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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 for details of the Moorea Biocode Project.

Getting Started

You will need to download two files, in addition to Geneious in order to use the Biocode plugin.

Plugin icons.png
  • The Biocode plugin itself
  • The Biocode Genbank Submission plugin, which allows you to submit your completed contigs to Genbank.


You can download Geneious from

See Getting Started for detailed instructions on how to install and configure the plugins in Geneious.

Getting Help

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

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


Frequently asked questions will appear here shortly.


Biocode Plugin 2.8.9 - 8 June 2015

  • Fixed a bug that prevented the creation of PCR plates from existing 8 strip extraction plates.
  • Fixed a problem preventing the use of the same extraction within PCR or cycle sequencing plates.
  • Other minor fixes.

Biocode Plugin 2.8.8 - 2 March 2015

  • The LIMS now actively tries to prevent duplicate extraction barcodes. It will ask if extractions should be moved if duplicates are detected.
  • LIMS data will now be annotated with sequencing primers in addition to PCR primers if using GenBank Submission plugin v1.5.0 or greater.
  • Cherry picking an extraction plate will now correctly set the previous plate and well fields.
  • Fixed an issue where plates with errors could still be saved.
  • Fixed crash that would occur when changing columns in Primer Overview table.
  • Fixed a bug that would cause all plates with no workflows to be returned in addition to normal search results when searching solely on FIMS fields.
  • Fixed a problem where 8-strip plates would be displayed with incorrect well numbers in some views.
  • Fixed a problem where annotating an assembly would prevent generation of a consensus with quality scores.
  • Removed the ability to move extraction reactions via the reaction editor invoked from the workflow document viewer.
  • Other minor fixes and improvements.

Biocode Plugin 2.8.7 - 14 January 2015

  • Added modifications in response to upcoming changes that will be made to the Biocode FIMS REST service.
  • Added the handling of the presence of duplicate document fields in the FIMS.
  • Fixed slow trace downloads from plates without workflows.
  • Other improvements and fixes.

Biocode Plugin 2.8.6 - 12 December 2014

  • Fixed a bug that caused Geneious to crash trying to index sequences or traces that had been downloaded or annotated while using the new Biocode FIMS.

Note: Documents that have already been annotated with 2.8.5 will need to be re-annotated with 2.8.6 to avoid these errors from occurring.

Biocode Plugin 2.8.5 - 8 December 2014

  • Added cytB to the example loci list.
  • Fixed a bug where taxonomy fields that are below the species field on the connection options were not being incorporated into the values of annotated taxonomy fields.
  • Fixed a bug where the reporting module could not copy records from FIMS into MySQL based LIMS.
  • Other minor fixes.

Biocode Plugin 2.8.4 - 20 November 2014

  • Remove development changes that were accidentally included in 2.8.3.

Biocode Plugin 2.8.3 - 19 November 2014

  • Add the ability to bulk add traces to plates of any size.
  • Provide more information for connection errors.

This version was accidentally released with some development changes included. The plugin requires a database schema from the beta version (2.99.x). This schema is still compatible with the release version and there will have been no data loss caused by applying it.

However since the development changes have not yet undergone our normal testing process, it is advised that all users use 2.8.4 instead of this release as it may contain undiscovered bugs and instability.

Biocode Plugin 2.8.2 - 28 October 2014

  • Fixed a bug that was causing the Sequencing Primer document note to sometimes not show up on downloaded sequences.
  • Fixed a bug where traces downloaded directly from the plate viewer would not be annotated with FIMS information.
  • Fixed a bug that caused the FIMS plate to be set as the Sequencing Plate when annotating assemblies using the FIMS.
  • Other minor fixes and improvements.

Biocode Plugin 2.8.1 - 23 September 2014

  • Made 'Forward Plate' and 'Reverse Plate' fields on assembled sequences support more than one value.
  • Fixed a bug where workflows were being added to search results when downloading sequences
  • Made the 'Mark as Passed' operation work even when links to the original chromatogram documents has been lost.
  • Fixed a problem where a background maintenance task would fail when using the Built-in MySQL LIMS.
  • Other minor fixes and improvements.

Biocode Plugin 2.8.0 - 19 August 2014

  • Added '# Passed' and '# Sequences' fields to cycle sequencing plate views.
  • Added 'Forward Plate' and 'Reverse Plate' fields to assembled sequences.
  • Annotate from FIMS/LIMS now works with any FIMS field in addition to well number.
  • Added extraction barcode as a displayable field on all plate types.
  • Improved performance when using the Biocode FIMS.
  • Fixed a bug where the # Traces field would not be populated in the Tabular Plate View.
  • Fixed a bug where searching the Moorea FIMS on Collection Date could return additional results.
  • Other minor fixes and improvements.

See the Release Notes for details on previous releases


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.


Viewing And Editing Contigs - How to make base calls, edit gaps etc.

Alignment Of Consensus Sequences - Directly compare your contigs by aligning their consensus sequences.

Verify Taxonomy And Loci - Use BLAST to check the taxonomy of your sequences.


Collating Workflows - Workflows can be combined into summary views for project managers and troubleshooters.

Generating Reports Charts - Tabular reports and charts can be generated from field and lab data.


Preparing your documents for submission - Make sure your sequences are correctly annotated.

Genbank Submission - Submit your sequences.

Mark as Submitted - Mark your sequences as being submitted in the LIMS.