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MBP-627 Release Biocode LIMS 3.0 & GenBank Submission 1.6.4
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| <PluginVersions> | ||
| <LatestVersion>2.8.9</LatestVersion> | ||
| <LatestVersionURL>http://assets.geneious.com/plugins/biocode/Biocode_2_8_9.gplugin</LatestVersionURL> | ||
| <ReleaseNotes>==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. | ||
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| ==Biocode Plugin 2.8.10== | ||
| Beta release of 2.8.11. | ||
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| ==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. | ||
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| ==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. | ||
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| ==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. | ||
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| ==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. | ||
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| ==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. | ||
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| ==Biocode Plugin 2.8.4 - 20 November 2014== | ||
| * Remove development changes that were accidentally included in 2.8.3. | ||
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| ==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. | ||
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| ==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. | ||
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| ==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. | ||
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| ==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. | ||
| <LatestVersion>3.0.0</LatestVersion> | ||
| <LatestVersionURL>http://assets.geneious.com/plugins/biocode/Biocode_3_0_0.gplugin</LatestVersionURL> | ||
| <ReleaseNotes>==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. | ||
| </ReleaseNotes> | ||
| <ExtraInformation> | ||
| Upgrading to 2.8.0 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 [email protected] for instructions. | ||
| 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. | ||
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| Downloading or annotating sequences or traces using 2.8.5 could cause problems for users of the new Biocode FIMS. | ||
| Users of this FIMS should update to 2.8.6 and re-annotate/re-download documents causing errors. | ||
| The schema upgrade script can be found at http://software.mooreabiocode.org/index.php?title=Download | ||
| </ExtraInformation> | ||
| </PluginVersions> |