Accelerating Genomics Research at Synpromics

Dominick Zheng

Dominick Zheng is an Application Scientist at Benchling, where he handles configuration, implementation, and ongoing support for our customers around the world. Recently, Dom traveled to Edinburgh, Scotland, to onboard one of our new customers, Synpromics.

Most people know of Edinburgh, Scotland, for its castles and rolling hills, but as a molecular biologist, I had my own reason to be excited: this was the birthplace and resting place of Dolly the sheep, the first mammal to be successfully cloned from an adult cell. I had read countless articles about Dolly as a student, so visiting her in person at the National Museum felt like a pilgrimage of sorts — though it also made the decision to have haggis for dinner that night a real moral dilemma.

In truth, I was almost as excited to see Dolly as I was for the main purpose of my trip: to get a groundbreaking local genomics company, Synpromics, up-and-running and trained on their first ever R&D informatics platform.

In some ways, Synpromics’s work is a distant descendent of Dolly. Synpromics is the leading developer of synthetic gene promoters for the biotech industry. Synpromics's promoters are designed to be active only in specific cell types, which means scientists can regulate genes of interest with much greater granularity. Fine-tuned gene regulation is vital to the most cutting-edge drug modalities, including cell and gene therapy. Synpromics’s particular approach makes manufacturing and scaling these therapies much more efficient, which means drugs not only get to patients faster, but are also more affordable and widely available.


Dolly the sheep on display at the National Museum of Scotland.


Deploying R&D Informatics at Synpromics

With Synpromics's previous systems – paper notebooks, spreadsheets, and emails – scientists spent roughly 30% of their time manually entering data, searching across unstructured records for up-to-date results, and unintentionally duplicating efforts. By the time I entered Synpromics, it became clear that its leadership team had done a great job of aligning everyone in the company on how a unified informatics system would solve these problems.

The first person to greet me was Bala Bendi, an enthusiastic Project Manager who was already well-versed in Benchling from our preliminary meetings. Over the course of four weeks prior to the training, Bala and other members of Synpromics worked remotely with our team to configure Benchling for their specific workflows and data models.

Bala’s enthusiasm was shared by the others—even before our training sessions began, scientists with technical backgrounds were telling me about inefficiencies they’d found in the ways that they currently track data, while scientists with less software experience were vocal about their excitement to learn. Over the next two days, I trained Synpromics's scientists on Benchling's Bioregistry & Sample Tracking system in addition to the Electronic Lab Notebook.

In the Bioregistry & Sample Tracking sessions, we went through examples of simultaneously creating and registering new entities and physical batches. We also walked through plasmid tracking, which is fundamental to Synpromics’s work, with a focus on metadata standardization and sample tracking compliance. This was a necessary shift from their previously uncentralized and unstructured tracking methods. Scientists wanted to spend less time on data entry and querying, and more time on the actual development of synthetic promoters that drug companies rely on. Now, they'd have a single, easy-to-use system where they could quickly surface relevant and trustworthy data.

Similarly, Synpromics’s paper lab notebooks previously made each scientist operate as a silo, making tracking and reporting research progress very difficult. As a rapidly growing organization, Synpromics made it a priority to address this issue. Benchling's Lab Notebook would enable Synpromics to have a centralized, searchable, and collaboration-friendly system of records across the entire R&D organization.

The enthusiasm of the Synpromics team to upgrade their informatics really came through during our sessions on the Lab Notebook, when a Senior Researcher (who had never used an electronic lab notebook) asked barrage after barrage of questions. At one point, she apologized to the group for asking so many questions, but it was clear that she – along with everyone else at Synpromics – was determined to get things right.

By the end, the scientists who had no prior informatics experience admitted that while they initially felt nervous about keeping up with the software transition, they left thinking everything was much easier than expected.


Tea, Cakes, and Genomics

Following our trainings, Synpromics had “tea-and-cake time” (a classier equivalent to our happy hours). I was consistently struck by the friendliness and foresightedness of the Synpromics team throughout my visit, and I couldn’t help but think about how far we’ve come since Dolly – both in terms of groundbreaking science and advancements in informatics. The intricate genomics work at Synpromics is lightyears ahead of the work done at contemporaries of the Roslin Institute in the '90s; and similarly, the systems we have today for tracking and measuring research are lightyears ahead of the paper and spreadsheets that previously impeded scientific progress.

I knew, then, that I would return home changed by my trip: with even greater respect for today's scientists, and with a newfound love for haggis.

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