pepkio-serial-dilution-planner 0.1.1

Python client for pipette-aware serial dilution protocols via the Pepkio API

Pepkio Serial Dilution Planner

Python client for the Pepkio Serial Dilution Planner API: pipette-aware multi-step protocols, standard curves, and optional 96/384-well plate layouts from scripts or notebooks.

What It Does

Serial dilution prepares a geometric concentration series from one stock solution. Researchers use it for dose–response setups, ELISA and qPCR standard curves, inhibitor titrations, antibody working dilutions, and protein standards.

Planning by hand or in a spreadsheet often mixes unit conversions, total dilution ratio, and step count inconsistently. Transfer volumes that look correct on paper (for example 18.37 µL) may not match pipette increments. Mapping tubes to microplate wells adds separate bookkeeping.

This package calls the same Pepkio Tools calculation engine as the hosted web application. Use PepkioClient.run() from Python, Jupyter, or automation pipelines to obtain step-by-step protocols with pipette-rounded volumes, diluent amounts, concentrations per step, optional plate maps, and shareable run links.

Programmatic runs require a network connection and a Pepkio API key. Calculations are not bundled for offline use.

Features

• Concentration units: molar (M, mM, uM, nM), mass per volume (mg_per_mL, ug_per_uL, ng_per_uL), and percent
• Pipette-aware volumes: declare pipettes (min_ul, max_ul, resolution_ul); receive rounded transfer_ul and pipette_label per step
• Step-by-step output: concentration display, transfer volume, diluent volume, and warnings
• Economy mode to reduce reagent use within pipette limits
• Automatic extra steps when a single-step dilution would exceed roughly 1000×
• Mass–molar conversion via molecular_weight_g_per_mol
• Optional plate_map for 96- or 384-well layouts
• Manifest and named examples: get_manifest, list_examples, get_example_input
• CLI: pepkio-serial-dilution-planner manifest and run
• Configuration via PEPKIO_API_KEY and PEPKIO_API_BASE_URL

Installation

pip install pepkio-serial-dilution-planner

Set an API key with tools:run scope before calling run():

export PEPKIO_API_KEY="your-key"

Create a key in your Pepkio account API keys settings.

Quick Example

from pepkio_serial_dilution_planner import PepkioClient

with PepkioClient() as client:
    inp = client.get_example_input("standard_4step")
    result = client.run(inp)
    for step in result.result["steps"]:
        print(step["step"], step["concentration_display"],
              step["transfer_ul"], step["pipette_label"])

CLI:

pepkio-serial-dilution-planner run --example standard_4step

Manifest inspection does not require an API key.

Typical Use Cases

• Serial dilution planning (for example 10 mM to 10 µM in four steps)
• Standard curve preparation for ELISA and immunoassays
• qPCR template dilution and standard series
• Antibody dilution from mg/mL stock to molar working concentration
• 96- or 384-well plate layout for high-throughput assays
• Limited reagent volume with economy mode and small pipettes
• Large stock-to-target concentration span with automatic step expansion

Scientific Background

In a constant-ratio serial dilution, each step uses the same dilution factor DF = Cᵢ / Cᵢ₊₁. After n steps from initial concentration C₀, the concentration is Cₙ = C₀ / DFⁿ.

When the total dilution is large, one step may need a transfer volume below the pipette minimum or above its maximum. Splitting into multiple serial steps keeps each transfer pipettable and improves mixing.

Standard curves for ELISA, qPCR, and binding assays are often built as a geometric (log-spaced) concentration series from a concentrated stock.

Protocols should use volumes rounded to the pipette you will use at the bench; otherwise the achieved concentration differs from the ideal calculated value.

Web Application

For researchers who prefer a graphical interface, an interactive Serial Dilution Planner is available in the browser.

The web interface adds bench mode (check-off steps at the hood), economy mode, 96/384-well plate maps with CSV or PNG export, printable worksheets, and shareable links that restore the same plan as API permalink values.

Documentation and Resources

Source code and issue tracking: github.com/pepkio/pepkio-serial-dilution-planner

About Pepkio

Pepkio develops software tools and bioinformatics services for life science research.

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