{"id":23640143,"url":"https://github.com/logan169/egnize","last_synced_at":"2026-05-02T11:34:09.423Z","repository":{"id":115933272,"uuid":"91112241","full_name":"logan169/EGNize","owner":"logan169","description":"EGN web server for Network analysis and visualisation","archived":false,"fork":false,"pushed_at":"2017-05-12T20:21:38.000Z","size":4282,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-11T20:39:17.215Z","etag":null,"topics":["angularjs","egn","flask","flask-server","full-stack","interactive-visualizations","network-analysis","perl","python-2","sigmajs","visualization"],"latest_commit_sha":null,"homepage":"","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/logan169.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":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-05-12T16:54:58.000Z","updated_at":"2021-03-10T17:18:20.000Z","dependencies_parsed_at":null,"dependency_job_id":"4d77d40c-5e6c-48dd-b8e0-d71194e3db48","html_url":"https://github.com/logan169/EGNize","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/logan169%2FEGNize","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/logan169%2FEGNize/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/logan169%2FEGNize/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/logan169%2FEGNize/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/logan169","download_url":"https://codeload.github.com/logan169/EGNize/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239576799,"owners_count":19662113,"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":["angularjs","egn","flask","flask-server","full-stack","interactive-visualizations","network-analysis","perl","python-2","sigmajs","visualization"],"created_at":"2024-12-28T08:32:07.404Z","updated_at":"2025-11-09T20:30:19.276Z","avatar_url":"https://github.com/logan169.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# EGNize\n## EGN web server for Network analysis and visualisation\n\n![Alt text](/network_example4.png?raw=true \"intro network\")\n\nEGNize is a fullstack web application (Python2/AngularJS) based on an encapsulated modified version of\n[EGN](https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-13-146) (Perl). It allows users to create networks (based on gene and genome similarities) and visualize them through an\ninteractive visualization tool (SigmaJS).\n\nAs analyzing data could take some times (depending on dataset size), a mail server was implemented to keep user\ninformed of analysis status and send output files directly to user mail when done.\nOutput files produced by EGNize could then either be visualized directly using EGNize's interactive visualization tool or any\nother network analysis software (Cytoscape or Gephi).\n\nThe visualisation tools are highly customizable to anyone that would like for example to associate keyboard/mouse inputs in order to display any kind of metrics over a color gradient.\n\n#### Actual available interaction are :\n- Mouse wheel           =\u003e zoom in and zoom out\n- Click and hold        =\u003e slide throught the network\n- Right click on a node =\u003e display gene/genomics similarities with neighbours nodes represented with a color gradient\n- Left click on a node  =\u003e display only nodes sharing similarities with it\n- Double click anywhere =\u003e reset to default display where nodes are colored according to the biological group they belong\n\nFor more information about EGNize, please read appDescription.pdf and EGN User Guide.pdf.\nIf you have any questions send a mail to \u003clogan1691987@gmail.com\u003e\n\n#### Dependencies\n- Python 2\n- Flask\n- Flask mail\n- Blast (should be executable through terminal)\n\n### Initialization\n\n#### To launch the server (Back-end)\nAfter installing dependencies, and editing mail account information in config.py, type the following commands from 'egn_server' folder:\n\n        $ chmod +x launch_srvr.py\n        $ ./launch_srvr.py\n\n#### How to use it (Front-end)\n\nOnce the server is up, type URL displayed in the terminal (after executing the last command) in your browser's URL bar.\nPer default, it should be \u003chttp://localhost:8084\u003e but may change depending on your flask configuration.\n\n##### Create a network\n\nOnce connected, click on 'new analysis' in the top right corner and fill up inputs form and upload your .faa input file.\nPlease refer to EGN documentation for input value.\n- Don't forget to enter your mail address to get back your zip archive (containing all outputs files) when the analysis is done.\n- Be aware that starting several runs (with different parameters) on the same input file will return a zip archive that also contains all previous outputs analysis from same input file.\n\n\n##### Visualize a network\n\nAfter receiving the zip archive, reconnect to EGNize page, click on the \"load a network\" button and upload a json or gexf file.\nAfter clicking on ok, modal window should close and visualization tool should display your network.\nReport to the 'Actual available interaction' section above for possible interactions.\n\n#### Example pictures\n\n![Alt text](/network_example.png?raw=true \"biological group network\")\n\n![Alt text](/network_example2.png?raw=true \"neighboorhood\")\n\n![Alt text](/network_example3.png?raw=true \"gene similarity\")\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flogan169%2Fegnize","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flogan169%2Fegnize","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flogan169%2Fegnize/lists"}