Release Notes

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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

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 2.8.9 - 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.

Warning

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.

Additional Notes This version will apply a schema fix to MySQL LIMS databases which may take anywhere between a minute and an hour to perform. The amount of time depends on the number of traces stored in the database. If your database has over 30,000 traces then it is recommended that an administrator perform it beforehand. Contact support@mooreabiocode.org for instructions.

Biocode Plugin 2.7.1 - 18 July 2014

  • Fixed a problem where seqeunces could be downloaded without annotated FIMS data.
  • Fixed a crash that happens when trying to view/edit traces when a cyclesequencing reaction has no existing traces.
  • Fixed a problem where a local LIMS database wouldn't be closed until Geneious was shutdown.
  • Fixed a bug where traces could not be added or removed from reactions using the traces editor.
  • Other minor fixes and improvements.

Biocode Plugin 2.7.0 - 27 June 2014

  • Enable cherry-picking from extraction plates.
  • The MySQL JDBC driver is now bundled with the plugin.
  • Fixed issues with template system occasionally not saving or displaying templates correctly.
  • Fix incorrect cyclesequencing cocktail calculations.
  • Other minor fixes and improvements.

Biocode Plugin 2.6.4 - 20 May 2014

  • Plate bulk editor now starts at the top rather than the bottom.
  • Changed date search conditions "Less/Greater Than" to "Before/After".
  • Replaced Last Modified (LIMS) search field with Sequencing Pass/Fail Date and Extraction Date search fields.
  • Fixed bug that was causing date searches to be off by one day.
  • Fix searching issues with Biocode FIMS connector.
  • Other minor fixes and improvements.

Biocode Plugin 2.6.2 - 24 April 2014

Biocode Plugin 2.6.0 - 14 April 2014

  • Improved LIMS search performance.
  • Greatly improved memory usage and search performance when searching on FIMS fields.
  • Fix a bug that was causing failed sequences to not be returned from searches.
  • Fix a bug that was causing reactions that had no associated workflow to be missing from plate searches.
  • Fix a bug that disabled the clean up method field.
  • Fix a bug that prevented traces or sequences from being deleted from plates.
  • Other minor fixes and improvements.

Biocode Plugin 2.5.3 - 7 January 2014

  • Annotate from FIMS/LIMS can now use the annotated workflow name in addition to the annotated plate/well.
  • Improved plate bulk editor. Changed wells are now highlighted. Pasting doesn't shift existing wells down. Pressing Enter at the end of a line no longer inserts a new row.
  • Export of original chromatograms can now be done when selecting assemblies or consensus sequences.
  • Fixed a bug that could cause all chromatograms to be unannotated if there was an empty row in an Excel FIMS.
  • Lists of FIMS fields are now sorted.
  • Old FIMS fields from MySQL and older Excel connections are now detected when annotating from FIMS/LIMS and can be removed.
  • A text filter can now be used when bulk adding traces to sequencing plates.
  • Added # Traces field to the display options in the plate view.
  • Added 2 new failure reason fields for marking sequencing results as fail. These can be configured in the database.
  • Sequencing results now belong to a specific reaction rather than a workflow.
  • Other minor fixes and improvements.

Additional Notes

  • The minimum required version of Geneious is now 6.1.1.
  • This version includes an update to the LIMS database format. 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.

Biocode Plugin 2.4.5 - 7 October 2013

  • Fixed compatibility with Geneious R7.
  • Fixed a problem with advanced searches returning all plates without workflows in addition to search results.
  • Other minor fixes and improvements.

Biocode Plugin 2.4.4 - 13 September 2013

  • Bulk adding traces now displays problems found after completing the batch rather than stopping immediately.
  • Fix crash when search results contain plates with no reactions.
  • Fix crash when there are no search results.
  • Fix workflow documents missing reactions when searching by plate field.
  • Other minor bug fixes.

Biocode Plugin 2.4.3 - 2 September 2013

  • Much faster searching
  • Support for ABCD schema when using a Tapir FIMS connection
  • Support for working with consensus sequences when marking as pass/fail
  • Fixed crashes related to use of new Google Fusion Tables API
  • Fixed a crash that could occur when copying FIMS values to LIMS if they exceeded 128 characters.
  • Fixed a crash that would happen when connecting to a MySQL LIMS with a Tapir FIMS
  • Numerous small fixes and improvements

Biocode Plugin 2.4.2 - 27 August 2013

This release consisted of the wrong build and therefore included the following partial developments.

  • Support for ABCD schema when using a Tapir FIMS connection
  • Fixed crashes related to use of new Google Fusion Tables API
  • Fixed a crash that could occur when copying FIMS values to LIMS if they exceeded 128 characters.

Biocode Plugin 2.4.1 - 21 January 2013

  • Fixed a crash that could occur when connecting to a FIMS
  • Fixed a crash that could happen when copying FIMS to LIMS
  • Fixed a crash that could occur if users chose a numerical column for a taxonomy field

Biocode Plugin 2.4.0 - 19 December 2012

  • Added support for new Fusion Tables API
  • Improved handling of excel files
  • Numerous small fixes and improvements

Biocode Plugin 2.3.2 - 8 February 2012

  • Fixed a crash bug in verify taxonomy
  • Fixed an issue where the plugin could log users out under certain conditions
  • Improved support for non standard well names in bulk loading operations
  • Numerous small fixes and improvements

Biocode Plugin 2.3 - 22 December 2011

  • Added a reporting and charting module
  • Added support for strip reactions
  • Made improvements to the login interface
  • Added support for specimen photos stored on flickr
  • Added a tabular view and printout for plate documents
  • Numerous small fixes and improvements


Biocode Plugin 2.2 - 16 August 2011

This is a maintenance release, bringing many small usability tweaks and bug fixes, as well as improving performance.

  • Improved cherry picking documents - they now display all FIMS fields (e.g. taxonomy) associated with each reaction
  • Adding traces to reactions no longer requires delete permissions on remote LIMS databases
  • Added the ability to delete cocktails and thermocycles
  • Improved options for bulk adding traces
  • Improved performance creating plates
  • More informative error messages if the user does not have delete permissions

Numerous other fixes and usability improvements


Biocode Plugin 2.1 - 13 May 2011

Interoperability We have improved the ability for LIMS users to collaborate. If you are a medium sized lab with no existing field management system, you can upload your specimen data to Google Fusion Tables, and access your data directly in the plugin. If you have an existing system based on MySql, then you can connect the plugin directly to your database. We have also added the ability to save sequence and assembly binning parameters as profiles in Genieous, and share them with your colleagues.

Workflow Streamlining We've made a lot of small tweaks to the assembly workflow to make it easier (and faster) to bulk process sequences. You can assemble to a curated reference sequence database (which removes the need to trim before the assembly step, and the need to verify taxonomy after), and the addition of the "number of ambiguities in consensus" binning parameter makes processing assembly binning much faster (Geneious makes obvious calls on disagreements itself, and leaves just the ambiguous ones up to the technician).

Detailed list of changes:

  • Added a connection manager - save and choose multiple accounts, connect automatically on startup
  • Added support for FIMS databases stored in Google Fusion Tables
  • Added support for FIMS databases stored in MySQL
  • Summary table views of workflows now contain taxonomy fields - right click on the table headers to choose them
  • Added a tabular view for plates - select a plate and click "Tabular plate view"
  • You are now required to specify a locus when creating workflows
  • Added a button to export primers in the LIMS to your local database - edit a reaction on a plate to see it
  • Added the ability to zoom in plate views
  • You can now mark as pass/failed in LIMS from consensus alignments - select the sequences you want to mark within the alignment
  • Added a new "Run" reaction state to PCR and sequencing reactions
  • New sample loci for reactions
  • It is now easier to change the locus of existing plates using the bulk editor
  • Added a 'mark as submitted' action to sequences

Numerous other fixes and usability improvements