{"id":20930541,"url":"https://github.com/intermine/cytoscape-intermine","last_synced_at":"2026-04-16T09:04:33.294Z","repository":{"id":57118929,"uuid":"145102443","full_name":"intermine/cytoscape-intermine","owner":"intermine","description":"Widget to allow intermine gene interactions to be viewed using cytoscape.js","archived":false,"fork":false,"pushed_at":"2021-06-15T10:04:04.000Z","size":5385,"stargazers_count":2,"open_issues_count":1,"forks_count":1,"subscribers_count":10,"default_branch":"master","last_synced_at":"2025-02-21T05:07:03.283Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"JavaScript","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/intermine.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":"2018-08-17T09:42:18.000Z","updated_at":"2021-06-15T10:36:40.000Z","dependencies_parsed_at":"2022-08-23T04:40:29.855Z","dependency_job_id":null,"html_url":"https://github.com/intermine/cytoscape-intermine","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2Fcytoscape-intermine","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2Fcytoscape-intermine/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2Fcytoscape-intermine/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/intermine%2Fcytoscape-intermine/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/intermine","download_url":"https://codeload.github.com/intermine/cytoscape-intermine/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243324506,"owners_count":20273113,"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":[],"created_at":"2024-11-18T21:34:51.022Z","updated_at":"2025-12-25T09:47:33.587Z","avatar_url":"https://github.com/intermine.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Build Status](https://travis-ci.org/intermine/cytoscape-intermine.svg?branch=master)](https://travis-ci.org/intermine/cytoscape-intermine)\n\n## About\nThis project takes gene interaction data from [Intermine](https://github.com/intermine/intermine) and visualises it using [cytoscape.js](http://js.cytoscape.org/), a fabulous network visualisation tool.\n\nDemo at [yochannah.github.io/cytoscape-intermine/](http://yochannah.github.io/cytoscape-intermine/).\n\n## Quick Start\n\nTL;DR: See the [source](https://github.com/yochannah/cytoscape-intermine/blob/master/index.html) of the [demo page](http://yochannah.github.io/cytoscape-intermine/).\n\n### Detailed steps:\nIf you don't care about building the script, just download or check out **dist/bundle.js** and **dist/style.css**.\nInclude links to both in your project page, e.g.:\n\n    \u003clink href=\"dist/style.css\" rel=\"stylesheet\" type=\"text/css\"\u003e\n    \u003cscript src=\"dist/bundle.js\"\u003e\u003c/script\u003e\n\n#### To initialise the graph:\n\nYou'll need to pass an object that contains the following properties:\n\n* `service`: An object, that at a minimum contains a `root` property pointing to [Intermine Service](http://iodocs.labs.intermine.org/), e.g `service : {root : 'http://www.flymine.org/query/service/'}`. Optionally can take a `token` property as well.\n* `queryOn`: This is a **term to query on** (e.g. a gene name or 'primaryIdentifier'). This is in the format of an object, such as `{\"value\" : \"FBgn0034249\"}` or `{\"value\" : \"PPARG\", \"extraValue\" : \"H. sapiens\"}`.\n* `parentElem`: An **element to insert the graph into**, e.g. `document.getElementById('myAwesomeElement');`. If this isn't specified, the graph will try to find an element with the ID `cymine`.\n* `nodeType`: Optional, will default to gene. Mandatory for Protein queries. Values are `Gene` or `Protein`.\n* `compact`: optional. If there are no results, if this argument is truthy, the 'sorry, no interactions for this search' message is 1.5em high, not 350px.\n\n#### Gluing them all together, the body of your HTML page might look something like this:\n\n    \u003cdiv id=\"myAwesomeElement\"\u003e\u003c/div\u003e\n    \u003cscript\u003e\n    cymine({\n      parentElem : document.getElementById('myAwesomeElement'),\n      service : {\n        root : \"http://beta.flymine.org/beta/service/\", //mandatory\n        token : \"\" //optional\n        },\n      queryOn : {\n        \"value\" : \"FBgn0034249\"\n      },\n      nodeType : \"Gene\",\n      compact : true //optional\n    });\n    \u003c/script\u003e\n\n## Modifying / running the project locally\n### Dependencies\nWe'll assume you have [npm](https://nodejs.org/download/) installed already.\n\n### Installation\n\nIn terminal:\n\n    $ npm install\n    $ bower install\n\nIf you get error `bower: command not found`, then run:\n    \n    $ npm install -g bower\n    $ bower install\n\nThat should be it!\n\n### Running the project\n\nTo serve the project in browser, run:\n\n    $ npm start\n\nIf you get error `Error: listen EADDRINUSE: address already in use :::3344`, then, either kill that port(not recommended) or you can use any other port.\nSay, If you want to use port `8080` then run:\n\n    $ export PORT=8080\n\n\nIf you want to modify the script and let Browsersync live-reload your changes, run:\n\n    $ npm run gulpDev\n\nIf you just want a one-off build, gulp's default task will do it:\n\n    $ npm run gulp\n\nBoth tasks will compile your less (make sure to prefix partials with `_`, e.g. `_button.less`) and bundle up your js, then move it to the dist folder.\n\n#### Testing\n\n  Run `$ mocha` (to run the suite once) or `$ mocha --watch` (to re-test when you make changes).\n\n### Query notes\n\nTo get this working with objectId arguments, initialise with `\"op\" : \"=\"` on the queryOn object, e.g.\n\n    \u003cdiv id=\"myAwesomeElement\"\u003e\u003c/div\u003e\n    \u003cscript\u003e\n    cymine({\n      parentElem : document.getElementById('myAwesomeElement'),\n      service : {\n        root : \"http://beta.flymine.org/beta/service/\", //mandatory\n        token : \"\" //optional\n        },\n      queryOn : {\n        \"value\" : 1449024,\n        \"op\" : \"=\"\n      },\n      nodeType : \"Gene\"\n    });\n    \u003c/script\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fintermine%2Fcytoscape-intermine","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fintermine%2Fcytoscape-intermine","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fintermine%2Fcytoscape-intermine/lists"}