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Benchling Partners With Gen9 on DNA Library Design Tool as Software Suite Grows


This article has been update to correct Singhal and Bond's respective titles.

NEW YORK (GenomeWeb) – Digital lab notebook software firm Benchling has partnered with synthetic DNA maker Gen9 to create a DNA library design tool. Launched earlier this month at SynBioBeta in California, the partners intend for the online tool to streamline the process of ordering large libraries of DNA variants. It's the latest in a series of moves for the startup firm as it tries to build its user base.

The synthetic biology space was where San Francisco-based Benchling's initial users came from, Co-founder Ashu Singhal told GenomeWeb. As it builds out its applications, it's looking for ways to raise awareness of what it can offer the industry.

"Partnering with a name like Gen9 that's known to have output that is good and trusted by companies allows [synthetic biology companies] to realize the functionality of our tools and bring our software to more researchers in the field," he said. The partnership with Gen9 is one way to add applications on to its CRISPR/Cas9 design tools and enterprise digital lab notebook functionality.

Boston-based Gen9 is trying to position itself as a mass producer of synthetic nucleic acids. It counts Harvard University and Broad Institute Professor George Church and Stanford University Professor Drew Endy as co-founders.

Its DNA products are used by a number of biotechnology companies in the pharmaceutical, ag-bio, and even clean tech spaces, Gen9 CEO Kevin Munnelly told GenomeWeb. The DNA is used to make antibodies, enzymes, molecular standards, and even flavors and fragrances.

"Customers have hit this bottleneck on how they can get things designed quickly," Gen9 Senior Director of Product Strategy Andrew Bond said. There are several rules governing sequence design and the design process used to be carried out manually.

The collaboration between Gen9 and Benchling now allows customers to upload a sequence into an online portal and generate variants in a slick point and click interface. So far, the portal is only designed for customers looking to create antibodies or enzymes, Gen9 said, but it represents the firm's ability to "rationally design" libraries," Bond said.

"In the past, when other companies made libraries, they were doing it in a degenerate approach. There was not necessarily uniform representation of all the variants," he said. "We allow for every library product. Everything is built at the oligo level."

Gen9 said it can make hundreds of thousands of oligos at a time and can create pooled libraries where the number of variants reaches 10 billion. The firm also makes arrayed libraries in 96-well plates.

The new design tool allows users to open a sequence and make any number of changes at any of the positions. The software analyzes the sequence and allows the viewer to see the sequence in terms of the codons. With the tool, the user can choose new codons at a position to create variants for the synthetic library. The number of variants can multiply quickly, with multiple changes at multiple positions, but the software can keep track of the combinations. The tool even offers the bonus feature of removing certain variants from the library.

"When we started selling pooled libraries, we were selling them as fully combinatorial, but customers didn't want all of the variants, they only wanted a subset of them," Bond said. "Here we can allow customers to remove some combinations. It gives them a lot of freedom in design."

The range of design possibilities could form the start of a bigger design collaboration. Gen9 is interested in moving past proteins to designing entire gene and protein pathways for its customers. When pressed for details about the deal between the two companies, Gen9 officials would only say that it was "mutually beneficial." Singhal added that it "benefits [Benchling] financially." 

Elsewhere, Benchling is pushing the use of its digitized laboratory notebooks. It released the lab notebook application in April, Singhal said, and has landed both academic and enterprise customers.

"It's a product where it's going to take more work to get it to be the fully optimal lab notebook for any biology researcher to use, but we're planning out a lot of extra features for it, he said. "You can think of it as trying to make [note-taking software] fully optimized for how research actually does work."

Singhal also said that CRISPR design remains a big draw for Benchling. "We've seen the usage of that grow a lot in the last year. A lot of our [customer's] requests are to make that type of design a lot easier."

With the Gen9 tool launched, CRISPR-related tools and the lab notebook remain Benchling's main focus, Singhal said, but he's keeping an eye on how to move to the mobile platform.

"Anything we can do that brings Benchling to the bench," he said.