NEW YORK (GenomeWeb) – Qiagen and BioTeam are seeking early testers for a microbial genome analysis solution jointly developed by the companies that couples a number of bioinformatics software tools from Qiagen with a BioTeam-developed server appliance.
The partners have put together a proof of concept of the so-called BioTeam Appliance, Microbial Genomics Edition that they will showcase at the Bio-IT World conference in Boston this week. The purpose of the demonstration is to gauge the market interest in the solution as well as to secure a limited number of users willing to participate in an early access program that will put the solution through its paces, Anushka Brownley, a senior scientific consultant for BioTeam, told GenomeWeb.
Ten users will have a chance to try out the appliance and provide feedback that will be used to improve the system ahead of its full launch, planned for the end of the year. Interested customers can sign up at the BioTeam booth during the Bio-IT meeting and the partners plan to start shipping systems to EAP customers in July.
BioTeam has worked on consulting projects in the past where it had to integrate Qiagen's bioinformatics solutions with infrastructure it designed and built for clients. "We are already familiar with their software applications," Brownley said. "We realized that we have an opportunity to package this expertise into a product to help both of our companies deliver some of our best practices to a wider market."
The planned system will provide easy-to-run infrastructure for analyzing microbial genomes, from sequence assembly to microbe identification. It will include many of the existing tools in Qiagen's bioinformatics portfolio, including some of the software solutions it acquired when it bought CLC Bio in late 2013.
The so-called Microbial Genomics Pro suite includes the CLC Genomics Workbench and CLC Genomics Server software packages, which offer tools for using and analyzing next-generation sequence data, including de novo assembly and mapping; and the Microbial Genomics Module, which offers pre-configured workflows for microbiome profiling. Also available is the CLC Genome Finishing Module, which provides tools for improving assembly quality; the MetaGeneMark Plugin, which allows for gene finding in bacterial genomes and metagenomes; and a number of reference databases. The suite is currently used by the US Food and Drug Administration for infectious disease research and outbreak analysis.
In addition to these programs, customers have the option to install and run other bioinformatics applications on the appliance, such as laboratory information management systems.
In terms of hardware, BioTeam is using the same infrastructure for microbial analysis that it uses for its other products, like the BioTeam Appliance Galaxy edition, which was launched in 2013. That product couples the server appliance with the open-source Galaxy analysis software and costs $35,000 for a base unit. The hardware was previously called the SlipStream appliance and was renamed the BioTeam appliance. The hardware component of the microbial analysis product features a Dell T630 server with 20-core Intel Xeon E5 processors. A base model comes with 384 gigabytes of random access memory, with a larger system offering as much as 512 gigabytes, and 32 terabytes of storage, with larger models offering up to 96 terabytes. It also includes a genomics server that lets users add custom functionality to the system.
Setting up the system is straightforward and does not require specific computing expertise, according to Brownley. To get their appliances configured, all users need to do is connect them to a mobile device or laptop computer. Each appliance comes with a key that allowsitto set up its own wireless network, she explained. When users connect the system to their mobile phone or laptop, the appliance's network shows up in the list of wireless networks that they see on their device. Connecting to that network sends the user to a web address that pulls up an interface to the appliance through which users access, control, and manage the appliance. "You don't have to buy BioTeam consulting time to set up the appliance and you don't have to bring in your IT expert to set up the appliance," she said. "A researcher can do it with their mobile phone."
Potential applications for the BioTeam microbial appliance include infectious disease profiling and biosurveillance, Frank Schacherer, Qiagen Bioinformatics' vice president of discovery genomics, told GenomeWeb. The system could easily be deployed in an infectious disease outbreak in a resource-poor setting, he said, adding that limited or no Internet connectivity is often an issue in these settings, rendering cloud-based solutions rather ineffective for genome analyses.
"You need to have some way to bring all that analysis capacity onsite," he said. "And that makes a very strong case for this kind of appliance approach. You just ship it out there, plug in your laptop to the appliance, and you are ready to go." However, the system can also be used in any research lab that analyzes microbial data, he added. "If you just prefer to not deal with setting up your own IT infrastructure, you can also get [the] appliance."
The BioTeam Appliance, Microbial Genomics Edition starts at around $70,000 for a base model that includes all of the Qiagen software, 384GB of RAM, and 96 terabytes of storage. That size system should be sufficient for most analyses that customers will need to run, Brownley said, but customers who need more capacity can purchase a bigger system.
Qiagen Bioinformatics offers the same maintenance services and software updates to appliance customers that it provides to customers of its standalone software solutions. As is the case with the standalone solutions, these services are included in the cost for the first year and are available afterwards for an additional cost, Schacherer said. However, appliance customers are not obligated to pay for these extras if they don't want them.
At that price point, the microbial genome analysis appliance should be attractive to potential customers, according to Stan Gloss, CEO and founding partner at BioTeam. In addition to being a viable option for researchers with limited Internet access, appliances could also be a boon for researchers in clinical contexts who want cheap hardware but are unwilling to use public clouds. However, high prices have hampered the adoption of some systems. Knome, for example launched its proprietary genome interpretation solution, KnoSys, as an appliance offering as an alternative to cloud solutions. But, as GenomeWeb reported, the company was unable to get the cost of the system down to under $100,000 and could not compete in the marketplace.
BioTeam, on the other hand, is not trying to market a proprietary solution, which helps keep costs down, Gloss told GenomeWeb. "Because we use commodity hardware, we are able to offer the [appliance] at a reasonable price." On the software side, "we are working with Qiagen but our platform is open, so if there is an end user and a different algorithm and application they want to use, no problem." Moreover, the system is plug-and-play and comes with everything that researchers need for genome analysis, he pointed out. Also, researchers don't need computing expertise to configure and run the appliance, so they don’t have to hire staff to maintain and run the system. It makes best practices in computing developed by BioTeam over the years "easily accessible" to a large number of scientists at a more affordable price, Gloss said.
The cost of purchasing the hardware and software independently, compared to buyingan appliance, are factors that could sway potential customers, Qiagen's Schacherer noted. "If you consider independently buying hardware, setting up pipelines, and keeping them up to date, and the costs of needing more powerful hardware when you have less efficient software, getting a ready-made, efficient solution may be the option that saves you considerable money and hassle," he said.
If this system does well in the market, Qiagen would consider making other software packages in its portfolio available in this manner, Schacherer said, but it's too early to say how big the market will be. "I think the microbial field use has the strongest case for an appliance as a preferred mode of deployment, which is why we are starting out with this," he said. "Part of this pilot's benefit is that we will get a bit better understanding of the market's appetite for such an appliance in traditional lab settings. We'd consider doing another one for those customers, if that interest is high and tells us this is something people want." The pilot also offers an opportunity for the partners to determine if the price point works for the market, he added.