Assembly plan build order

A multi-level assembly plan drawn as the graph it is: which parts and products go into which step, at which level, and which steps built.

What it doesCopy Anchor Link

A hierarchical build is not a list of reactions. A step at level 2 consumes the products of level 1, so the order the bench must work in, and the damage one failed reaction does, are both properties of a graph. This is that graph for the plan you simulated: the physical parts you start from along the first level, each step on the level where everything it needs already exists, and an edge for every part or product that goes into a step.

Each step carries its chemistry (Golden Gate, Gibson, BioBrick, BASIC, ligase cycling or oligo annealing) and is coloured by what happened to it. A step that built is marked as built, with how many constructs it produced. A step that failed is marked as failed. A step that was never attempted because something it consumes failed is marked as not attempted and names the failed step, so a dead branch traces back to its one root cause rather than to its immediate parent.

Selecting a step selects its construct, the same one the panel's Result tab highlights, so the graph and the per-level list always point at the same thing.

When you'd use thisCopy Anchor Link

• Before you start at the bench. The first level is the parts you have to have in hand; each later level can only start once the one above it is done.
• When a plan partly fails. One failed reaction can cancel a whole branch. The graph shows which steps are lost because of it and which are independent of it.
• When a plan mixes chemistries. Each step names its own, so a BASIC step built from the products of oligo annealing steps reads as exactly that.
• When the plan is wide. A plan with dozens of parts at its first level is drawn at full size, where it can be panned and zoomed rather than squeezed into a column.

What this computesCopy Anchor Link

• The build order: every step placed on the earliest level at which all of its inputs exist, with the parts it starts from on the first level.
• The inputs of every step: one edge per part or earlier product consumed.
• The outcome of every step: built (with its construct count), failed, or not attempted, and for a step not attempted, the failed step that cancelled it.
• The plan's totals: how many parts it needs, how many steps it has over how many levels, and how many steps built, failed and were cancelled.

Every outcome comes from simulating each reaction on the parts' real sequences.

What it does not doCopy Anchor Link

It draws a simulated plan, not an experiment. Reaction efficiency, colony screening, and the chance that a step which builds on screen gives the wrong clone at the bench are not modelled. It also does not reorder the plan for you: the levels are the earliest each step can run, not a schedule that balances work across days.