ca href=\"https://genometric.github.io/TVQ/api/\"\u003eSwagger API Documentation\u003c/a\u003e\n\u003c/p\u003e\n\n\nThe objective of this project is to study the impact of publishing tools \nto package management systems on their scholarly recognition and adoption. \nFor instance, how much the citation count of a scholarly paper increase after its \nrespective software is added to Bioconductor. Currently, the study is \nfocused on tools published to package management systems primarily used \nby the Bioinformatics community: \n[Bioconda](https://bioconda.github.io), \n[Bioconductor](https://www.bioconductor.org), \n[BioTools](https://github.com/bio-tools), and \n[ToolShed](https://toolshed.g2.bx.psu.edu). \n\n## Project Structure\n\nThe project consists of three major components (see the following figure):\n\n- [**Offline Crawlers**](https://genometric.github.io/TVQ/docs/offline_crawlers/about): \nScripts to retrieve those package metadata that require \nextensive time or resource consuming operations. These scripts are not run frequently, \nand their generated data is cached under the \n[`data`](https://github.com/Genometric/TVQ/tree/master/data) \nfolder to be used by the _Webservice_ \n(read [details]((https://genometric.github.io/TVQ/docs/offline_crawlers/about))).\n\n- [**Webservice**](https://genometric.github.io/TVQ/docs/webservice/about):\nCollects all the required metadata about software packages, it uses the cached \ndata and queries the package management systems for the \"cheap-to-retrieve\" data.\nIt then aggregates the information collected from different package management systems,\nand queries Scopus for the citation count of every scholarly paper. The service\ngenerates descriptive statistics about the packages and their citation count, and\noutputs raw data to be used for detailed statistical inferences by _analytics scripts_ \n(read webservice [details](https://genometric.github.io/TVQ/docs/webservice/about)).  \n\n- [**Analytics Scripts**](https://genometric.github.io/TVQ/docs/analytics/about): \n[Python Scripts](https://github.com/Genometric/TVQ/tree/master/analytics) \nfor statistical analysis and plotting. These scripts perform statistical tests \non the data collected by the _webservice_ and report results in tables and plots\n(read [detail](https://genometric.github.io/TVQ/docs/analytics/about) about \nthese scripts).\n\n\u003cbr/\u003e\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://genometric.github.io/TVQ/docs/\"\u003e\n    \u003cimg src=\"https://raw.githubusercontent.com/Genometric/TVQ/docs/static/img/overview_wbg.svg?raw=true\"/\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n\u003cbr/\u003e\n\n## 💖 Contributing\n\nWhen it comes to open-source, every contribution you \nmake, makes the software better for everyone, and \nthat is extensively valuable and warmly appreciated \nby the community. We have a \n[contributing guide](https://github.com/genometric/tvq/blob/master/CONTRIBUTING.md) \nto help guide you.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenometric%2Ftvq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgenometric%2Ftvq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenometric%2Ftvq/lists"}