http://mirmaid.org/ 2011-11-08T01:26:13+01:00 http://mirmaid.org/ http://mirmaid.org/lib/images/favicon.ico text/html 2011-11-07T00:22:23+01:00 Anders Jacobsen http://mirmaid.org/doku.php?id=start&rev=1320621743&do=diff miRMaid is data about microRNAs structured for easier access and integration, especially for computer-geeks * The core of miRMaid is the data contained in miRBase, which is the de facto accepted standard registry for microRNA information and nomenclature. * miRMaid takes miRbase data, reorganises it slightly and provides a programming interface to the data, which makes it much easier for the computer-savvy to perform complex data queries and analysis. * miRMaid is extendable, meaning t… text/html 2010-07-21T16:10:39+01:00 Anders Jacobsen http://mirmaid.org/doku.php?id=api_tutorial&rev=1279721439&do=diff There are two different ways of accessing the MirMaid programmatically * Use Ruby's ActiveRecord based models to access a local version of miRmaid on your own computer. For this you need a local installation of miRmaid. * Use the REST interface to query MiRMaid via the http-protocol. Most programming languages have standard REST client libraries. We demonstrate the REST-interface from a ruby and perl client. You can use this method without installing any miRmaid code or data on your local c… text/html 2010-06-14T09:58:50+01:00 Morten Lindow http://mirmaid.org/doku.php?id=plugins&rev=1276502330&do=diff The motivation for plugins in MirMaid The core of MirMaid is designed around data from the official miRNA registry, miRBase. But there are many other web sites and databases that provide unique and specialized information on miRNAs. Such data resources can be implemented as independent extensions to the core MirMaid framework. There are multiple benefits to such a strategy: text/html 2010-03-10T16:08:06+01:00 Morten Lindow http://mirmaid.org/doku.php?id=landgraf&rev=1268233686&do=diff Landgraf et al cloning data GitHub: <http://github.com/mortenlindow/mirmaid_landgraf> This plugin models adds data and appropiate model for miRNA cloning data reported by Landgraf et al. The data is downloaded from <http://www.microrna.org> text/html 2010-03-10T15:06:45+01:00 Morten Lindow http://mirmaid.org/doku.php?id=mir2disease&rev=1268230005&do=diff miR2Disease Homepage of the plugin: <http://github.com/andersjacobsen/mirmaid_mir2disease/>. This plugin is based on data from miR2Disease.org. miR2Disease is a manually curated database that aims at providing a comprehensive resource of miRNA deregulation in various human diseases. The plugin introduces two resources, m2d_diseases and m2d_disease_links. m2d_disease_links is a many-to-many map between the MirMaid mature miRNA resource and the diseases, m2d_disease. Once you have installed Mir… text/html 2010-03-01T20:14:33+01:00 Morten Lindow http://mirmaid.org/doku.php?id=install_quick&rev=1267470873&do=diff * Linux or Mac system with the following programs available on the command line: sed, wget and gunzip. These programs are available in most Linix distributions. * Ruby programming language (version 1.8.X), the RubyGems packaging system and Rake (Ruby 'make') - in Ubuntu: sudo apt-get install ruby ruby-dev rubygems and gem install rake. * One of the following database management systems: * Sqlite3 * PostgreSQL * MySQL