Reactions are entered into the Lab Bench Database by plates. Plates come in a number of sizes: 48, 96, or 384 wells, and also in a grouping of any number of reactions. Creating a plate opens that plate in the plate viewer.
The Biocode Plugin places a New Reaction button on the Geneious main toolbar. Click it to begin creating a plate. You can choose from extraction, PCR, or cycle sequencing reactions, and can also choose the plate size (one of the three predefined sizes, or a number of individual reactions)
Creating a plate from an existing document
Geneious can use an existing plate as a guide for creating a new plate, so that the genetic material in each well of the new plate corresponds to the genetic material in the existing plate. To do this, select a plate document in Geneious, click New Reaction, and select the Create plate from existing document checkbox. If the reaction types are the same (for example, you're creating a PCR plate from a PCR plate), then all reaction parameters will be copied to the new plate. If the reaction type is different (for example, an Extraction to a PCR plate), then only the extraction id's will be copied across.
Converting between 96 and 384 well plates
It is possible to create a new 384 well plate from a group of 96 well plates, and to create a group of 96 well plates from a 384 well plate. Each 96 well plate corresponds to one quadrant in the 384 well plate (see below). To create a 384 well plate, select up to four 96 well plates in Geneious, and click New Reaction. Select the Create plate from existing document checkbox, and choose 384 well plate. A panel will appear at the bottom of the dialog which will allow you to choose to which quadrant each 96 well plate corresponds.
The Cherry Picking function allows you to select reactions from one or more plates, based on criteria that you specify (e.g. failed reactions, or genes of a particular taxonomy). You can use these selected reactions to create a new plate (or plates), or have them returned to you as a list. To perform Cherry Picking, select the plates containing the reactions you want to pick, and click on Cherry Picking in the Biocode toolbar menu. Choose your destination, and then choose the criteria to select your reactions.
The Plate Editor
The plate editor is a customizable viewer and editor for your plate documents. It is shown both when creating new plates, and when viewing existing plates in the database. You can select wells in the plate by dragging the mouse across the plate, or select a single well by clicking it. You can hold down the shift and ctrl (command on mac) keys to help you select wells. If you click the edit selected wells in the toolbar, you will only edit the wells you have selected.
You can select reactions in a plate by dragging a rectangle, or clicking individual wells. You can combine rectangles and wells by using the shift and ctrl (command on mac) keys. Click Edit Selected Wells to edit the currently selected wells. The edit dialog has a column of checkboxes on its left hand side. Values in the checked fields will be applied to all selected reactions, and unchecked fields will be left as they are. Most values can simply be entered into the dialog, with the exception of Primers and Cocktails, which require prior preparation.
The plate editor can display any number of fields from your FIMS or LIMS database. Click the Display Options button in the toolbar to open the display dialog.
The bulk-editor allows you to edit all the reactions in the plate at once by pasting in fields from an EXCEL file or similar.
To add traces to individual reactions in the plate view, open the reaction for editing (double click the reaction), and click Add/Edit Traces in the Edit Wells dialog. You can then click Add Sequences to add one or more sequences to the well. To remove one or more sequences from the well, select the sequences you want to remove, and click Remove Sequence(s). You can also import the sequences into Geneious as documents by clicking Import Sequence(s) into Geneious.
Bulk Adding traces
You can attach trace files to the wells of your sequencing plates. The traces can be downloaded into Geneious, and will have all FIMS and LIMS metadata preattached, ready for assembly (see Importing Trace Data).
To add traces when viewing a sequencing plate, click the Bulk Add Traces button on the viewer toolbar. The traces are matched to the appropriate well by field or well number, which are found the filename of the trace file. You also need to tell Geneious where to look in the filenames. For the example in the screenshot Match 2nd part of name, separated by Underscore, Geneious would find the well number in filenames such as 3726294_A01_capture.ab1.
You can attach GEL images to all types of plates. Click the Add/Remove GEL Image button in the plate editor toolbar, and click Add, then browse to the image file on your hard disk. You can also add notes to each GEL image. Geneious will accept images in JPEG, GIF, PNG, and TIFF formats.
You can split a GEL image, and attach the segments to each well by clicking the Split GEL button (located above the GEL image in the gel viewer window). GEL images are split into wells using a dragable grid, where each cell in the grid represents a well. Choose the number of rows and columns, the start row and column, and the direction of the wells in the grid, then drag your mouse on the image to create the grid. If you misplace the grid, you can start again by dragging the mouse. Click ok when done