dilution-calculator

name	dilution_calculator
description	Calculate C1V1=C2V2 dilutions, serial dilutions with plate-based replicates, and budget-conscious volume planning that accounts for micropipette systematic error.
category	bio/molecular_lab
version	2
requires_tools	["python_repl"]
requires_network	false
user_invocable	true
tags	["dilution","serial-dilution","plate-planning","wet-lab"]
aliases	["c1v1_calculator","serial_dilution_planner"]
species	any
modality	wet_lab
stage	utilities
stability	stable
safety_level	low

Dilution Calculator

Purpose

Calculate simple dilutions, serial dilutions, and plate-aware dilution plans while accounting for realistic wet-lab overage and replicate structure.

When to use

User asks for any dilution calculation: simple C1V1=C2V2, serial dilution from a protein stock, or plate-based experiment volume planning.

Required inputs

• stock concentration
• target concentration or concentration series
• final volume or plate format plus number of concentrations
• units for concentration and volume
• overage factor (optional; default to the lab rule below)

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Key Lab Rules (always apply)

1. Serial dilution — stock used only once

• Use the stock concentration only for the first step: diluting stock → highest concentration tube/well.
• All subsequent steps dilute from the previous step's concentration. Stock is ignored after step 1.

2. Replicate count = wells ÷ concentrations

• Do not default to 3 replicates. Calculate from plate format:

Plate format	Wells	Example: 6 conc. → replicates
6-well	6	1
12-well	12	2
24-well	24	4 (not 3)
48-well	48	8
96-well	96	16

• Always compute: replicates = total_wells / n_concentrations

3. Volume per well (standard lab values)

Plate format	Volume per well
6-well	2 mL
12-well	1 mL
24-well	500 µL
48-well	250 µL
96-well	100–200 µL

4. Micropipette systematic error — prepare slightly more

Micropipettes tend to under-aspirate (air bubbles, worn seals). E.g. a 1 mL pipette may only deliver 995 µL.

Overage rule: prepare 1.05–1.10× the nominal volume per tube.

• Want accuracy → lean toward 1.10×
• Want to save media → lean toward 1.05×
• Default: 1.05× for ≥500 µL volumes, 1.10× for <100 µL volumes

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Steps

Use python_repl for all arithmetic and show units clearly.

Simple dilution (C1V1 = C2V2)

1. Parse known values (C1, C2, V1, or V2).
2. Solve: V1 = C2 * V2 / C1 → add (V2 - V1) of diluent.
3. Print result with units.

Serial dilution from protein stock

Step 0: stock → tube_1 (highest concentration)
  V_stock = C_target_1 * V_tube_1 / C_stock
  V_diluent_0 = V_tube_1 - V_stock

Step i (i ≥ 1): tube_{i-1} → tube_i
  C_prev → C_i  (dilution factor D_i = C_{i-1} / C_i)
  V_transfer_i = C_i * V_tube_i / C_prev
  V_diluent_i  = V_tube_i - V_transfer_i

Apply overage multiplier to each V_tube_i before computing volumes.

Plate-based experiment volume planning

# --- User inputs ---
plate_format   = 24          # 6, 12, 24, 48, 96
n_conc         = 6           # number of concentrations
stock_conc_uM  = 95          # stock concentration (µM or any unit)
target_concs   = [10, 5, 2.5, 1.25, 0.625, 0.3125]  # µM, highest first
overage        = 1.05        # 1.05 to 1.10

# --- Derived ---
plate_volumes = {6: 2000, 12: 1000, 24: 500, 48: 250, 96: 150}  # µL
vol_per_well  = plate_volumes[plate_format]
replicates    = plate_format // n_conc
vol_per_tube  = vol_per_well * replicates * overage   # µL including overage

# Step 0: stock → tube for highest concentration
V_stock = target_concs[0] * vol_per_tube / stock_conc_uM
V_diluent_0 = vol_per_tube - V_stock

# Steps 1..N-1: serial dilution
for i in range(1, n_conc):
    V_transfer = target_concs[i] * vol_per_tube / target_concs[i-1]
    V_diluent  = vol_per_tube - V_transfer
    print(f"Tube {i+1} ({target_concs[i]} µM): transfer {V_transfer:.1f} µL, add {V_diluent:.1f} µL diluent")

---

Output format

For each tube/step, report:

• Concentration (with unit)
• Volume to transfer from previous step (µL)
• Volume of diluent to add (µL)
• Total tube volume (= vol_per_well × replicates × overage)
• One-line bench instruction: "Transfer X µL from tube N-1, add Y µL buffer."

Finish with a summary table and a note on the overage factor chosen and why.

Failure modes

• Missing units: ask the user to confirm units before calculating.
• Impossible dilution: explain why the requested concentration or volume cannot be achieved from the provided stock.
• Plate setup mismatch: if total_wells / n_concentrations is not an integer, warn the user and ask how they want to allocate replicates.

Examples

• "How do I make 100 mL of a 1 mM solution from a 100 mM stock?"
• "Plan a 24-well serial dilution with 6 concentrations from a 95 uM stock."
• "How much extra media should I prepare for a 12-well plate with 2 replicates and 5 concentrations?"