Key Concepts

These are the key concepts which you should understand before beginning to use the biocode software.

There are four components to the Biocode software:

• The Field Database (FIMS) – This stores information relating to field work (e.g. specimen records, collecting events etc). The Biocode plugin does not contain a FIMS database, but rather links to a FIMS database of your choosing (see Getting Started).
• The Lab Database (LIMS) – This stores data relating to lab work (e.g. reaction records, plates, etc). It links to data from the Field Database
• The Assembler Component – This automates the process of assembling your reads, as well as providing useful tools for troubleshooting and analysis. It links to data from both the Field Database and the Lab Database.
• Genbank Submission - This automates the process of submitting your sequences to Genbank. It combines metadata from the FIMS database with reaction information from the LIMS database to generate a submission.

Reactions are connected in two ways in the LIMS:

• Plates – You create reactions in plates, which simply groups reactions together in the same way they are in the lab. This grouping represents either physical plates, or a group of reactions run at the same time.
• Workflows – Reactions are also linked by workflows. A workflow represents the work done in the lab on one extraction, for a particular locus. It links together a number of reactions carried out at different times, but on the same extraction, and so has information about different PCR reactions tried, what passed and failed etc. See Workflows.

Note: Although a workflow is intended to link all the reactions for a single locus, you can create more than one workflow per locus (for example if two researchers are working independently on the same locus and the same tissue sample).