simulate_taqman_curve
Read-only
Predict the amplification curve a hydrolysis-probe (TaqMan) qPCR assay will draw, and the Cq read off it, from the assay's own sequences and its thermocycling programme - a forward simulation, not a fit to data. Ports DYNAMIC (Kreitmann et al., Anal. Chem. 2026, 98(12):9089-9101): thirteen species, four phases per cycle, mass-action annealing integrated as a stiff ODE, with primer-dimer formation and amplicon re-annealing competing for the primers. It is SINGLEPLEX, which is the paper's own stated limit and not an omission here - one target per run, no interassay competition. Two things it needs said about their provenance every time they are quoted: the primer-dimer free energy is upstream's NUPACK quantity and primer3's thal is explicitly NOT a substitute for it, and the association rate constants are one assay's FITTED values reused, not physical constants.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| beta | No | stretching exponent of the decay, exp(-(k_deg*t)^beta). Upstream ships 1, which makes the decay a plain exponential. Advanced. | |
| k_deg | No | polymerase thermal-decay rate constant. Upstream SHIPS this at 0 - no decay, efficiency identically 1 at every cycle - with its own code commenting 'original value: 1.9e-4'. Left at 0 you are running the model upstream ships; raise it and the plateau bends down. Advanced. | |
| probe | Yes | the hydrolysis probe, 5'->3'. Fluorescence in this model IS probe cleavage, so without a probe there is no curve to predict - this is a TaqMan simulator and not a SYBR one. | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| cycles | No | how many cycles to run. In cycles. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| amplicon | Yes | the amplicon, forward strand, 5'->3'. The whole product, not the region between the primers: the amplicon's own re-annealing is a species in the model and it competes with the primers for template late in the run, which is what bends the plateau. | |
| probe_molar | No | probe concentration, mol/L (150 nM in upstream's assay). It caps the plateau: fluorescence cannot exceed the probe you put in. In M. Advanced. | |
| annealing_time | No | seconds at the annealing temperature. A real parameter of the answer, not a formality: the system is NOT at equilibrium when a 15 s anneal ends, so a longer hold binds measurably more. In s. | |
| forward_primer | Yes | forward primer, 5'->3'. | |
| reverse_primer | Yes | reverse primer, 5'->3'. | |
| primer_dimer_dg | No | free energy of the forward-reverse primer dimer, kcal/mol, negative. NOT computed for you, and that is deliberate: the paper computes it with NUPACK and says why nothing simpler does - 'the nonspecific binding of P_for and P_rev into PD is not in perfect match', so nearest-neighbour formulas are the wrong class of tool. primer3's `thal`, which this repo does ship, is that class: on upstream's own C22 assay it returns -4.40 against upstream's -8.880. Pass the `thal` figure if it is the best you have and treat the answer as carrying that estimator's name, or pass a NUPACK value to reproduce the paper. In kcal/mol. | |
| template_copies | No | template copies in the reaction at cycle 0. This is the quantity Cq is a readout OF, so sweeping it is how you get a standard curve out of this node. In copies. | |
| denaturation_time | No | seconds at the denaturation temperature. It reaches the answer only through polymerase decay, so with `k_deg` at 0 it changes nothing. In s. Advanced. | |
| forward_primer_molar | No | forward primer concentration, mol/L (450 nM in upstream's assay). In M. Advanced. | |
| reverse_primer_molar | No | reverse primer concentration, mol/L (460 nM in upstream's assay). In M. Advanced. | |
| annealing_temperature | No | annealing temperature, °C. Every binding constant in the model is evaluated here, so this is the single knob that moves the whole curve rather than scaling it. In °C. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| cq | Yes | the predicted Cq, as a whole cycle number - upstream reads it as the cycle maximising the curve's SECOND derivative, so it is not interpolated and never fractional | |
| notes | Yes | what the run wants said about itself, in the panel's own words | |
| plateau | Yes | the final cycle's reading - what the curve levels off at, capped by the probe you put in | |
| curvePlot | Yes | the predicted amplification curve as a plot, one point per cycle | |
| estimators | Yes | which model produced each quoted quantity, so nothing here is read as upstream's when it is ours (§10 r11) | |
| fluorescence | Yes | the predicted curve: one reading per cycle, in mol/L of cleaved probe | |
| probeConsumed | Yes | fraction of the probe cleaved by the last cycle. Near 1 the plateau is probe-limited and the Cq is still trustworthy; well under it something else stopped the reaction |