Pinetree: a step-wise gene expression simulator with codon-specific translation rates.

Area of Science:

• Computational Biology
• Molecular Biology
• Systems Biology

Background:

• Stochastic gene expression simulations often simplify transcript levels or focus solely on transcription.
• Existing simulation tools lack accessible programming interfaces, limiting their widespread use.

Purpose of the Study:

• To introduce Pinetree, a novel, step-wise gene expression simulator.
• To provide a tool that models both transcription and translation with high biological detail.

Main Methods:

• Developed a stochastic simulation framework incorporating codon-specific translation rates.
• Modeled individual polymerase and ribosome dynamics.
• Implemented Pinetree in C++ with a Python front-end for user accessibility.

Main Results:

• Pinetree simulates gene expression with codon-specific translation rates.
• The simulator captures transcription and translation at the polymerase and ribosome level.
• Designed for efficiency and scalability to large genetic elements like plasmids and viral genomes.

Conclusions:

• Pinetree offers a powerful and accessible platform for detailed stochastic gene expression simulation.
• The tool's design facilitates research in areas requiring precise modeling of transcription and translation dynamics.