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Numerate Sees Opportunities for its Cloud-based Infrastructure in NGS, Sys Bio Markets

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Numerate, a privately-held biotechnology company, is expanding its cloud-based product portfolio to include analysis capabilities it can sell to clients first in the next-generation sequencing arena, and eventually in the systems biology market.

The firm is currently beta-testing a new product dubbed the BitMill data analytics platform that when launched next year will provide access to a suite of commonly used open source tools for NGS analysis such as TopHat, SAMTools, and Cufflinks. These tools will run on Numatix, a distributed computing infrastructure developed by Numerate that sits on Amazon Web Services. It plans to launch capabilities for systems biology research later on.

Initially, Numerate developed Numatix to run proprietary drug design algorithms that were used to help pharmaceutical companies such as Boehringer Ingelheim and Merck (BI 12/9/2011 and 3/16/2012) generate small-molecule drug leads in silico. However, Numerate saw opportunities for its platform to be used more broadly in biomedical science. It is currently targeting NGS research applications where scientists often have to crunch large quantities of data and require solutions that save time and are priced attractively, Brandon Allgood, Numerate's co-founder and chief technology officer, told BioInform.

"We are a drug design firm but internally we are a technology platform company," he said. "We felt that we had a system that existed already and, being in a closely related space, actually had both internal expertise … as well as advisors for the company in this area. It seemed like a natural place to launch this type of technology."

Numerate is using many of the same open source software that existing NGS analysis companies already offer as part of their platforms. However, the firm believes that by combining them with its distributed computing system it is creating solutions that are faster and more cost-competitive than similar products.

It saves time because scientists don't have to cobble together their own analysis solutions and they don't have to wait in line for time on the system because Numatix adds on compute resources as the number of users and submissions increases, Allgood said. It's also flexible so customers can request that Numerate add tools that they routinely use in their projects if they aren't already available in BitMill. They can also choose to run Numatix on infrastructure from other cloud providers, such as Google Compute Engine (BI 6/29/2012).

Finally, it's cost-effective because customers are only charged for the compute resources they use, he said. Pricing for BitMill's NGS capabilities depends on several factors, such as the software used and the type of AWS instance. However, pricing is also influenced by the AWS spot market, a system set up by Amazon to essentially sell compute time on idle machines. Through the market, customers can bid for time on these unused processors, and the cost can be on the order of ten times less than Amazon's on-demand prices, according to Allgood.

"Our framework can handle the spot market [while] many of the different current solutions cannot" because "they are more based on a traditional static cluster system that can't handle ephemeral resources very well," he said. It's one of the things "that we do to be price competitive."

Furthermore, "we've built a lot of expertise over the years in building parallel solutions so that we can rapidly come up to speed on implementing and modifying existing codes to be parallel," he added. This should give Numatix a performance advantage in addition to cheaper prices, he said.

Numerate is still accepting participants for the BitMill beta and hopes to receive applications from a wide variety of users so that it can test the platform thoroughly. It expects to continue testing the platform until Q1 2014 after which it will do a "soft launch."

"We are trying to follow an agile development and agile launch approach where we'll just continue to add users to the beta," Allgood explained.

In an attempt to drum up some interest in its forthcoming NGS capabilities, as well as highlight the flexibility of its platform for a wider set of research problems, Numerate officially unveiled BitMill this week as part of a statement announcing its participation in the eighth Dialogue on Reverse Engineering Assessment and Methods, or DREAM, project, a systems biology challenge organized and supported by Sage Bionetworks and IBM.

Numatix has been tapped to provide a testing platform and to support algorithms that will be used for DREAM's whole cell parameter estimation challenge — one of four in this incarnation of the project (BI 4/26/2013). This particular task requires participants to estimate the model parameters for specific biological process using a simulated whole cell model of Mycoplasma genitalium that was developed by researchers at Stanford University and published in Cell last summer (BI 8/3/2012).

Allgood said that Numerate plans to take some of the capabilities being used for DREAM and make them available as part of BitMill at a later date. Although the commercial product is currently focused on NGS, the DREAM partnership shows that "it's a platform that can approach many different types of verticals," he said.

Numerate doesn’t have any immediate plans to develop solutions for other life science research spaces outside of NGS and systems biology but "we are certainly open to exploring different things," Allgood said.

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