OMP Developer Edition™

The core of DNA Software’s product line is its computational environment, the Oligonucleotide Modeling Platform.
OMP is a programmable predictive modeling environment, which is used to develop customer-specific applications that access the computational and storage capacity of a local server. OMP takes all of the chemical and biological knowledge and expertise developed by DNA Software, Inc. and encapsulates it into a single design and simulation PCR script software platform. Key technology features of OMP include:

  • Fully encapsulated design and simulation platform that precisely designs and predicts oligonucleotide hybridization that will result from monomer, homodimer and heterodimer species under your specific oligo concentrations and temperature and salt conditions.
  • A defined scripting language that allows OMP to be programmed to perform specific tasks such as batch runs or weeding through simulation data to more easily see what’s important to your application.
  • Cutting edge peer-to-peer distributed high-performance computing architecture with an API for Perl script access to the OMP engine that can run on most any Windows, Linux or Unix machine.
  • Customizable gadgets to help you rationalize and organize cross-hybridization and melting curve data which is particularly useful for large multiplex design and simulation.
  • Simulation data can be visualized using Visual OMP™ and assay specificity can be evaluated using ThermoBLAST™.
  • Improve sensitivity with modified backbones and nucleotides.

The Science Behind OMP

Efficiently designing high-throughput, accurate diagnostics requires the ability to predict in advance precisely how oligonucleotides behave under the conditions of a given assay.

To address this challenge, DNA Software has developed the Oligonucleotide Modeling Platform (OMP), the computational environment which forms the foundation of the company’s product line. With OMP, it is possible to predict the melting temperature (Tm) of a duplex within 2 ˚C, on average; significantly more accurately than other popular commercial software packages or freeware, which simply lack the rigor and precision needed for today’s demanding, high-throughput assays. DNA Software’s CEO, Dr. John SantaLucia, has spent over 20 years developing a nearly complete database of thermodynamic parameters derived from 1000’s of empirical observations. He also developed a better model for calculating thermodynamics that produces more accurate and reproducible results.

Oligonucleotide Modeling Platform

The core of DNA Software’s product line is it’s computational environment, the Oligonucleotide Modeling Platform (“OMP”). OMP is a programmable predictive modeling environment, which is used to develop customer-specific applications. OMP takes all of the chemical and biological knowledge and expertise developed by DNA Software scientists and Dr. SantaLucia’s previous work, and encapsulates it into a single, simulation platform. Key technology features of OMP include:

  • A defined scripting language, allowing OMP to be “programmed” for specific tasks necessary to users or client applications,
  • Fully encapsulated hybridization science functions which precisely predict the DNA hybridization that will result from any specific oligo experiment under a variety different design conditions, including;
    • Single-strand optimal and sub-optimal unimolecular structure prediction, recursive bimolecular hybridization algorithm,
    • Customized numerical analysis code for the solution of multiple coupled hybridization equilibria,
    • DNA secondary structure display,
    • Display of species concentrations as a function of temperature,
    • Interface with the sequence and annotation data in the SNP database,
    • Interface with the Oracle, SQL and MS ACCESS database format,
  • Rich modeling functionality, including capabilities to predict DNA microarray effectiveness, PCR and PCR multiplexed efficiency, and oligo probe and primer interactions (dimerization),
  • A cutting edge peer-to-peer distributed computing architecture which allows OMP to run across a cluster or network of PCs, making OMP scalable and extremely fast,
  • Cross-platform capability to run on most any commercial Windows, Linux, or Unix machine.