CHICAGO (GenomeWeb) – While working on their respective PhDs at the Centre for Genomic Regulation in Barcelona, Spain, about five years ago, Maria Chatzou and Pablo Prieto noticed something about analysis of genomic data.
"We found ourselves using around 80 percent of our time on computational tasks rather than on actual research and results," Chatzou recalled.
So Chatzou, Prieto, and some other researchers there decided to create a new, open-source programming framework to make processes more efficient. They called it Nextflow, and it was an immediate hit; Chatzou estimated that half of all organizations worldwide involved in any sort of DNA analysis use Nextflow for at least some processes, as do four of the world's 10 largest pharmaceutical companies.
"The fast adoption of Nextflow really highlighted the fact that there is a huge need and that this problem was not just our problem. It was a problem of everyone doing genomic analysis," Chatzou said. "Now, Nextflow is being massively used by a large community."
Indeed, a paper that appeared in the journal Nature Biotechnology in April — with Chatzou and Prieto among the listed authors — concluded that Nextflow was "superior" to and more numerically stable than other open-source workflow management systems that can be limited by storage constraints for very large computational projects such as gene annotation.
"Nextflow is a solution to the numerical instability issue that occurs when data-analytic pipelines are used on different computational platforms," the authors stated in the paper.
"Numerical instability affects most types of in silico analyses, and although the overall impact of numerical stability on final readouts may seem modest, the lack of effective solutions to date has left users with a daunting challenge when it comes to choosing which platform to use," they noted. "Careful monitoring of database and software versions is simply not enough. A lack of numerical stability can have problematic consequences when processing experimental data, such as compromising verification and updating of previous results."
Still, the free software had its limitations.
"What we actually soon realized is that all of these people using Nextflow, they still need to build on top of it custom software and hardware solutions in order to be able to further analyze this data and get insight," Chatzou said.
"The second problem is that in order to use Nextflow, you need to be able to program and you need to be a bioinformatician. That means that only about 20,000 people on this planet can really use Nextflow. That's a huge barrier."
These shortfalls led Chatzou and Prieto to form a company called LifeBit earlier this year. In April, they set up shop in the high-performance computing hub of Cambridge, England, the home of Lifebit Chairman Alan Barrell, an angel investor and entrepreneur in residence at the University of Cambridge's Centre for Entrepreneurial Learning.
"We are not trying to commercialize Nextflow because Nextflow is open source in the research domain," said Chatzou, who is CEO of Lifebit. Prieto serves as chief technology officer and chief security officer.
Instead, Lifebit is trying to add services and components, including interfaces and artificial intelligence, to the basic Nextflow platform. "We're building on top of it a high-performance, big data solution combined with very powerful AI," Chatzou explained.
"We are putting the right high-performance computing technologies together and the right applications together and we are building on the cloud a completely scalable and modular application ecosystem," Chatzou said.
Lifebit has developed several proprietary algorithms and also has been collecting and parsing data to standardize ontologies.
"On top of that, we have already started implementing the first algorithm of machine learning," Chatzou said. The first task is to train the infrastructure on how to optimize combinations of resources and applications in pursuit of faster processing at lower cost.
The fledgling company now is trying to raise £1.2 million to £1.5 million ($1.6 million to $2.1 million) in private equity. Chatzou is optimistic that the money will come in soon because of some early successes.
High-tech business accelerator Techstars chose Lifebit for its most recent three-month program in London, which came with a €120,000 ($141,000) award and the opportunity to present its technology to potential investors.
The program ended last week with London Demo Day, where Chatzou's presentation was captured on video. She said investors were "queuing to talk to us" at the end of the Techstars event on Oct. 11.
"What if DNA analysis was so simple, anyone could do it?" Chatzou posited during Demo Day. "That would radically transform pharma research, and that is exactly what Lifebit does."
During the three-month Techstars accelerator program, Lifebit cut monthlong DNA analyses down to about one day, and lowered computational costs from $10 to $1 per sample, according to Chatzou.
"Our intelligent platform technology understands DNA data and generates meaningful insights at scale," she said in the video.
"We are now building the infrastructure for the entire genomic industry," Chatzou said during her presentation. "We enable pharma companies [to] develop better therapies and better drugs while saving them money and time."
The technology also should be able to help smaller hospitals and independent laboratories start precision medicine programs by addressing the global shortage of bioinformaticians. Chatzou believes Lifebit's cloud-based platform can bring the necessary expertise to the estimated 5 million biomedical experts worldwide without informatics training.
"Existing processes just aren't keeping up" with the data explosion, Chatzou said, noting that 80 percent of time is "wasted on computational tasks rather than on actual research and results," based on her experiences in Barcelona.
"What this [platform] does is expand the number of users able to analyze this data today from 20,000 specialized bioinformaticians to over 5 million biomedical experts."
Lifebit certainly is not the first player trying to address the shortage of bioinformatics professionals. For example, Israeli genomic analysis startup Genoox has expressed a desire to accelerate the clinical uptake of next-generation sequencing by making its variant classification technology accessible to community hospitals and laboratories, not just academic medical centers. That company quietly entered the US market this year, then raised $6 million in a Series A round of private equity investment that closed in June.
However, Lifebit is building on the rapidly adopted phenomenon called Nextflow, with two of the latter's creators at the helm. Lifebit is now is in closed beta at several pilot sites and will open up its beta testing in January, Chatzou said.
The UK-based startup is looking beyond Western labs and pharma companies as well, working on a deal with a major technology vendor to bring genomic informatics and basic sequencing to low-resource parts of the world in the fight against malaria.
Chatzou said she is not ready to disclose details, but said that the company would likely announce something by the end of the year.