Basic experiment templates
Original planning blocks for assembling your own experiment. Select a block, provide your own validated parameters and check the source protocol and equipment instructions before use.
These cards describe inputs, outputs and decisions. They contain no paper-derived procedure, recipe or ready-to-run protocol.
Article-based planning maps
Examples of how to select reusable blocks; these are not reconstructions of the papers.
Flow cytometry staining → Flow cytometry analysis
Choose sample conditions and a marker panel; define controls and interpretation rules before running.
Source publication
DNA extraction → PCR amplification → Quantitative PCR assay
Choose a sample route, design independent assays, then decide what follow-up evidence is needed.
Source publication
Lipid nanoparticle formulation → Particle characterization
Choose a formulation route and define quality checks before any downstream evaluation.
Source publication
Reusable blocks
Parameter notes stay in this browser. They are not uploaded or turned into an executable protocol.
Amplify a user-selected DNA target.
Input: DNA template, primer pair, polymerase class
Output: Amplicon
Set before use: Target and primer design; enzyme and buffer; reaction volume; cycling program; controls
Reaction mix · Listen Step table layout
Enter values from your own validated assay. The final column is the per-reaction volume used by Listen Step’s Mix × N calculation.
| Component | Selection / role | Volume per reaction (µL) |
|---|---|---|
| PCR enzyme or master mix | Choose enzyme system | µL |
| Forward primer | User-designed sequence | µL |
| Reverse primer | User-designed sequence | µL |
| DNA template | User-selected input | µL |
| Optional additive | Only if required | µL |
| Nuclease-free water | Calculate from total | µL |
Enter volumes to check the mix total.
Set primer sequences, thermal cycling program and controls in your own notes. The App treats a cycling program as a separate step table.
Prepare DNA from a selected sample type.
Input: Sample
Output: DNA
Set before use: Sample type and amount; extraction chemistry; quality check; storage
Separate and recover DNA or RNA after an upstream operation.
Input: Nucleic-acid mixture, bead class
Output: Recovered nucleic acid
Set before use: Bead ratio; binding conditions; wash; elution; size-selection intent
Inspect approximate fragment size and sample integrity.
Input: Nucleic-acid sample, size marker
Output: Gel observation
Set before use: Gel percentage; buffer; loading amount; run conditions; expected size
Join compatible DNA ends using a ligase class.
Input: DNA insert and compatible ends, ligase
Output: Ligation product
Set before use: End compatibility; molar ratio; enzyme and buffer; reaction conditions; controls
Measure a selected target relative to appropriate controls.
Input: DNA or cDNA, primers or probes
Output: Amplification measurement
Set before use: Target and reference; assay design; standard or calibration; controls; acceptance criteria
Prepare samples for marker measurement.
Input: Cells, selected markers and dyes
Output: Stained cells
Set before use: Cell type; marker panel; titration; compensation controls; acquisition window
Interpret acquired events using a documented gating plan.
Input: Event data and controls
Output: Population summary
Set before use: Instrument settings; exclusion gates; control-derived thresholds; reporting rule
Combine user-selected lipid and payload streams.
Input: Lipid mixture and payload
Output: Formulation candidate
Set before use: Lipid identities and proportions; mixing method; flow or mixing conditions; target particle properties
Assess a formulation against user-defined release criteria.
Input: Formulation candidate
Output: QC observations
Set before use: Size; dispersity; loading or encapsulation measure; acceptance limits