Connecting with the Geneious Biocode Plugin

BWP Biocode Plugin connection details

Install the latest version of the Biocode Plug-in. Check the Updates section of the Home Page to see the latest version available. If you do not have the latest version, then follow the instructions in the Geneious plugins section of the previous page.

Once the Biocode plugin has been successfully installed, you can now connect by right-clicking on the Biocode icon in the Sources panel and click “Login”.

_images/biocode_login.png

This will open the Biocode Connections window that looks like this:

_images/biocode_connection_details_empty.png

Connection Name and Method

Enter a value in the Connection Name so that the plug-in saves this information.

Field Database Connection

In the Field Database Connection section, select “Biocode FIMS” from the dropdown.

_images/biocode_fims_options.png

This will auto-fill the Host box with “http://www.biscicol.org:80” however this needs to be replaced with “http://www.biscicol.org/”. Enter the FIMS Username and Password that Mike Trizna assigned to you. Make sure to click the “Save” box, and then the “Authenticate” button to ensure you can connect to FIMS.

After authenticating, the Project drop-down will now be populated with only the FIMS projects that you have access to. Choose “SI Barcoding CBOL”.

Tissue ID field
For “Tissue ID field”, select “tissueID”.
Specimen ID field
For “Specimen ID field”, select “voucherID”.

Make sure to check the box next to “The FIMS database contains plate information”.

Plate name field
For “Plate name field”, select “extractionPlateID”.
Well field
For “Well field”, select “extractionWell”.

Finally, click the “Autodetect” button to automatically populate the different taxonomy fields.

The completed Field Database Connection should look like this:

_images/SIBN_biocode_connection_details_fims.png

LIMS Database Connection

In the LIMS Location section, start out by selecting “Remote MySQL Database” from the dropdown.

Server Address
For “Server Address”, copy and paste in “nmnh-lims.si.edu”.
Port
For “Port”, make sure it is set to “3,306”.
Database Name
For “Database Name”, enter “lims”.
Username and Password
Finally, for the “Username” and “Password” boxes, enter the LIMS database Username and Password that John Keltner assigned to you via email.

Make sure that the checkbox next to “Save” is selected.

Your fully-completed Biocode Connection window should look like this:

_images/biocode_connection_details_completed.png