Consulting

Extensive Scientific Consulting Experience:

Dr. John SantaLucia, DNA Software's Chief Scientific Officer, has served on numerous scientific advisory boards of international companies. He helps by deeply interacting with customers to understand their technology and then brainstorms to help them solve their critical path issues and bottlenecks as well as providing general advice to improve the science and engineering of the customers’ products.

The team at DNA Software brings deep expertise in helping customers to solve problems. Typical examples include helping to trouble shoot problematic multiplex PCR assays, molecular beacons, Taqman probes, etc. We have also worked with customers to conceive of the best plan to coordinate wet lab research and integration into software.

DNA Software has previously engaged several customers who wanted large scale computational simulations for the design of "orthogonal" probes and primers and order to anticipate the expected statistics of assay performance and identify areas where assays needed to be improved.

Training:

Customers who purchase Visual OMP^TM or OMP Developer Edition^TM are encouraged to take advantage of one and two day intensive training courses. These courses are offered periodically at various locations worldwide, and can also be delivered on-site.

This unique, hands-on, one day training course covers the science and software of Visual OMP^TM. The course is taught by the expert scientists and developers who created Visual OMP. You will cover the science behind OMP^TM, and use Visual OMP^TM in an interactive, application oriented hands-on session to help you gain confidence and competence getting the most out of this powerful software tool.

Bioinformatics Algorithms Expertise:

Dynamic programming algorithms for nucleic acids. The first bimolecular folding algorithm was done at DNA Software, Inc. Our algorithm also has unique features for the accurate prediction of DNAs and RNAs with multi-branched loops.
ThermoBLAST^TMalgorithm developed at DNA Software.
Windows compatible version of BLAST first developed at DNA Software.
Algorithms for predicting the 3D structure of RNA and DNA currently under development.
Algorithms for designing DNA nanostructures currently under development.
Novel sequence alignment algorithm for RNA which takes into account secondary structure.
Novel partition function algorithms for computing the concentrations of all species (unimolecular folded, bimolecular hybridization, and higher order structures).
Algorithms for simulating the kinetics of DNA hybridization currently under development.
Simulation of PCR product distribution at each cycle of PCR (under development).
Novel algorithms for automated design of various assays using state-of-the-art algorithms from the artificial intelligence and operations research communities (including genetic algorithms, branch and bond, Monte Carlo, and Simulated Annealing, Linear programming, Discrete event simulations, Dynamic programming algorithms).
Experience with a variety of Database software including MySQL, Oracle, and Access databases.