Getting Started

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What you need to get started

The first thing you will need to do, is download Geneious. It is available from The Biomatters Website. To run the biocode software, you currently need Geneious 6.1.1.

The Biocode LIMS software comes as two plugins for Geneious. You can download these files from the download page.

To install the plugins, just drag them into Geneious. You will see three new icons appear - two in the toolbar and one in the service tree: New toolbar.png New service.png

Logging In/Setting up Databases

The Biocode plugin login screen

To log in, right click on the Biocode icon in the service tree, and click "Log in" to display the biocode login screen. You can create a number of connections (which are visible on the left hand side of the connection window). To connect to a saved connection, select it in the list, and click Connect. If you are connecting for the first time, click the Add Button in the bottom left corner of the window to create a new connection.

Creating a new Connection

Each Connection has two sections - one for FIMS and one for LIMS.

You can connect to one of five types of FIMS, and two types of LIMS databases


  • TAPIR FIMS - This is most useful for groups who want to store their lab information in a single FIMS, or for collaborative projects. The TAPIR FIMS will read tissue data from a TAPIR server.

The following table-based FIMS connections allow you to specify your own data structure:

  • MySQL FIMS - This is most useful for groups of users who have an existing FIMS system backed by a MySQL database, but do not want to set up a TAPIR server. Geneious will read the data directly from the database.
  • Google Fusion Tables FIMS - This is most useful for groups of users who want to access their FIMS data remotely, and do not already have a compatible way of storing it.
  • EXCEL FIMS - This is most useful for single users, or people who cannot set up a TAPIR server. The EXCEL FIMS will read tissue data in from an excel sheet.


  • Remote LIMS - The plugin will store your lab workflows on a remote MySQL server. This is the best option for labs, or collaborative projects.
  • Local LIMS - The plugin will store your lab workflows on your local machine. This is intended for single users.