News

April 20th 2021

We are rolling out several new biophysical models in the coming weeks & months, including ...

The Promoter Calculator! The Promoter Calculator uses a biophysical free energy model to calculate the interaction energies between RNAP/sigma & promoter DNA and to predict the promoter's transcription initiation rate. Input any DNA sequence. Predict transcription rates for each possible transcriptional start site. We've already experimentally determined that the Promoter Calculator can accurately predict transcription rates across multiple datasets containing over 25000 promoters with highly diverse sequences. We then leverage these predictions to carry out automated design of synthetic promoters (inverting the model). Type in your upstream sequence & mRNA sequence. Select your target transcription rate. Generate a custom designed promoter! We've experimentally validated that the model can de novo design synthetic promoters with well-targeted transcription rates. There are several additional design modes that will generate promoters with either a single forward transcriptional start site, bidirectional promoters with two transcriptional start sites, or promoters with multiple TSSs with higher cumulative transcription rates. We're still exploring all the applications of the Promoter Calculator and we encourage you to try it out. In one example, we found that it could predict the locations of cryptic and anti-sense promoters inside protein coding sequences that were causing a genetic circuit to malfunction.

In this update, we've also released a site-wide "Leaderboard" that shows the academic & research institutions that are using the design platform the most. It's not a contest, but it is fascinating.

January 4th 2021

Updated Business Model for Academics

For a very long time (almost 10 years now), we've offered De Novo DNA's software platform for free to all academic users. In the beginning, Synthetic Biology was a new field, struggling to overcome the technical challenges of engineering organisms while also searching for high-impact, high-value applications that would demonstrate its importance. Collectively, we've achieved critical mass. There are now many examples of engineered organisms that solve an important challenge (e.g. treating disease, reducing fertilizer usage, producing new materials, and making your veggie burgers so much more tasty). Notably, many successes began in academic labs with researchers who routinely used our software platform to accelerate their organism engineering efforts. We are delighted and proud to play such a role in the field's development and success.

Now is a good time to plan for the next 10 years. De Novo DNA's platform has a sprawling user-base of over 10,000 registered researchers who have designed more than 700,000 genetic systems. Growth has been increasing; thousands more join each year. Overall, there are three types of people who use our software platform. There are the newly joined academic researchers who read about our models & design algorithms, try them out, and continue to use them sporadically for projects whenever they happen to need them. Second, there are the academic researchers who routinely use our models & design algorithms (intensively!) as a *key* part of their research workflow. They use our software to design and engineer hundreds to thousands of genetic system variants (sensors, circuits, pathways). They achieve technical success, publish great papers, and often ... they take the next entrepreneurial step with their best engineered organisms. Finally, there are the researchers at several companies who continue to license & use our platform. If you've read any Synthetic Biology / Metabolic Engineering "Top 20" list, you know about them; many of their fantastic products were designed with help from our software (but I shall write no more as we take our confidentiality clause seriously). We're grateful for their support as they've helped to keep our servers running for so long.

We have several good reasons to change our business model for academics, but we don't want to over-dramatize it. Our pricing changes will only affect the roughly 400 academic labs who routinely use our software platform as a key part of their research workflow. The academic price for unlimited usage across an entire lab is only $138 / month. That's roughly the same price as a Gibson/HiFi assembly kit or a tube of Q5 polymerase. Again, the subscription covers the entire research lab (within a reasonable limit of 20 active researchers per lab). If that sounds like a low, low price to you, that's our goal. We don't want to inhibit anyone from tackling a challenging research project. There is also an annual option ($1380 / year with 2 free months) for those who want to avoid the hassle of dealing with monthly reconciliation forms (us too!). Payments can be made on-line via credit card or off-line via purchase orders.

But if you're one of those researchers who sporadically uses our software platform, we have another option for you. Every academic researcher will receive some "coins" (either now or when they create a new account). They're not real coins. You can't sell them or trade them. But you can use the coins to submit model predictions and design jobs. The number of coins to use each algorithm depends on its computational cost and the amount of compute time that we need to purchase (those are real dollars coming out of our pocket). For example, at the extremes, an RBS Calculator prediction costs only one coin whereas an Operon Calculator design job uses 50 coins. And many of our newest models & design algorithms don't cost any coins to use (so feel free to try them out). What happens if you run out of coins? Academic researchers can purchase 200 coins for $100 USD (euros and yuan accepted as well). For commercial researchers, it's 100 coins for $100 USD. This is called our "Pay As You Go" option. If you only sporadically utilize our software platform, then you only need to pay for what you use.

As you'll notice, this is not a plan to "get rich" (whatever that means), but rather the best way of creating a sustainable business that is constantly innovating & empowering the field. Please feel free to reach out with any feedback. And it's totally OK if your University has stingy rules for purchase cards, we've created a way for you to automatically download a quote for purchase orders.

Design Organisms. Save Time. Save the World.

January 1st 2021

Happy New Year!

We had some "spare" time in this past week so we began to formally document De Novo DNA's software platform, including a glossary full of molecular biology jargon. We're not finished yet, of course. We plan on adding several guides and an extensive FAQ. But just having a written description for each of our models & algorithms (more concise than the original research articles) should be helpful, particularly for researchers new to our platform. Let us know if we missed anything!

December 6th 2020

Welcome to the latest improvement to De Novo DNA's software platform ... a place to share the latest news and changes!

It's been about a year since we relaunched our web portal to make it even easier to design genetic systems, leveraging the latest in Web technologies. During that time, we've upgraded several of our biophysical models (the RBS Calculator, RBS Library Calculator, and the Operon Calculator) and added new design algorithms (the Synthesis Success Calculator, the ELSA Calculator, and the Non-Repetitive Parts Calculator) to engineer ever larger, more complicated genetic systems with improved genetic stability. We've added easy ways for you to search, sort, and select the genetic parts that you need from huge toolboxes of well-characterized and non-repetitive genetic parts. And if you can't find your favorite host organism in our database, we've automated our genome-specific calculations so that you can add it with a single click. We have more news to share in the upcoming weeks and months. We'll also use this space to describe the latest developments in the field.

But what hasn't changed? Our mission!

Our objective is to transition Synthetic Biology into a mature engineering discipline so that you can design genetic systems that function correctly on the first try.