CellPD

BACKGROUND: The increased availability of high-throughput datasets has revealed a
need for reproducible and accessible analyses which can quantitatively relate
molecular changes to phenotypic behavior. Existing tools for quantitative
analysis generally require expert knowledge. RESULTS: CellPD (cell phenotype
digitizer) facilitates quantitative phenotype analysis, allowing users to fit
mathematical models of cell population dynamics without specialized training.
CellPD requires one input (a spreadsheet) and generates multiple outputs
including parameter estimation reports, high-quality plots, and minable XML
files. We validated CellPD's estimates by comparing it with a previously
published tool (cellGrowth) and with Microsoft Excel's built-in functions. CellPD
correctly estimates the net growth rate of cell cultures and is more robust to
data sparsity than cellGrowth. When we tested CellPD's usability, biologists
(without training in computational modeling) ran CellPD correctly on sample data
within 30 min. To demonstrate CellPD's ability to aid in the analysis of high
throughput data, we created a synthetic high content screening (HCS) data set,
where a simulated cell line is exposed to two hypothetical drug compounds at
several doses. CellPD correctly estimates the drug-dependent birth, death, and
net growth rates. Furthermore, CellPD's estimates quantify and distinguish
between the cytostatic and cytotoxic effects of both drugs-analyses that cannot
readily be performed with spreadsheet software such as Microsoft Excel or without
specialized computational expertise and programming environments. CONCLUSIONS:
CellPD is an open source tool that can be used by scientists (with or without a
background in computational or mathematical modeling) to quantify key aspects of
cell phenotypes (such as cell cycle and death parameters). Early applications of
CellPD may include drug effect quantification, functional analysis of gene
knockout experiments, data quality control, minable big data generation, and
integration of biological data with computational models.

Quantifying differences in cell line population dynamics using CellPD.

CellPD (cell phenotype digitizer) is a software tool for quantitative phenotype analysis to analyze cell population dynamics.

CellPD

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