Getting Started

Related Topics: Frequently Asked Questions  |  Terminology  |  How Do I ..?  |  Schema Overview |  Contents

The following information is available to help you get up-to-speed with using maxdLoad.

Please note that this documentation is in the early stages of development and that much of it is very minimal or missing altogether. If you require assistance with any aspect of using this software, please contact maxd_info@cs.man.ac.uk.

• Creating a database
• Starting the application
• Connecting to a database
• Creating the database tables
• Getting accustomed to the user interface
• Modelling your experimental design
• Loading data by hand
• Loading data from a file
• Browsing and editing data

The first step in using maxdLoad is to create a new database into which the data will be loaded.

The procedure differs between the different database servers that are supported by maxdLoad but in general, the steps are:

1. If you have not already done so, you may have to create a new database user and set up suitable access permissions for that user. See your database server documentation for details on how to do this.

2. Connect to the database server using the console tool specific to that server, for example with MySQL the console tool is called mysql and with Oracle the tool is called sqlplus.

3. Create a new database by executing the SQL statement "CREATE DATABASE maxd;". The database name ('maxd' in this case) can be anything you want.

The maxdLoad application is written in Java and is distributed as an executable JAR file. This means that you do not have to unpack or do anything special to install it. Assuming that you have got the Java Runtime Environment successfully installed on your machine, then the application can be started by:

• Windows ® platforms:
     Double-clicking on the icon corresponding the JAR file

   

• Unix based systems (including Linux ® and Mac OS X ®):
     Running the command "java -jar maxdLoad.jar".

If everything goes according to plan then the licence agreement should appear in a new window. If you agree to the licensing conditions, press the "Accept" button and the application will start.

Once the application has started, the connection panel will be displayed. This panel is used to specify the parameters that tell maxdLoad how to connect to the database that you have created, see here for full details on how to provide this information.

After the connection parameters have been successfully specified, press the "Connect" button to establish a connection with the new database.

If the database is brand new, then the tables which will store the data need to be created. maxdLoad will notice that these tables do not exist and will offer to create them for you.

The "Create Database Tables" panel offers a variety of configuration settings, most of which can be left on their default settings. The only information that must be provided is:

• A descriptive name for the database which can be used by users to easily distinguish between different databases on a particular server.
• A string identify the location of the database, again for use by users who subsequently connect to this database.

More information on creating the database tables can be found here.

In particular, the way that panels 'stack up' on top of one another...

The most important step in creating a new microarray expression database is deciding how to represent your experiment within the constraints defined by the maxdLoad database schema.

Some aspects of the mapping from the real-world experimental design to the database representation are fairly trivial, for example the concept of Source (i.e. an organism from which samples can be taken) maps nicely onto the actual biological entities which are sources of material used in hybridisations. Other aspects will prove to be more complex and choosing the 'correct' representation will require a reasonable level of understanding of the maxdLoad schema.

More information on choosing an appropriate representation for your experimental design can be found here.

Using "Create" mode....

Using "Load" mode....

Using "Browse" and "Edit" modes....