Metadata-Version: 2.5
Name: pepkio-confluency-split-passage-planner
Version: 0.1.0
Summary: Python client for Pepkio confluency-split-passage-planner tool
License-File: LICENSE
Requires-Python: >=3.11
Requires-Dist: click>=8.4.1
Requires-Dist: httpx>=0.28.1
Requires-Dist: pydantic>=2.13.4
Description-Content-Type: text/markdown

# Pepkio Confluency & Split Passage Planner

A Python interface for calculating cell culture split ratios, seeding densities, harvest yields, and passage schedules based on cell growth kinetics and vessel surface areas.

# What It Does

Passaging adherent or suspension cell cultures requires calculating split ratios, seeding densities, total cell yields, and liquid transfer volumes. Manual rule-of-thumb split ratios (such as 1:3 or 1:5) fail to account for variations in current confluency, cell doubling kinetics, and vessel geometry, often causing inconsistent cell growth or weekend over-confluency.

This package provides programmatic access to the Pepkio cell passage planning engine. Researchers can input current vessel confluency, cell doubling time ($T_d$), target seeding density (cells/cm² or cells/mL), and vessel formats to calculate exact split ratios, harvest yields, transfer volumes, and passage timing.

Programmatic runs require a network connection and a Pepkio API key.

# Features

- **Adherent and Suspension Support**: Computes surface-area seeding densities (cells/cm²) for adherent monolayers and concentration-based seeding (cells/mL) for suspension cultures.
- **Standard Vessel Surface Area Database**: Built-in surface areas and working volumes for 96-well through 6-well microplates, T-25, T-75, T-175, and T-225 flasks, and 60mm, 100mm, and 150mm dishes.
- **Growth Kinetics Forecasting**: Uses cell doubling time ($T_d$) to project cell accumulation kinetics and predict hours or days required to reach target harvest confluency.
- **Multi-Mode Seeding Calculations**: Computes subculturing parameters by target seeding density, target split ratio, or total cell count per vessel.
- **Pipetting Reserve Allowance**: Includes configurable safety overhead percentages (5% to 15%) to prevent liquid deficits during multi-vessel transfers.
- **Programmatic & CLI Interfaces**: Access via Python `PepkioClient` or the `pepkio-confluency-split-passage-planner` command-line tool.

# Installation

```bash
pip install pepkio-confluency-split-passage-planner
```

Set an API key before invoking `run()`:

```bash
export PEPKIO_API_KEY="your-api-key"
```

# Quick Example

```python
from pepkio_confluency_split_passage_planner import PepkioClient

with PepkioClient() as client:
    # Load example input for a standard HEK293 split in a T-75 flask
    inp = client.get_example_input("hek293_t75_split")
    result = client.run(inp)

    split = result.result["split"]
    print("Split Ratio:", split["split_ratio_label"])
    print("Harvest Total Cells:", f"{split['harvest_total_cells']:.2e}")
    print("Required Suspension Volume:", split["required_suspension_volume_ml"], "mL")
    print("Hours to 80% Confluency:", split["predicted_hours_to_80_percent_confluency"], "h")
```

CLI command:

```bash
pepkio-confluency-split-passage-planner run --example hek293_t75_split
```

# Typical Use Cases

- **Adherent Cell Subculturing**: Determining exact split ratios and cell suspension transfer volumes to passage confluent culture flasks (e.g., HEK293, HeLa, CHO, NIH-3T3).
- **Weekend Passage Scheduling**: Calculating reduced seeding densities on Friday to ensure cultures reach 80% target confluency on Monday morning.
- **Vessel Format Scale-Up**: Translating seeding protocols across different culture vessel sizes (e.g., scaling from 6-well plates to T-75 or T-175 flasks) while maintaining constant density per unit surface area.
- **Suspension Culture Maintenance**: Calculating dilution ratios and fresh media volumes for suspension cell lines (e.g., Jurkat, K562, CHO-S) to remain within log-phase growth windows.
- **Multi-Well Assay Seeding**: Calculating master mix suspension volumes and cell counts required to seed 24-well or 96-well assay plates.

# Scientific Background

Cell population growth during logarithmic phase follows first-order exponential kinetics:

$$N(t) = N_0 \cdot 2^{\frac{t}{T_d}}$$

where $N(t)$ is the cell population at time $t$, $N_0$ is the initial seeded population, and $T_d$ is the cell doubling time in hours. The incubation duration $t$ required to reach a target cell yield $N(t)$ is given by:

$$t = T_d \cdot \log_2 \left( \frac{N(t)}{N_0} \right)$$

For adherent cells, total harvest yield $N_{\text{harvest}}$ is derived from vessel surface area $A$ ($\text{cm}^2$), maximum monolayer cell density $D_{\text{max}}$ ($\text{cells/cm}^2$), and percentage confluency $C_{\%}$:

$$N_{\text{harvest}} = D_{\text{max}} \cdot A \cdot \left( \frac{C_{\%}}{100} \right)$$

The split ratio $R$ represents the proportion of harvested cells required to seed $m$ new target vessels at density $D_{\text{target}}$:

$$R = \frac{N_{\text{harvest}}}{m \cdot D_{\text{target}} \cdot A}$$

Pipetting reserve volume accounts for liquid hold-up during multi-vessel transfers by applying a safety overhead factor $P_{\text{reserve}}$ to the net transfer volume.

# Web Application

For researchers who prefer a graphical interface, an interactive [Confluency & Split Passage Planner](https://www.pepkio.com/tools/confluency-split-passage-planner) is available in the browser.

The web interface offers interactive split visualizations, passage schedule timelines, plate layout summaries, and shareable permalinks.

# Documentation and Resources

GitHub Repository: https://github.com/pepkio/pepkio-confluency-split-passage-planner

Web Application: https://www.pepkio.com/tools/confluency-split-passage-planner

# About Pepkio

Pepkio (https://www.pepkio.com/) develops software tools and bioinformatics solutions for life science researchers, including laboratory calculators and analysis services (https://www.pepkio.com/cro).

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A semantic, AI-native version of this document in the K2F format is available at https://k2f.dev (https://k2f.dev/v/a82d9704864e08d2f4f4d1ce029f690138c4c3d832afd844c100740fa7205918)
