Benchling: Enabling the Next Generation of Data and Workflow Tracking

By Allison Proffitt  

December 2, 2019 | Benchling’s value proposition is easy to see. For researchers—whether in an academic lab, small biotech, or big pharma—keeping track of research using paper lab notebooks, email, and spreadsheets is cumbersome and inefficient. But the challenges to science are much bigger than just misplaced notes or forgotten results. That is the lowest hanging fruit—the returns for an isolated scientist.  

The real value, says Saji Wickramasekara, comes from enabling a new level of collaboration and data provenance.  

Wickramasekara is Benchling's co-founder and CEO. In 2012, Benchling started with that low-hanging fruit. “We started by building tools for the individual academic scientist working at the bench, and those are tools for designing experiments that had to do with nucleic acid sequences for DNA in proteins and then tools to document and track experiments,” Wickramasekara told Bio-IT World.  

Wickramasekara and his co-founder, Ashu Singhal, had work experience on both the wet lab and computer science sides, and Wickramasekara said the collaboration differences between the two disciplines was stark. “Software engineers have great tools for working with one another; it's very easy to collaborate on code… If you're a software engineer, you can make new tools and so I think every year that productivity bump has consistently gone up,” he said. “I don't think the same thing has happened for scientists.”  

Even with recent technical advances like CRISPR and cheap, fast genome sequencing, “more or less the entire industry is working together using paper, email, and spreadsheets,” Wickramasekara said. “The scientific complexity of what they've done has gone tremendously up, but the tools have stayed relatively the same.”  

The industry needed more than the laboratory information management systems and electronic lab notebooks that had been around for years, Wickramasekara argued. “I think that's from a different era of science research.” Organizations—and even individual researchers—have great volumes of structured and unstructured data and a host of different solutions to manage those data: a LIMS for this, a notebook for that, a spreadsheet for this.  

“We're taking a very different approach, which is sort of like a unified platform with a set of applications based on it. That unification is key because it means scientists and managers and executives are all using the same tool, and that the data is actually structured when it comes out. Whereas, you could have a LIMS for one specific workflow… but it’s going to be specific to that one team or group, and then I think you lose the value of having structured it throughout the entire organization and easily query-able.”  

The Benchling platform includes a host of applications including Molecular Biology, Notebook, Registry, Inventory, and Workflows, as well as tools for compliance and administration, sharing and permissions, a developer platform, and more. Benchling keeps both structured and unstructured data together in the same interface, an approach that facilitates workflows for the researcher. “One thing we've really worked hard on is the connective tissue between the different applications,” Wickramasekara said.  

“If I'm a scientist, I can work in my notebook, but if I create something new for example, it's going to get automatically tracked and registered with the rest of my inventory. I don't have to leave that screen. There're some fill-in-the-blank [sections] in addition to some unstructured areas, and that information is just being automatically sent to the right places in Benchling, so I can focus on just doing work.” 

Product Suite 

Today Benchling’s offerings address those problems in all research settings: grad students in the lab who want to collaborate with others; startup biotechs with two researchers, a molecule, and a vision to scale quickly; and big pharma and universities who need to track their data and their IP.   

“The system really went from the individual productivity tool to something that was more of a platform and system of record for entire organizations,” Wickramasekara said. “Not just the tools for defining and documenting experiments, but how you track and manage all the biological materials you're working with, how you manage the process of research and the actual workflows, things like how you hand-off experiments from team to team,” he explained. “The key thing throughout all of this is scientists being able to do their work with the best of applications and then the business being able to extract structured data pretty seamlessly from that.”  

Wickramasekara quotes user numbers in the hundreds of thousands. About 100,000 academics use it, he said, and more than 250 companies are either using or validating the platform, ranging from fresh startups to nine of the top 25 life science organizations by revenue.  

The different editions of Benchling vary in price and which applications are included. Benchling is free for academics to use. Anyone can sign up for a free account with an institutional email address. Principle investigators love Benchling, Wickramasekara said, because with a constant flow of students in and out of labs, graduate students can “easily package up the work they've done to hand it over to PI with one click and then there's continuity.”  

But last September the company launched Benchling for Institutions, a product that enables research organizations, universities, and medical centers to offer Benchling to their research staff, delivering more efficient collaboration and enabling institutions to systematically protect and manage their intellectual property by centralizing recordkeeping, data tracking, and administration. 

As an example, Wickramasekara mentions the CRISPR patent dispute between the Broad Institute and UC Berkeley. “With our new Institution Edition, if I'm a student at some university and I'm going to go to a different university, if I were to download all of my data and graduate, the administrators would know that this happened,” he said. “These folks are bound by confidentiality agreements and so you can't just take your data and assign access to it from one university to another. The Institution Edition helps the school administrators keep an eye on that, and alert someone that's happening.”  

Benchling for Startups, also launched last September, offers a core toolset from the Benchling platform for any early-stage life sciences research company at a dramatically reduced cost.  

“There's been tremendous growth in the number of new fledgling biotechs that are being created and we have created an offering that could be used at the very beginning of these companies' formation,” Wickramasekara said. “There’s been more and more of these startups spinning out of universities, and they actually used Benchling in the lab in university already, and so they want to keep using it, even if they're two minds and a molecule and they don't have their lab operational. So I wanted to create a new program where we could provide these companies with support and capabilities from day one, also help them with their data hygiene and best practices early on rather than waiting to the point where they're getting ready to grow like crazy. It's sometimes a little hard to build the plane while you're flying it, so to speak.”  

Finally, Benchling Enterprise includes access to all of the Benchling tools. This gives industry new insight into the data, Wickramasekara said, as well as ensuring traceability for samples.  

For example, an administrator might want to track down which experiments, protocols and plasmas results in the highest yields, Wickramasekara said. “That's a question I can just ask and with a couple of clicks get the answer to, and have full traceability back to all the different models and keys that were referenced.” Or perhaps an executive is ranking programs. Wickramasekara envisions the questions she can ask: “We thought that we had a number one program and a number two program. How our resources split between that? Is our number one program actually our number one program?” The platform enables “scientific questions that have to do with experimental context and a lot of operational questions about how resources are being allocated,” he said.  

“Our job is to help customers create high quality data, help them centralize, help them standardize it and then it will be really easy for them to get the data out and then do whatever they have to it.”