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The new Biocode LIMS home can be found at https://github.com/biocodellc/biocode-lims/wiki


Releases can be found at https://github.com/biocodellc/biocode-lims/releases


LEGACY INSTRUCTIONS:

The following instructions were current for plugin releases prior to v3.0.4. For up to date instructions, please follow the links above. The instructions here are maintained in their current form to support older releases of the plugin. In addition, the documentation here contains images which have not yet been ported to the current documentation at the Github wiki site.


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. If you have and questions or suggestions that you don't want to post to the community, you can email support@mooreabiocode.org

LIMS

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

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.

Analysis

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.

Reporting

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.

Submission

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.