Expert Bioreactor Designer

About this guide

Model a cell-culture run from inoculation to harvest: the cells, the feeds, and the DO and pH control that hold them, all solved together. This takes about three minutes. For how the model works, and where its numbers stop being reliable, see the detailed guide.

1. Open a design

The first page gives you four ways in:

• Start with an example. The featured design, Fed-Batch - Intermediate lactate (controlled), is a 14-day fed-batch in a 15 L bench vessel. Click Open example. Standard designs, under it, holds the other ready-made batch, fed-batch and perfusion designs. Each one is built to show one effect.
• Start from a culture profile. Each card is the featured fed-batch with its cells reshaped: denser, slower, a lactate curve that crashes or rises late, or a published culture. Click a card to compare it with the design as shipped, then click Open in the Designer.
• User defined lists the designs you have saved.
• Start from scratch opens the Designer on the design you last worked on, ready to change by hand.

2. Find your way around

The Designer runs the design as soon as it opens, so you start with a result.

• Left: Process settings. This holds the Design list, and sliders for the settings most runs change: the DO and pH setpoints, growth, volume, temperature, duration and feed rates.
• Right: the results. Five numbers across the top, then the charts.
• Top: the design’s name and its feasibility badge, then Messages, Assistant, Engineering, Help, Save As, Save, Assess and Run simulation. ← Designs takes you back to the first page.

3. Change the design

• Drag a slider under Process settings. The title becomes Custom run, and ● unsaved — run to refresh reminds you that the charts show the run before your change.
• Turn on Engineering to see the design’s eight parts: Reactor, Initial state, DO control, Biology, Basal medium, Feed strategy, pH control and Solver. Click a part to open it.
• In a part’s drawer, pick another Configuration from the list, or change its settings. Tweaker shows the few settings most runs need, Designer adds the equipment limits, and Builder shows everything.

4. Check and run

• The badge beside the title checks the design against its vessel before you run. ✓ means it fits. ⚠ means it will run, with warnings. ✕ not feasible means the vessel can’t do what the design asks, and Run simulation is blocked. Click the badge to read why.
• Run simulation runs 10 to 14 days of culture in a few seconds.
• Assess runs the design with everything the vessel has, then reports in Messages what the culture demanded and whether the vessel could meet it. It changes nothing.

5. Read the results

• Across the top: peak cell density, peak lactate, doubling time, and how closely DO and pH were held to their setpoints.
• Time series has four views:
  • Signals: every measurement.
  • Cause → effect: what the cells demanded, what the vessel could deliver, what the controllers moved, and what happened.
  • Control loops: each loop on its own.
  • Limits & headroom: what is holding the run back, and how much room is left.
• Detailed analysis explains one moment of the run. Click any point on a chart to move to it.
• pH & DO loops splits each loop into what pushed it and how it was held.
• Messages lists warnings before a run, and the controllers’ log after it. If the vessel runs out of room, the run still finishes, but it is marked not feasible, and the charts dim from that moment on.

6. Save your work

• Save keeps the design in your workspace, and asks for a name if it has none. Save As always asks for a new name. Saved designs appear on the first page, under User defined.
• Save As in a part’s drawer keeps that part on its own, so other designs can use it. The Configuration library, on the first page, is where you rename, duplicate and delete saved parts, and see which designs use each one.

Need more?

• The Assistant can build and run a design from a plain-language request and read the result back to you. Its / commands, such as /assemblies and /run, work even without an AI model.
• The detailed guide explains the model: what the cells respond to, how oxygen and pH are controlled, and how far to trust the numbers.