Skip to main content

Ahead of Planned Q1 2014 Launch, Lab7 Puts Workflow Management Software through Its Paces

Premium

Lab7, a bioinformatics startup based in Austin, Texas, is hoping to carve a niche for itself in the bioinformatics space by providing a complete solution for managing samples, data, and analysis pipelines that are used in next-generation sequencing-based laboratories.

The company is beta testing components of Lab7 Dashboard, its flagship software product that combines laboratory information system capabilities and pipeline management and reporting tools in a single system. It began testing several components of Dashboard at a number of undisclosed sites this past summer. Specifically, the company previously released a management tool for testing that helps users connect and manage the analysis pipelines they use for downstream analyses tasks like generating sequence alignments and calling variants. It also released Dashboard's capabilities for visualizing and reporting analysis results at that time (BI 6/21/2013).

Now the company is preparing to test another Dashboard component that will provide tools for tracking samples from submission through the sequencing and analysis steps. Varshal Davé, vice president of sales and marketing for Lab7, told BioInform this week that the company is still building this part of the software but plans to wrap up both development and testing ahead of a full roll out planned for the first quarter of next year.

Lab7 hasn’t disclosed Dashboard's pricing yet but the company said that it will offer a lower priced option for small research laboratories, and a more expensive enterprise option for core labs and sequencing service providers.

When it brings the complete solution goes to market, Lab7 will target clinical researchers working in commercial and academic laboratories, as well as scientists working in other applied markets such as agriculture, food safety, and veterinary science, where it expects the product to appeal to newcomers to the NGS arena, as well as more established users.

It tackles "a lot of the basic problems that you run into when you are running a sequencing facility" including how to move sequencing data between workflows and how to generate and send reports back to sample submitters, enabling these customers to process data much faster and cheaper than they normally can, Christopher Mueller, the company's president, chief technology officer, and founder, told BioInform.

Furthermore, "for someone who is just getting into the space [who needs] pipeline management and reporting … you don't need to buy three different systems. It's one platform that's priced a lot more competitively than buying those things separately," he said. On the other hand, "if you already have a lot of existing infrastructure … a lot of our value add is being able to integrate your existing infrastructure and really get true sample-to-answer information and provenance on your data."

Lab7 has already been able to test the Dashboard in some of its target markets through its beta program. Although the company isn't naming any of it beta testers, Davé described some ways in which participants have put the software through its paces. One group, for instance, implemented the solution in a clinical laboratory, which also provided an opportunity to check that the system meets necessary regulatory requirements, he said. Another group is testing the system as part of efforts to transition from microarray-based technologies to NGS.

"We are working with them to help curate a lot of the data that they've collected over the years of microarrays and make that translatable to their NGS environment and [to] make that transition a bit more seamless," he said.

Besides selling software, Lab7 also runs a services business that offers custom development and consulting to customers that need help selecting infrastructure that they can use in the lab or making their existing analysis environments more efficient. Through one of these services, called SeqSigma, the company works with customers to design and implement computational infrastructure that best supports their goals and budgets.

A second service, dubbed Dash03, focuses on tackling inefficiencies and analysis bottlenecks in computational workflows to help clients improve the performance of their systems and get results faster. It's a service that the company believes should be particularly attractive to clients that are trying to adapt pipelines that were developed for research environments for clinical use.

"We've got a lot of expertise in high performance computing and in computational biology and as well as in writing a lot of those tools," Davé said. "We can look at the code that people are using for managing those pipelines, help them streamline that code [and] improve the … turnaround time by two- to 10-fold."

Furthermore, since the company already markets software, it can use components from its system to create custom infrastructure for clients, Mueller noted. As a result, "we end up being cheaper than a lot of consulting groups that will develop everything from scratch."

In addition to selling software and consulting services, Lab7 also offers BioBuilds, which is a collection of pre-built binaries for common open-source bioinformatics tools, such as BedTools, Bowtie2, BWA, Cufflinks, SAMTools, and TopHat. The company offers these for free.

Filed under

The Scan

Possibly as Transmissible

Officials in the UK say the B.1.617.2 variant of SARS-CoV-2 may be as transmitted as easily as the B.1.1.7 variant that was identified in the UK, New Scientist reports.

Gene Therapy for SCID 'Encouraging'

The Associated Press reports that a gene therapy appears to be effective in treating severe combined immunodeficiency syndrome.

To Watch the Variants

Scientists told US lawmakers that SARS-CoV-2 variants need to be better monitored, the New York Times reports.

Nature Papers Present Nautilus Genome, Tool to Analyze Single-Cell Data, More

In Nature this week: nautilus genome gives peek into its evolution, computational tool to analyze single-cell ATAC-seq data, and more.