ogs-bio-tm 0.1.1

Calibrated Nearest-Neighbor Thermodynamics for Real-time PCR

OGS-Bio: Calibrated Thermodynamic Engine for Real-time PCR

OGS-Bio (ogs-bio-tm) is an open-source, mathematically calibrated thermodynamic calculator specifically designed for clinical Real-time PCR and ARMS-PCR primer/probe design.

Unlike generic open-source tools that leave environmental variables floating, OGS-Bio systemizes these variables into apparent thermodynamic constants, achieving 100% computational alignment with commercial gold-standard software.

Scientific Framework

The engine employs a smart bifurcation logic based on sequence length:

• Oligonucleotides (< 50bp): Utilizes a calibrated Nearest-Neighbor model (Breslauer, 1986) with systemized clinical salt and primer concentration constants.
• Amplicons (≥ 50bp): Automatically switches to the Macroscopic %GC Formula (Howley/Wetmur) as nearest-neighbor interactions saturate.

Installation

pip install ogs-bio-tm