multiMiR-db

Database and server code to support the multiMiR R package.

This contains two seperate components which include code(html,cgi) for the web-server and R code to load data from the source files into an SQL Database(MySQL).

The data from the 14 supported databases is not packaged with the multiMiR R package due to its size. Instead the R package submits an SQL query to the server which performs the database query and returns results. The code to accomplish this on the server is in the cgi folder. The code to build database tables from the source files is in the database folder. The R package does allow you to change the URL of the server for requests so it is relatively easy to use the R package on your own server.

Why might you want to use this code?

• Unsuported Organisms - you could modify the code to support additional organisms
• Improved performance - if the server is not performing adequately you can create a mirror that should in most cases perform better. If you experience problems with our server performance please let us know.

Database code

R code to process the initial files available from each datasource and load into the MySQL database is provided. You can run these individually or all at once.

• additional details

Server code

The cgi script is required to allow requests. Configure using documentation for your web server. Note you will need to edit multimir_univ.pl with your database connection details. The html is not nessecary for the package to function, but the html folder of the webserver will need to contain the cutoff files generated at the end of loading the database.

Steps to setup a server

1. Install a Web Server(Apache recommended).
2. Setup a database server(MySQL recommeded).
3. Run database code to setup/load database tables.
4. Setup and test the cgi and cutoff files(edit db connection details etc).
5. Setup R package and change the URL to point to your server.