The Venus Worktable: Why You Build the Deck Before You Write a Single Step

The mistake almost every new Venus user makes

Open Hamilton Venus for the first time and the instinct is to head straight for the method editor, the panel where you drag and drop steps to build your protocol. This is understandable. The method editor is where the script lives. It looks like the place to start.

It isn't.

The first thing you build in Venus is the worktable. Everything else follows from it. A method that references sequences not defined on the worktable won't run. A method built on an incorrect worktable will run badly: wrong positions, wrong liquid volumes, wrong tip types, or a crash into labware the robot didn't know was there.

This article explains what the worktable is, what it contains, and why getting it right before writing a single method step is the most important practice in Venus scripting.

What the worktable is

The worktable is Venus's graphical representation of your physical STAR deck. It's a 2D overhead view that shows:

• The deck tracks (the numbered horizontal slots where carriers sit)
• The carriers loaded on those tracks (plate carriers, tip carriers, reagent carriers, active devices)
• The labware placed in those carriers (plates, tip racks, troughs, tubes)
• The sequences defined across all of that labware (the named lists of positions your method will address)

When you open the Deck Layout Editor in Venus, you're editing the worktable. Every item you place here, every carrier, every plate, every tip rack, creates the software model of the physical deck that your robot will operate against.

The method you write in the method editor doesn't talk directly to the hardware. It talks to the worktable. The worktable talks to the hardware. This is why the worktable must accurately represent reality before your method can do anything useful.

What goes on the worktable

Carriers

Carriers are the structural pieces that sit on the deck tracks. A plate carrier holds plates. A tip carrier holds tip racks. A reagent carrier holds troughs or reservoirs. Each carrier has a specific track width; a 6-track plate carrier takes up positions 1 to 6 on the deck, for example.

In the Deck Layout Editor, you drag carriers from the labware catalogue onto the correct deck track positions. The carrier must match the physical carrier on your instrument, not just in type but in specific variant. A Hamilton 5-position plate carrier (PLT_CAR_L5MD) has different dimensions and position offsets than a Hamilton plate carrier optimised for deep-well plates. Using the wrong carrier definition means every plate position it holds is defined incorrectly.

Identify the exact carrier type on your physical instrument (the part number is typically stamped on the carrier) and match it to the corresponding labware definition in Venus. Don't use the closest-looking option.

Labware

Once a carrier is on the worktable, you place labware into its positions. A plate definition goes into a plate carrier slot. A tip rack goes into a tip carrier slot. A trough goes into a reagent carrier slot.

Each labware definition specifies the geometry of that specific item: the number of wells, their X/Y positions relative to the labware origin, the well depth, the well shape (flat, round, V-bottom), and the maximum pipetting depth. The same considerations that apply to dead volume calculations apply here. A labware definition that doesn't match your physical labware will produce systematic errors.

A common mistake is placing a generic "96-well plate" definition when the actual plate in use is from a specific manufacturer with a non-standard well depth. Always use the labware definition that matches your specific product. If it's not in the Venus library, you need to create or import a custom definition before building the worktable.

The waste position

The waste position is not optional. Track 55 of the Hamilton STAR deck is reserved for the tip waste container, and the waste labware definition must be on the worktable. Every tip eject step that directs tips to the default waste destination references this position. If the waste position isn't defined on the worktable, tip eject steps will fail or eject to an undefined location.

Active devices

If your deck includes active devices such as a Heater Shaker (HHS), an On-Deck Thermal Cycler (ODTC), or a Hamilton Heater Cooler (HHC), these also appear on the worktable as specific labware/carrier combinations. Each active device has its own deck position definition, and the method steps that control it (temperature commands, shaking commands) reference that worktable position.

What sequences are and why they matter

A sequence is an ordered list of positions on the worktable. It's the fundamental reference unit in every Venus pipetting step. When you write an aspirate step, you don't tell the robot "go to well A1 of the plate on carrier position 3." You tell it "aspirate from this sequence." The sequence contains the list of positions, and the aspirate step works through them one by one.

Every aspirate, dispense, tip pickup, and tip eject step in a Venus method references a sequence. The method editor can't reference a raw XYZ position; it must go through a named sequence. This means sequences must be defined on the worktable before they can be used in the method.

Sequence counting

Sequences maintain a current position pointer. When a step uses a sequence and sequence counting is set to 1 (Automatic), the pointer advances after each use. If you aspirate from position 1 of a sequence, the next aspirate from the same sequence goes to position 2, then position 3, and so on. If sequence counting is set to 0 (Manual), the pointer doesn't advance. The same position is used every time until you manually move it in the method logic.

This counter behaviour sits at the heart of many method logic patterns. An 8-column dispense across a 96-well plate works by defining the plate wells as a sequence, then letting the counter advance through all 96 positions. A fixed reagent dispense that always reads from the same reservoir position uses Manual counting to stay at position 1 throughout.

Understanding sequence counting before you write methods saves a significant amount of debugging time — the full mechanics are covered in the sequences article.

How sequences are created on the worktable

In the Deck Layout Editor, sequences are created by:

1. Selecting the labware positions you want to include
2. Naming the sequence
3. Setting the order in which positions are addressed (column-wise, row-wise, or custom)

The order matters. A 96-well plate sequenced column-wise (A1, B1, C1 ... H1, A2, B2 ...) processes wells in a different physical order than the same plate sequenced row-wise (A1, A2, A3 ... A12, B1, B2 ...). For multi-channel pipetting, column-wise sequencing allows all 8 channels to aspirate or dispense simultaneously into a complete column. Row-wise does not, and attempting an 8-channel operation on a row-wise sequence will produce channel conflicts or wrong positions.

Venus automatically creates a default sequence for any labware you place on the worktable. These default sequences cover all wells and default to column-wise order. For many methods, the default sequence is fine. For methods that process only a subset of wells, or in a specific non-standard order, you'll need to create a custom sequence that covers only those positions in that order.

Checking the worktable before you script

Before moving to the method editor, run through this checklist on every new worktable:

Carrier verification. Does every carrier definition on the worktable match the physical carrier type and part number on the deck? Are all carriers placed on the correct track numbers? A carrier placed one track off from reality will make every position it holds incorrect.

Labware verification. Does every labware definition match the physical labware? Check manufacturer, well format, well depth, and skirt type (full, half, no skirt). Well depth errors are particularly common when using plates from multiple suppliers.

Waste position. Is the waste position defined at track 55 and does it match the physical waste container?

Sequence order. For every sequence that will be used in a pipetting step, is the position order appropriate for the head configuration? Column-wise for 8-channel aspirations; row-wise or custom only when you have a specific reason.

Active devices. Are all active devices placed at the correct track positions with the correct labware definitions? Is the deck physically configured to match?

Tip racks. Do the tip rack definitions match the physical tips, not just the rack format but the tip volume (300 µL vs 1000 µL) and filtered vs non-filtered status? The tip type used by a tip rack labware definition directly filters which liquid classes Venus will make available in aspirate/dispense steps.

The worktable is a living document, but change it carefully

Once your method is in use, the worktable isn't static. A new labware type requires a new definition. Moving a carrier to a different deck position requires updating the track assignment on the worktable. Adding an active device requires both a labware update and a method step update.

Make worktable changes in the Deck Layout Editor, not by guessing in the method. Every change to the worktable must be followed by a re-verification of the methods that reference it, because moving a carrier can break every sequence that pointed to its old position.

Treat the worktable as the ground truth for your physical deck configuration. Version-control your worktable files alongside your method files. If you need to run the same method on a different STAR instrument with a different deck layout, create a separate worktable file. Don't edit the production worktable in place.

Summary

The worktable isn't a setup step before the real work. It's the foundation the real work runs on. Every sequence, every pipetting position, every tip pickup, every plate transport operation ultimately traces back to a definition on the worktable. Getting the worktable right, with correct carrier types, correct labware definitions, correctly ordered sequences, and a defined waste position, is the prerequisite for every other scripting decision covered in this series.

The next article covers the step that validates your worktable against physical reality: teaching.