{"id":15599599,"url":"https://github.com/hypercubed/connectome","last_synced_at":"2025-10-10T22:12:01.111Z","repository":{"id":33209026,"uuid":"36851746","full_name":"Hypercubed/connectome","owner":"Hypercubed","description":"Web tool for exploring cell-cell ligand-receptor mediated communication networks","archived":false,"fork":false,"pushed_at":"2016-08-18T05:02:09.000Z","size":2443,"stargazers_count":24,"open_issues_count":0,"forks_count":8,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-04-28T10:56:08.632Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://hypercubed.github.io/connectome/","language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Hypercubed.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-06-04T06:11:56.000Z","updated_at":"2024-01-23T21:46:30.000Z","dependencies_parsed_at":"2022-07-29T18:49:53.515Z","dependency_job_id":null,"html_url":"https://github.com/Hypercubed/connectome","commit_stats":null,"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"purl":"pkg:github/Hypercubed/connectome","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Hypercubed%2Fconnectome","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Hypercubed%2Fconnectome/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Hypercubed%2Fconnectome/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Hypercubed%2Fconnectome/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Hypercubed","download_url":"https://codeload.github.com/Hypercubed/connectome/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Hypercubed%2Fconnectome/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279005463,"owners_count":26083900,"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","status":"online","status_checked_at":"2025-10-10T02:00:06.843Z","response_time":62,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":[],"created_at":"2024-10-03T02:00:26.759Z","updated_at":"2025-10-10T22:12:01.094Z","avatar_url":"https://github.com/Hypercubed.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# connectome\n\nWeb tool for exploring cell-cell ligand-receptor mediated communication networks\n\n## Introduction\n\nIn Ramilowski et al. ‘A draft network of ligand-receptor mediated multicellular signaling in human’ 2015 [doi:10.1038/ncomms8866](http://dx.doi.org/10.1038/ncomms8866) we present the first large-scale map of cell-to-cell communication between 144 human primary cell types using 2,422 putative and literature supported ligand-receptor pairs. With up to hundreds of potential interactions between any two of these 144 primary cell types, there are millions of possible cell-cell communication paths across the entire network. Static visualization of such complex networks not only can be obscure and impractical but also difficult. With that, and to benefit the research community, we provide an online resource that visualizes, on demand, our cell-cell communication network for any given subset of the ligand-receptor pairs and profiled primary cells. An online version of the resource is located at: [Ramilowski_et_al_2015](http://fantom.gsc.riken.jp/5/suppl/Ramilowski_et_al_2015/vis/) and mirrored at [forrest-lab.github.io/connectome](http://forrest-lab.github.io/connectome).\n\nWe developed the online connectome visualization application using various open source and custom tools.  The vector graphic visualization is generated using the [D3.js visualization library][d3].  The application interface was developed using the [AngularJS web application framework][angular] and the [twitter bootstrap front-end framework][twbs].\n\nThe visualization interface takes the the expression files generated in this study along with other metadata in tabular format [Ramilowski_et_al_2015](http://fantom.gsc.riken.jp/5/suppl/Ramilowski_et_al_2015/) to generate the network/hive visualization as shown in figure 5 in the paper.\n\n# For Developers\n\n## Background\n\nTo install a copy of this application you will need [node and npm](http://nodejs.org/), Grunt, and Bower. If you are not familiar it would be worthwhile to read up on [node and npm](http://www.joyent.com/blog/installing-node-and-npm/), [Grunt](https://github.com/gruntjs/grunt/wiki/Getting-started) and [bower](http://bower.io/).\n\n## Download and Install\n\n```\ngit clone https://github.com/Hypercubed/connectome.git\ncd connectome\nnpm install\nbower install\n```\n\n## Summary of Directory Layout\n\n    app/                --\u003e all of the files to be used in development\n      bower_components/    --\u003e AngularJS and 3rd party JavaScript libraries installed using bower\n      components/          --\u003e Application components\n      data/                --\u003e data files\n    test/               --\u003e test source files and libraries\n    package.json        --\u003e npm's config file\n    bower.json          --\u003e bower's config file\n    Gruntfile.js        --\u003e Grunt config file\n    README.md           --\u003e This file\n\n## Adding data\n\nThis git repository include the data files that acompany the above referenced paper. You add your own into the app/data/ folder. All data files should be Tab-Seperated-Value (TSV) files.\n\n## Grunt\n\nGrunt is a JavaScript based task runner.  In this project Grunt is used for many tasks including testing, minification, and even deployment.  If you are not familiar with Grunt please read the [Getting started guide](https://github.com/gruntjs/grunt/wiki/Getting-started).\n\nSummary of Grunt tasks:\n\n             clean  Clean files and folders.\n              test  Run all tests\n             build  Prepare project for deployment.\n             serve  Run a test server\n             deploy Build and deploy to github\n\n## Running the app during development\n\nRunning `grunt serve` will run a test server on the local host and open your default web browser to http://localhost:9000/.\n\n# Contact\n\nFor more information please contact J. Harshbarger\n\n## Acknowledgments\n\nThis work was supported by a research grant from the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT) to the RIKEN Center for Life Science Technologies.\n\n## Reference\n\n\u003e **A draft network of ligand–receptor-mediated multicellular signalling in human**\n\n\u003e Jordan A. Ramilowski,\tTatyana Goldberg,\tJayson Harshbarger,\tEdda Kloppman,\tMarina Lizio,\tVenkata P. Satagopam,\tMasayoshi Itoh,\tHideya Kawaji,\tPiero Carninci,\tBurkhard Rost \u0026 Alistair R. R. Forrest\n\n\u003e Nature Communications 6, Article number: 7866 [doi:10.1038/ncomms8866](http://doi.org/10.1038/ncomms8866)\n\n## License\n\n[MIT License](http://en.wikipedia.org/wiki/MIT_License)\n\nCopyright (c) 2015 RIKEN, Japan.\n\nPermission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the \"Software\"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.\n\n\n[d3]: http://d3js.org/ \"Data-Driven Documents\"\n[angular]: http://angularjs.org/ \"AngularJS Framework\"\n[twbs]: http://getbootstrap.com/2.3.2/ \"Twitter bootstrap\"\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhypercubed%2Fconnectome","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhypercubed%2Fconnectome","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhypercubed%2Fconnectome/lists"}