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Welcome to the home of the Moorea Biocode LIMS (Laboratory Information Management) Software. The Biocode software comprises everything you need to manage your lab and sequence analysis workflows. This wiki serves both as a repository for the plugins themselves (with release notes and links to downloads), and an extensive online manual. You can download the plugin by following the Getting Started instructions in the green section on the right. If you run into trouble, or want to unlock the full power of the LIMS, read through the blue manual section on the right hand side. See www.mooreabiocode.org for details of the Moorea Biocode Project.
The Biocode plugins are complex, and while learning how to use them can seem like a daunting task, help is available. Your first port of call should be the introduction video, which walks you through the plugins. You can find a more detailed reference in the manual (available on the right of this page), and a list of frequently asked questions below.
A user community, and technical support is available from http://connect.barcodeoflife.org/group/lims
Here, you can engage with the wider community, get help from experienced users, and make suggestions about how to improve the plugins.
If you have and questions or suggestions that you don't want to post to the community, you can email [email protected]
By downloading and installing these plugins, you agree to the terms of use
All releases of the LIMS plugin can be downloaded from:
For the Genbank Submission Plugin, please visit
If you want to use the LIMS plugin with a MySQL database, you will need the the following database creation script.
Version 11.0 (Current): http://assets.geneious.com/plugins/biocode/labbench_11.0_mysql.sql
If you have been using the previous version of the plugin with a MySQL database, you may need to upgrade it. If the plugin tells you that your database version is out of date, then you can upgrade it with the following database upgrade scripts.
The scripts must be executed in order. Start at the version which mentions your current database version. For example if you are running version 9, then you only need to run upgrade_9_mysql.sql. If you need help, please contact [email protected].
http://assets.geneious.com/plugins/biocode/upgrade_9.1_mysql.sql
http://assets.geneious.com/plugins/biocode/upgrade_9_mysql.sql
http://assets.geneious.com/plugins/biocode/upgrade_8_mysql.sql
If you have been using either the 2.9.x beta or the 2.99.x beta versions then you may have already been using the latest schema and can set the correct version number by running: http://assets.geneious.com/plugins/biocode/upgrade_9.2_sqlite.sql
If you have problems or are unsure, please contact [email protected]
- Key Concepts - Key concepts that you need to know before using the biocode plugin.
- Workflows - It is important that you understand how workflows work before entering data.
- Entering Data - How to enter data into the LIMS, from your first plate through to cherry picking failed reactions for a second try.
- Searching- How to intelligently search your data in the LIMS
- Collating Workflows - Workflows can be combined into summary views for project managers and troubleshooters.
- Printing- All views of the LIMS data are fully printable. This section explains how to get the most out of printing.
- Export - The biocode plugin supports exporting plates and summary views to excel, as well as a selection of other formats.
- Assembly Workflow - A flow diagram describing the full assembly workflow.
- Importing Trace Data - How to get your trace data into Geneious.
- Binning - Group your traces/contigs based on overall quality to speed up the assembly workflow, and quickly identify problem sequences.
- Trimming - Trim low quality data and primers from the ends of your sequences.
- Mark as Pass/Fail - Mark sequences as having passed or failed in the LIMS
- [Assembly] - Assembling the prepared reads into contigs.