{"id":13743598,"url":"https://github.com/ryanbressler/Lichen","last_synced_at":"2025-05-09T01:31:18.158Z","repository":{"id":558832,"uuid":"189676","full_name":"ryanbressler/Lichen","owner":"ryanbressler","description":"Client side Network Viewer, Rectangular Heatmap and Visualization Template implemented in actionscript and javascript using the google visualization API.","archived":false,"fork":false,"pushed_at":"2010-12-16T05:10:09.000Z","size":8008,"stargazers_count":8,"open_issues_count":5,"forks_count":3,"subscribers_count":4,"default_branch":"master","last_synced_at":"2024-08-03T05:02:26.174Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"www.systemsbiology.org","language":"ActionScript","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/ryanbressler.png","metadata":{"files":{"readme":"README","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":"2009-04-30T20:36:31.000Z","updated_at":"2019-08-13T14:22:45.000Z","dependencies_parsed_at":"2022-08-16T10:30:52.180Z","dependency_job_id":null,"html_url":"https://github.com/ryanbressler/Lichen","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/ryanbressler%2FLichen","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryanbressler%2FLichen/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryanbressler%2FLichen/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ryanbressler%2FLichen/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ryanbressler","download_url":"https://codeload.github.com/ryanbressler/Lichen/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224796490,"owners_count":17371500,"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":"2024-08-03T05:00:52.717Z","updated_at":"2024-11-15T14:31:33.083Z","avatar_url":"https://github.com/ryanbressler.png","language":"ActionScript","readme":"Copyright (C) 2003-2009 Institute for Systems Biology\n                        Seattle, Washington, USA.\n\nThis library is free software; you can redistribute it and/or\nmodify it under the terms of the GNU Lesser General Public\nLicense as published by the Free Software Foundation; either\nversion 2.1 of the License, or (at your option) any later version.\n\nThis library is distributed in the hope that it will be useful,\nbut WITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU\nLesser General Public License for more details.\n\nYou should have received a copy of the GNU Lesser General Public\nLicense along with this library; If not, see \u003chttp://www.gnu.org/licenses/\u003e.\n=======================================================================\n\n\nThis is a provisional readme file for BioVisualization, a set of  browser \nindependent Google Visuailzation API compliant biology oriented visualizations \nimplemented in javascript and actionscript 3. Please feel free to \nedit and expand it. If something you need to do is not covered here contact \nus and we will update it.\n\nBefore starting you should read the google Visualization API documents \nto learn the basics of creating a data table and using API compliant \nvisualizations:\n\thttp://code.google.com/apis/visualization/\n\t\nTable of Contents\n\n1.  Getting set up in Flex Builder and building code.\n2. BioNetwork Parmaters\n3. BioHeatmap Parmaters\n4. Deploying on a server\n5. Creating your own visualization using flexvistemplate\n6. List of Dependencies\n\n1.  Getting set up in Flex Builder and building code.\n\n\t-creat your own fork on github if you wish to develop against the code\n\t(see: http://github.com/guides/fork-a-project-and-submit-your-modifications)\n\n\t-check out from github using a command like: \n\tgit clone git@github.com:YOURUSERNAME/Lichen.git (if you have forked)\n\tgit clone git://github.com/ryanbressler/Lichen (if you do not wish to fork)\n\t\n\t- open flex builder and go to file\u003eNew\u003eActionScript Project\n\tset the path to your Lichen dir and the name to Lichen\n\tand hit finish.\n\t\n\t- go to project\u003eproperties. Go to actionscript build path, and then go to the\n\tlib dir tab, click the add swc folder hit 'browse' button, and choose the \n\tLichen/lib sub dir.\n\t\n\t- Set bionetwork.as, bioheatmap.as or flexvistemplate.as as your default \n\texecutable (use theright click menu)\n\t\n\t- delete the contents of your html-template dir  and src/lichen.as \n\t(to get rid of all auto generated stuff).\n\t\n\t- go to the Lichen dir in a shell and run: \n\t\tgit checkout html-template\n\t to recreate the files in html-template from github.\n\t\n\t- Hit the build button and wait. A browser with bionetwork.html should come\n\tup, you can open any of the other html files at this point.\n\t\n\t- If you encounter a security zone error there are two possible fixes:\n\t\t1) Ensure there are no spaces in the path to the html file.\n\t\t\n\t \t2) Serve the Lichen/bin-debug directory with a web server then go to Project/Properties, \n\t \tActionScript Build Path, and set Output Folder URL to the URL where the bin-debug file \n\t \tcan be found (example: http://localhost/Lichen).\n\t\n\t- Make sure the swf is built in bin-debug. Then you \n\tcan go to bin-debug folder and open any html files under that folder.\n\t\n\tYou may need to change the font family being embeded if your system does not have helvetica installed\n\n2. BioNetwork Parameters\nDocumentaton had been moved to: \nhttp://ryanbressler.github.com/Lichen/bionetwork.html\n\n\n3. BioHeatmap Parmaters\n\thttp://ryanbressler.github.com/Lichen/bionetwork.html\n\t\t\n4. Deploying on a server\n\tTo deploy a visualization on a server you need to host the associated js and swf files. \n\tCurrentley, if you wish to host these files in a seperate directory you need to edit the path\n\tto the swf file in two places in the embed tag string. You can do this using find and replace \n\t(EX bionetwork.swf -\u003e /js/bionetwork.swf).\n\t\n\tWe are looking for a more maintainable solution if anybody has any ideas.\n\n5. Creating your own visualization using flexvistemplate\n\n\tThe easiest way to start work on your own visualization is to create a copy of flexvistemplate.as,\n\tflexvistemplate.js and flexvistemplate.html. and use find and replace to update all occurences of\n\tflexvistemplate (should be mostly file names) and FlexVisTemplate (class names).\n\t\n\tAfter you have done this you can verify that everything is working using the debuger. Set your \n\tnew as file as the default executable, set a break point in the draw function after data import and \n\tcompile and run in debug mode.\n\t\n6. List of Dependencies (Track Versions Here as we update)\n\tcorelib.swc\n\t\thttp://code.google.com/p/as3corelib/\n\tflare.swc\n\t\thttp://flare.prefuse.org/\n\tcom.clevr.*\n\t\thttp://clevrlib.riaforge.org/\n\tFlexUnit.swc (Not currentley used?)","funding_links":[],"categories":["Multimedia"],"sub_categories":["Data Visualization"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fryanbressler%2FLichen","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fryanbressler%2FLichen","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fryanbressler%2FLichen/lists"}