Difference between revisions of "Main Page"

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The schema upgrade script can be found at http://software.mooreabiocode.org/index.php?title=Download
The schema upgrade script can be found at http://software.mooreabiocode.org/index.php?title=Download
'''Biocode Plugin 2.8.12 - Privately released '''
* Updated to work with 2016 New Biocode FIMS changes
'''Biocode Plugin 2.8.11 - 4 September 2015'''
* Fixed a crash that occurs when viewing the Reporting service in Geneious 8.1 or later.
* Fixed a crash that occurs when using the Bulk Editor to fetch PCR or Cycle Sequencing reactions from extraction barcodes.
* Fixed an error that prevented the use of compound queries that searched across both FIMS and LIMS fields.
* Changed default Moorea FIMS connection URL to gall.bnhm.berkeley.edu from darwin.berkeley.edu.
'''Biocode Plugin 2.8.10'''
Beta release of 2.8.11.
'''Biocode Plugin 2.8.9 - 8 June 2015'''<br>
* 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'''<br>
* 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'''<br>
* 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'''<br>
* 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'''<br>
* 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'''<br>
* Remove development changes that were accidentally included in 2.8.3.
'''Biocode Plugin 2.8.3 - 19 November 2014'''<br>
* 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'''<br>
* 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'''<br>
* 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'''<br>
* 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''
''See the [[Release Notes]] for details on previous releases''

Revision as of 04:52, 22 September 2017

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.

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 http://www.geneious.com.

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 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 support@mooreabiocode.org


Frequently asked questions will appear here shortly.


Biocode Plugin 3.0.4 - 11 September 2017

  • Fixed problem where the Biocode FIMS only retrieved field definitions from the Barcode of Wildlife project instead of the project that was specified. This would result in empty tissue fields

Biocode Plugin 3.0.3 - 21 August 2017

  • Updated for Biocode FIMS query system upgrades
  • Added the ability to use "match any" when searching the Biocode FIMS
  • Fixed a problem where users were not re-authenticated with the Biocode FIMS unless they clicked 'Authenticate'
  • Added support for more delimiters when loading barcodes from a file: tab, ";", ",", space, "-", "_"
  • Fix a rare crash that can occur when connecting to a MySQL FIMS or LIMS

Biocode Plugin 3.0.2 - 7 December 2016

  • Added Country (GenBank) and Lat/Long (GenBank) fields for use with submission to GenBank
  • Fixed column width in plate bulk editor when running on Windows with a HiDPI display
  • Fixed a crash that occurs when connecting to a Google Fusion Tables account that has no fusion tables
  • Fixed a crash when running Verify Taxonomy with Geneious R10

Biocode Plugin 3.0.1 - 15 September 2016

  • Fixed a crash that occurred when saving a display template that did not have a chosen "label wells by" field
  • Fixed bug that caused "Mark as Submitted in LIMS" to incorrectly say sequence did not exist

Biocode Plugin 3.0.0 - 9 June 2016

  • 'BOLD Trace submission': New function to create packages for submission of traces to BOLD.
  • Added the ability to create extraction plates from tissue documents.
  • Search performance improvements.
  • Faster download of sequences. Download of workflow documents is no longer required when downloading sequences.
  • The # Traces, # Sequences, # Passed Sequences and Sequence Progress fields now show up for workflow documents.
  • Added an operation to the plate bulk editor that allows for the importing of extraction barcodes from FIMS.
  • Added the ability to export tables to .xls, .csv and .tsv.
  • Increased the maximum number of individual reactions from 26 to 30.
  • Added advanded option to New Plate operation for copying reactions to a custom plate format (individual reactions only)
  • Added new Gel Quantification reaction type
  • Download Traces from LIMS can now work on a selection of passed sequences
  • Download Traces from LIMS can now re-assemble traces to selected sequences
  • You can now search for reference assemblies of traces to passed sequences in the Biocode service.
  • Many other bug fixes and improvements.

Additional Notes This version includes an update to the LIMS database format. This version is not compatible with older versions of the LIMS plugin. All users of the database will need to update the LIMS plugin to the latest version.

  • Built-in MySQL users will be upgraded automatically.
  • Remote MySQL users will need their database administrator to upgrade their database before using this version of the plugin.

The schema upgrade script can be found at http://software.mooreabiocode.org/index.php?title=Download

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.