Plan multi-condition microfluidic runs with flush-to-waste timing, fraction collection windows, and a printable bench checklist. Free. Client-side.
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Load example sample-to-waste scheduler data to see the full workflow
Use the Dead Volume Calculator to get this number.
| Time | Relative (min) | Action | Notes |
|---|---|---|---|
| 18:33 | 0.0 | Switch to condition 1 | Flush 3× dead volume (450 μL) to waste |
| 18:42 | 9.0 | Collect fraction 1.1 | 100 μL at 50 μL/min |
| 18:44 | 11.0 | Collect fraction 1.2 | 100 μL at 50 μL/min |
| 18:46 | 13.0 | Collect fraction 1.3 | 100 μL at 50 μL/min |
| 18:48 | 15.0 | Collect fraction 1.4 | 100 μL at 50 μL/min |
| 18:50 | 17.0 | Collect fraction 1.5 | 100 μL at 50 μL/min |
| 18:53 | 20.0 | Condition 1 complete | Advance to next condition |
| 18:53 | 20.0 | Switch to condition 2 | Flush 3× dead volume (450 μL) to waste |
| 19:02 | 29.0 | Collect fraction 2.1 | 100 μL at 50 μL/min |
| 19:04 | 31.0 | Collect fraction 2.2 | 100 μL at 50 μL/min |
| 19:06 | 33.0 | Collect fraction 2.3 | 100 μL at 50 μL/min |
| 19:08 | 35.0 | Collect fraction 2.4 | 100 μL at 50 μL/min |
| 19:10 | 37.0 | Collect fraction 2.5 | 100 μL at 50 μL/min |
| 19:13 | 40.0 | Condition 2 complete | Advance to next condition |
| 19:13 | 40.0 | Switch to condition 3 | Flush 3× dead volume (450 μL) to waste |
| 19:22 | 49.0 | Collect fraction 3.1 | 100 μL at 50 μL/min |
| 19:24 | 51.0 | Collect fraction 3.2 | 100 μL at 50 μL/min |
| 19:26 | 53.0 | Collect fraction 3.3 | 100 μL at 50 μL/min |
| 19:28 | 55.0 | Collect fraction 3.4 | 100 μL at 50 μL/min |
| 19:30 | 57.0 | Collect fraction 3.5 | 100 μL at 50 μL/min |
| 19:33 | 60.0 | Condition 3 complete | Advance to next condition |
| 19:33 | 60.0 | Switch to condition 4 | Flush 3× dead volume (450 μL) to waste |
| 19:42 | 69.0 | Collect fraction 4.1 | 100 μL at 50 μL/min |
| 19:44 | 71.0 | Collect fraction 4.2 | 100 μL at 50 μL/min |
| 19:46 | 73.0 | Collect fraction 4.3 | 100 μL at 50 μL/min |
| 19:48 | 75.0 | Collect fraction 4.4 | 100 μL at 50 μL/min |
| 19:50 | 77.0 | Collect fraction 4.5 | 100 μL at 50 μL/min |
| 19:53 | 80.0 | Condition 4 complete | Advance to next condition |
| 19:53 | 80.0 | Switch to condition 5 | Flush 3× dead volume (450 μL) to waste |
| 20:02 | 89.0 | Collect fraction 5.1 | 100 μL at 50 μL/min |
| 20:04 | 91.0 | Collect fraction 5.2 | 100 μL at 50 μL/min |
| 20:06 | 93.0 | Collect fraction 5.3 | 100 μL at 50 μL/min |
| 20:08 | 95.0 | Collect fraction 5.4 | 100 μL at 50 μL/min |
| 20:10 | 97.0 | Collect fraction 5.5 | 100 μL at 50 μL/min |
| 20:13 | 100.0 | Condition 5 complete | Stop pump and close collection valves |
When to use
Do not use for
A 5× flush on a 500 μL system wastes 2.5 mL of reagent per swap. For precious samples, drop to 3× and monitor the first fraction for carryover with a spike-in control.
Carryover in fraction 2A from condition 1 is invisible in the tube label but shows up in the data. Always flush at least 2× system volume, ideally 3×.
Most syringe pumps do not support programmed reservoir switches. You are the switch. Set a timer for each event and do not trust yourself to remember.
The last fraction per condition may be shorter than the others if the math does not work out cleanly. The scheduler drops any partial fractions rather than accepting a short tube.
Flush volume = systemDeadVolume flushFactor. Flush time = flushVolume / flowRate. Run time per condition = reservoir / flowRate. Fractions per condition = floor((reservoir − flushVolume) / fractionVolume). Timeline events emitted per condition: (1) switch/flush, (2) collect fraction 1..N, (3) condition complete. Absolute times computed from HH:MM run-start with wraparound past midnight.
Last validated 2026-04-07. Calculations are designed for planning and documentation support; verify procurement decisions against manufacturer specifications or institutional SOPs.
ConductScience Sample-to-Waste & Collection Scheduler (v1.9.0). ConductScience, Inc. 2026. Available at: https://conductscience.com/tools/microfluidic-sample-to-waste-scheduler
In a multi-condition microfluidic experiment, carryover is invisible until it ruins your data. If you start collecting fraction 2A one minute too early, it contains residual condition 1 fluid. At qPCR sensitivity, that is indistinguishable from a real signal.
The fix is a well-specified flush protocol: wait long enough for the new sample to fully displace the old one before collecting anything. The minimum wait is the system dead volume divided by the flow rate, multiplied by a safety factor (2× for routine, 3× for quantitative, 5× for sticky).
Writing this schedule on a scrap of paper at the bench invites transcription errors. A printable timeline with absolute clock times is the cheapest possible fix.
Fraction volume is a tradeoff: larger fractions give you more material per sample but fewer time points; smaller fractions give you better temporal resolution but less material per sample and more tubes to label.
For routine collection, 50–200 μL fractions work for most downstream assays. For gradient-based separations or time-resolved experiments, drop to 20 μL and expect to fill a 96-well plate per condition.
The scheduler drops any fraction that would overflow the reservoir after the flush — no partial tubes.
1. Load reservoirs for every condition and label them 2. Label collection tubes ahead of time (tube 1.A, 1.B, … 2.A, …) 3. Verify your flow rate on the pump display 4. Start the pump at the scheduled start time 5. Set a kitchen timer for each event from the printout
The scheduler is a plan, not a controller. The timestamps depend on you following the plan.
