Designing protocols - 9.3 - Editing assets

To add any asset other than a well array, click the ‘+’ icon on the Assets area, and select the item you want from the pop up menu.

Check ‘Available Deck Locations’ on the Status bar to make sure you are not adding more plates than there are deck locations. Reservoirs, the shaker module and the thermal modules do not take up deck locations.

If you need to use more plates, create user interaction steps to remove used items and add new ones at an appropriate point later in the protocol.

To delete any asset including a well array, select it and then click the bin icon for the Assets area.

Check the Errors (see section 9.5.7) list on the right of the screen in case deleting the asset has caused a problem in the loaded protocol.

9.3.1 Editing well arrays

To adjust the wells used in a well array, use the ‘Wells’ section of Properties, identifying your selection by rows and columns i.e. A1:E7.

If you increase the number of wells, check that you still have sufficient volume of reagents, and sufficient tips loaded.

If you are using an array of 96 tips to pipette between a 96 well plate and 384 well plate, a tiling pattern can be used to define the well array asset for the 384 well plate. In this way a single quadrant of the 384 well plate can be defined as a well array asset.

Array

9.3.2 Editing lids

You can either load plates which are lidded or load lids ready for use in a later protocol step.  

When you remove a lid it will be placed in an empty deck location, so every time you place a lid on a plate you will free up a deck location.

Check 'Available Deck Locations' on the Status bar to check you have enough free space, as you use lids and plates. If you need to use more lids, create user interaction steps to remove used items and add new ones at an appropriate point later in the protocol.  

When placing a lid on a plate, you are creating a stack. You can only use combinations of lids and plates which have a stack definition. Use Community to download stack definitions. If you cannot find what you need, contact reliance. You can continue designing with an undefined stack but you cannot run the protocol. 

firefly software will warn you if you try to use a dispensing or pipetting step without removing a plate's lid first.  

IMPORTANT: If you use Auto Deck Fill when you have an undefined stack in your protocol, collision detection would work based on the wrong stack definition so shouldn’t be trusted until this error is removed. 

Download the stack definition before using Auto Deck Fill. 

9.3.3 Editing tip sets

You will need to load sufficient tip sets for the quantity of tips you will use. Check the Errors list to see if you need to adjust the quantities. As tip sets can only be loaded on the lower deck, you may not be able to load all the tips you will need at the start of the protocol. Remove used tip sets and replenish tips in a user interaction step, ensuring that the tip type of the fresh tips matches those of the tips that have been removed.

9.3.4 Designing a scalable protocol

You can make your protocol scalable by using a variable size well array, number of strip tips or volume of reagents in each reservoir.

Scaling columns and strip tips usage

1. Select the Variables tab and create a column variable with an initial value, as shown. If variables are used in an existing protocol, they are shown with the variable name in white on a green background.

2. Select the ‘fx’ button on the tip set properties to open the Expression Builder (Strips)

3. Create an expression which replaces a fixed number of strip tips with your variable. This can be very simple, like the example shown above which just sets the number of strip tips used to match the number of well array columns.

Your variable now appears in the Strips property for the tip set.

Scaling well arrays

1. Select the ‘fx’ button on the well array properties to open the Expression Builder (Wells)

2. Create an expression which replaces fixed values in a well array with your variables. This can be very simple, like the example shown above which just allows you to vary the number of columns when running the protocol.

Your variable now appears in the Wells property for the well array.

Scaling starting volumes

Select the ‘fx’ button on the reservoir properties to open the Expression Builder (Starting Volume)

Create an expression which replaces a fixed value for the Starting Volume in a reservoir.

Click ‘OK’ and your variable now appears in the Starting Volume property for the reservoir.

Scaling dispense or aspirate volumes

Select the 'fx' button on the Volume property to open the Expression Builder (Volume). 

Create an expression which replaces a fixed value for the aspirate or dispense step volume.

Click 'OK' and your variable now appears in the appropriate property for the reservoir.

9.3.5 Editing reservoirs

When editing the reagents to be dispensed in a protocol, you will need to define Reservoirs for the materials.

Use Properties to increase or decrease the volume: you may find it more convenient to use multiple reservoirs for the same material if you are dispensing to a large quantity of wells, as parallel dispensing is faster. However, you will need more of your reagent, as you will always need the same additional volumes for the excess aspirate volume in the syringe and for the dead volume in the reservoir, irrespective of your dispense volume.

To add a new reagent, you will need to add a new Reservoirs Asset, then use the Reservoirs Property to select which Reservoir to use.

If you select a reservoir which had been in use, it will be reassigned and you will generate an error that the previous reagent is no longer loaded.

Color coding your materials will make it easier to keep track of what is in use, particularly in long protocols.

The Assets shown above includes two reagents in reservoirs, the first uses two, the second uses one.

9.3.5.1 Setting the required reservoir volume automatically

When you create a protocol step which aspirates from a reservoir, the feedback pane will warn you if there is insufficient reagent in the reservoir and calculate the volume required.

If you click 'set starting volume', the reservoir starting volume will be set to the correct value, provided the required volume is not more than the reservoir's capacity (in which case you would need to use additional reservoirs).

9.3.6 Editing magnetic blocks

Magnetic blocks are simple, passive devices which require no configuration. 

You can use multiple magnetic blocks in a protocol.

You can only use magnetic block types which you have already installed, so if you cannot see the one you want to use, you look in the ‘Community’, ‘Labware’ section and download it.

9.3.7 Editing risers

Risers are simple, passive devices which require no configuration. They are used to lift shallow
plates so that heads dispensing to them do not collide with taller labware in adjacent deck
locations.

You can use multiple risers in a protocol. There are specific types for upper and lower deck use.

You can only use riser types which you have already installed, so if you cannot see the one you
want to use, look in the 'Community', 'Labware' section and download it.

9.3.8 Editing thermal blocks

thermal blocks are used in conjunction with the plate thermal module, there are designs for use with 96 or 384 well plates.

After they have been heated or cooled to the required temperature while located on the plate thermal module, they can be moved with a plate to e.g. the dispense head, to keep the plate warm or cool for longer. 

You can use multiple thermal blocks simultaneously on firefly e.g. to cool both a source and destination plate.

Next Article - Designing protocols - 9.4 - Editing steps