OMP Developer Edition

OMP Developer Edition™ (OMP-DE) is a programmable predictive modeling environment developed by DNA Software, Inc. for integrating oligonucleotide folding and hybridization algorithms directly into custom design pipelines. It is intended for organizations that need to develop customer-specific applications requiring access to computational and storage capacity on a local server, particularly for high-throughput diagnostic assay design and PCR simulation workflows.

At the core of OMP-DE is the Oligonucleotide Modeling Platform (OMP), which encapsulates the chemical and biological knowledge developed by DNA Software scientists and Dr. John SantaLucia, whose work over more than 20 years produced a thermodynamic parameter database derived from thousands of empirical observations. OMP is capable of predicting the melting temperature (Tm) of a duplex within 2°C on average, which DNA Software states is more accurate than other commercial software packages or freeware for demanding, high-throughput assays.

Key Platform Features

• Fully encapsulated design and simulation platform that predicts oligonucleotide hybridization resulting from monomer, homodimer, and heterodimer species under user-specified oligo concentrations, temperature, and salt conditions.
• A defined scripting language that allows OMP to be programmed for specific tasks, such as batch runs or filtering simulation data to surface application-relevant results.
• Peer-to-peer distributed high-performance computing architecture with an API for Perl script access to the OMP engine, supporting scalable operation across a cluster or network of PCs.
• Cross-platform compatibility with most Windows, Linux, and Unix machines.
• Customizable gadgets for organizing and rationalizing cross-hybridization and melting curve data, particularly useful for large multiplex design and simulation.
• Support for modified backbones and nucleotides to improve assay sensitivity.
• Simulation data visualization via Visual OMP™, and assay specificity evaluation via ThermoSleuth™.

Hybridization Science and Modeling Capabilities

• Single-strand optimal and sub-optimal unimolecular structure prediction.
• Recursive bimolecular hybridization algorithm.
• Customized numerical analysis code for solving multiple coupled hybridization equilibria.
• DNA secondary structure display.
• Display of species concentrations as a function of temperature.
• Interface with sequence and annotation data in the SNP database.
• Interface with Oracle, SQL, and MS Access database formats.
• Rich modeling functionality covering DNA microarray effectiveness prediction, PCR and multiplexed PCR efficiency, and oligo probe and primer dimerization interactions.

Deployment and Integration

• Runs on local server infrastructure, providing access to computational and storage resources within an organization's own environment.
• API supports Perl script access to the OMP engine for programmatic integration into existing design pipelines.
• Compatible with major commercial operating systems including Windows, Linux, and Unix.
• Database integration supports Oracle, SQL, and MS Access formats for connecting to existing data infrastructure.

OMP Developer Edition is available for evaluation via a free trial or scheduled demonstration. It is positioned as a foundational computational tool for organizations building custom oligonucleotide design and diagnostic assay development applications.