The Intro Wizard

The first time you start Bio::POD, a default profile is in place so you are not required to go through the Intro Wizard. If you are presented with the Intro Wizard the first time you run Bio::POD, then the default profile could not be initialized on your system.

The Intro Wizard allows you to quickly and easily select new datasources and modify your preferences. To start the Intro Wizard, simply choose "Options > Intro Wizard..." as pictured here:

The Intro Wizard will take you through the following 6 steps:

Step 1:

This is simply a welcome page. Click "Next" to continue with the wizard.

Step 2:

With this screen, you will add a data source and test that it is working properly. Click "Add..." to continue.

If there are no options to choose from, then you need to download genomic data source plugins. See Step 3 of the Installation instructions.

Select "Ensembl" from the Data Source options. Enter the values for your own local mirror of ensembl or use the default options:

hostname: ensembldb.ensembl.org
port: 3306
username: anonymous
password: <blank>

Click "Ok".

Once you have chosen Ensembl as your data source, you must add two necessary drivers: ensembl and mysql. These two files should have been downloaded to the "lib" directory in your Bio::POD installation directory as part of your installation instructions and are probably named "ensj-<number>.jar" and "mysql-connector-java-<version>-bin.jar". Use the "Browse..." buttons to select the files. If you cannot locate these files, double-check your installation instructions or contact Bio::Neos for further technical support.

Once you have added the two drivers, click "Test All...". If everything is setup correctly the Test column will switch from "?" to "P" for passed.

Step 3:

In this step, you may add annotation data sources in the same way that you added genomic data sources in the previous step. If you do not add any annotation data sources, Bio::POD will work but you will not see any annotation (such as domains, SNPs, secondary structures, etc.). If you'd like to add annotation data sources but no options are available, then you need to download the plugins as described in Step 3 of the Installation instructions.

Step 4:

In this step, you have the option to modify the default parameters of the PAR algorithm. For more details on PAR, visit the "Prioritized Screening" help page.

Advanced: The "PAR Window Size" value is a key parameter to the PAR algorithm that determines the number of nucleotides over which an integration is performed. A larger value will cause the algorithm to include a larger surrounding region when determining the PAR value for a certain nucleotide. If you are not sure about changing the value, leave it at 150.

You may also wish to change the way regions are displayed. We recommend you use the "By regions" method as the range of values returned by PAR can vary greatly...making it difficult to choose a meaningful threshold value.

The "Number of Regions" dictates how many suggestion screening locations will be displayed. Setting this to one will display the single best region to start screening. Setting this to two will display the top two best, and so on...

The "Size of Regions" is the maximum width, in nucleotides, of a suggested screening area. If you typically design amplimers to span a larger or smaller region than this, you may wish to change the default value accordingly.

Step 5:

In this step, you have the option of changing annotation-specific options that affect how annotation is displayed and included in the PAR algorithm.

If desired, select the annotation type from the drop-down box. You may change the display name (how it is displayed in the program), whether it is displayed in Full, Small, or Hidden mode by default. See Understanding Annotation for more on these modes. And finally, you may choose whether or not this type of annotation is included in the PAR algorithm and override the default weight parameters for the annotation.

Once you are done, click "Next".

Step 6:

The final screen summarizes the options you have chosen as part of the Intro Wizard setup. If you are satisfied with the options, click "Finish". Otherwise, you may go back with the "Previous" button and make changes.

This concludes the use of the Intro Wizard. After clicking Finish, the main Bio::POD program will appear. To understand what to do next, you may wish to view the help documentation on Loading a Gene.