Software Created in Happy Valley Driving Biotech Innovation


Happy Valley-based De Novo DNA was founded in 2012 by Penn State University Professor Howard Salis and a team of scientists and engineers. Together, they’re reshaping how synthetic biology is carried out, maturing it into a fully-fledged engineering discipline by developing simple-to-use software capable of making the predictions necessary to improve the way organisms are engineered. The De Novo DNA platform empowers its user base to innovate everything from biofuels to renewable materials to medical therapeutics.

As Salis explains, “Before engineers build anything – whether it's a bridge, a car, a rocket or a factory – we carry out several types of design calculations to make sure that it will work on the first try.” In the growing field of synthetic biology, engineers are designing and building organisms used in various biotechnology applications — and that’s what De Novo DNA’s software platform enables. It empowers engineers with the tools they need to design microbial organisms that have the necessary functions without having to experiment extensively with trial and error.

Simplifying Synthetic Biology

There have been many advancements in the field of synthetic biology. Today, engineers can synthesize any DNA sequence to reprogram the capabilities and metabolism of an organism. But there are still challenges. With so many interactions going on inside of a cell, it’s hard to predict the best DNA sequence that will achieve everything that engineers are looking for, before inserting the sequence into an organism.

De Novo DNA solves the challenges that engineers face by developing and applying sophisticated models and design algorithms that make it possible to control the amount of protein produced inside of a cell by predicting the speed that specific DNA sequences will be transcribed and translated.

“Those predictions are then combined to create large, sophisticated genetic systems. For example, our algorithms are applied to engineer and optimize multi-enzyme metabolic pathways that manufacture biorenewable chemical products,” Salis notes. “The predictions are also useful in engineering biosensors used to detect and quantify metabolite concentrations.”

All the detailed models are packaged within De Novo DNA’s user-friendly web interface, so that researchers can design DNA sequences for their own applications.

“De Novo DNA's mission is to make engineering biology easier, by enabling researchers to predict what their DNA sequences will do before they are introduced into an organism's genome,” Salis says. By doing so, their platform radically decreases the amount of time and money that’s needed to engineer organisms that have a desired set of capabilities.

De Novo DNA’s Software Platform

More than 9,000 registered researchers have already used De Novo DNA's software platform, designing more than 650,000 synthetic DNA sequences. This Happy Valley company serves a broad customer base that spans the industrial, medical and agricultural biotech industries and De Novo DNA's software platform is the only one of its kind. There isn’t another platform available to provide these invaluable predictions to engineers working within biotechnology.

“We have continually advanced the state-of-the-art in the field by developing new algorithms to overcome our research community's challenges. As growth in the synthetic biology product space has continually grown (now well over $10 billion), De Novo DNA's software platform will remain the number one way that researchers design complex genetic systems without trial-and-error experimentation,” Salis says.

De Novo DNA in Action

So, how does it all work?

Consider a typical challenge, during which researchers aim to express six enzymes in a new, engineered organism. The goal is to improve the enzymes’ production rates to optimize the way the organism converts organic materials into usable products or energy sources. If the researcher’s successful, they stand to make a profit by developing the organism as a valuable component for bionewable products.

Salis explains, “Without our design algorithms, this type of project would require a great deal of brute force experimentation.” But by using the algorithms and workflow De Novo DNA’s platform provides, everything is simpler. Researchers can design their version 1.0 genetic system and go through small, designed experiments to optimize production rates.

“We use a combination of biophysics, machine learning and global optimization to learn sequence-function relationships and design optimal metabolic pathway variants,” says Salis.

In short, the software platform and solutions provided by De Novo DNA increases the odds of researchers’ and engineers’ success, which is key to future innovation.

After all, as Salis says, “No one builds thousands of bridges to see the few that will stand firm. De Novo DNA's platform enables researchers to only build the organisms that have the highest chance of success.” 

Happy in Happy Valley

As for the company’s location, Salis is happy to call Happy Valley home. Part of what makes the environment so unique as a hub of Industry 4.0 is the interwoven ties to Penn State University. That’s one of the ways that Happy Valley has supported the growth of many companies in the region, including this one.

“De Novo DNA's connection and proximity to Penn State University has been very advantageous,” he explains. “Penn State has been very supportive, for example, by providing De Novo DNA with access to an excellent laboratory space where we carry out experiments to validate and demonstrate our design platform.”

There are so many reasons that Happy Valley draws talented researchers, entrepreneurs and business leaders. Not only has it been hailed as one of the best areas for business and careers, it was also listed among the top cities in the United States for entrepreneurs by Entrepreneur Magazine.

Salis echoes the sentiment, noting that, “Overall, the ecosystem in Happy Valley is excellent for start-up companies. We can reach our target customers and markets while achieving lower-than-typical cash burn rates.”

Want to learn more about De Novo DNA? Visit




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