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UCSC Spinout Maverix Biomics Launches Cloud-based NGS Analysis Platform


Maverix Biomics, a San Mateo, Calif.-based bioinformatics startup, this week launched the first version of the Maverix Analytic Platform, a cloud-based offering for next-generation sequence data management, exploration, and visualization.

The newly minted firm was founded by Todd Lowe, an associate professor of biomolecular engineering at the University of California, Santa Cruz, and the company’s chief scientific officer; Patricia Chan, a research scientist at UCSC and the company’s chief technology officer; and David Mandelkern, the company’s president and CEO, who has a background in software development.

The 12-person firm is commercializing some applications that were developed at the University of California, Santa Cruz, such as the UCSC Genome Browser, which is integrated with the platform. The company has also licensed software dubbed make-browser, which was developed by two company founders —and enables “on-the-fly creation of new genome browsers for new organisms,” Mandelkern told BioInform.

Usually, “you have to do a lot of configuration and setup for each different type of organism that you want to visualize and that can be a very lengthy process if you are trying to do this manually,” he explained. With the technology licensed from the UCSC founders, "as you are uploading the GenBank file for a new organism … we can build a new browser on the fly in the cloud.”

Maverix is the second UCSC spinout to launch a commercial offering for the NGS analysis space in as many months. Five3 Genomics, which is commercializing technologies developed by three UCSC graduates, plans to offer cloud-based data processing and interpretation services to researchers, pharmaceutical companies, and healthcare organizations involved in developing and applying personalized cancer therapies (BI 10/26/2012).

While Five3 is focused on the oncology research market, Maverix hopes to appeal broadly to all researchers who require genome analysis tools, including those working with non-human genomes.

The Maverix Analytic Platform provides the UCSC technology alongside other open-source algorithms and applications such as TopHat, Blast, Annovar, AllPaths-LG, and more. The system also incorporates publicly available genomic data allowing users to analyze their data in the context of earlier study results.

The company offers pipelines for RNA-seq and ChIP-seq analysis, SNP detection, ribosome profiling, bisulfite sequencing methylation analysis, and de novo small genome assembly, among others.

Users can upload sequence data from a variety of organisms — human, animal, plant, virus, bacteria, and more — and access and run Maverix’s pre-configured tools on Amazon’s cloud infrastructure, eliminating the need for upfront investments in IT infrastructure and the services of bioinformatics experts, Mandelkern said.

The platform allows more advanced users to customize their analysis workflows as well as incorporate their own analytic tools if they need to. It also offers automated quality checks on data uploaded by users or imported directly from sequencing service providers to ensure valid and reliable analysis results.

The company also creates customized versions of the UCSC Genome Browser for customers based on their organisms of interest. These bespoke browsers include analysis results as persistent data tracks for visualization and further studies. It also includes other traditional two-dimensional data visualizations such as differential expression heatmaps as well as box, line, and scatter plots.

Users can also share their data and analysis results and analysis pipelines with collaborators via the Maverix platform and can create so-called “communities of discovery” around specific organisms or common research areas.

They also receive automatic notifications and alerts that provide current information about their research areas including relevant journal articles, availability of data sets, and new tool releases based on previously run analyses and specific areas of interest.

Maverix also offers specialized hardware for customers who are concerned about the privacy and security of their data. In addition to Amazon’s cloud, Mandelkern said that the company also offers a secure private cloud environment for use by pharmaceutical companies, for instance.

The company also has dedicated servers that handle applications that require large quantities of memory in order to run, he said.

“Depending on how proprietary you want to keep your data and what type of application you’re trying to do … applications may be running in a number of different cloud sites.” However, all the platforms are linked to one another so users don’t need to concern themselves with data transfer issues, he said.

Maverix operates a pay-as-you-go pricing model, which varies depending on the organism being analyzed, the size of the dataset, and the type of analysis that needs to be done, Mandelkern said.

The starting price range for hosting up to a terabyte of data and accessing “some of the search and alert capability that we provide” would be around $4,000 per month for a commercial customer and around $1,000 for an academic customer, he said.

Maverix is targeting its tools to a broad range of life science researchers in academia as well as pharma, biotech, diagnostics, and agri-business.

In these markets, the company expects to go up against smaller informatics companies whose offerings tend to appeal to users with some bioinformatics experience, as well as larger companies like CLC Bio and Ingenuity, Mandelkern said.

In terms of the former, “we [are] pretty unique in terms of who our target audience is” — which is the biologists as opposed to bioinformaticians, he said. On the other hand, Maverix's cloud-based approach sets it apart from companies like CLC Bio, which only offer software that run on internal infrastructure, he said. So, even if these companies decide to switch to the cloud, “we have got a head start.”

He also noted that while Maverix’s nearest competitor, DNANexus, offers a “great proprietary browser,” its accompanying analytic capabilities are “limited.”

Maverix is also working to tie its platform into Illumina’s BaseSpace, Mandelkern said, adding that the company will provide details about this effort at a later date.

Maverix currently has several pilot customers working on projects in areas such as biofuel design, diagnostic test development, and plant genome analysis although Mandelkern could not divulge any specific names.