Scalable, Adaptable LIMS Software for Next-Generation Genomics Labs
Product News May 10, 2011
By incorporating a set of comprehensive features over the next year in the GenoLogics LIMS, the company is building on its deep experience in genomics to meet the standardization, flexibility and user requirements of next-generation genomics labs.
Specifically, GenoLogics announced that the enhancement of its LIMS will offer the following new features:
• Pre-configured integrations and interfaces to major next-generation sequencing (NGS) instruments, with the immediate availability of the GenoLogics LIMS pre-configured for Illumina NGS systems. Additional pre-configured system offerings will be available in the second half of 2011.
• Immediate availability of GenoLogics Rapid Scripting™ Application Programming Interface (API), empowering scientific programmers and bioinformaticians to quickly and easily reconfigure or customize workflows as laboratory protocols change.
• Role-based user interfaces that address the specific needs of laboratory managers, laboratory technicians and external collaborators. The first role-based user interface, for lab technicians, will be available by the end of 2011.
“Today’s approach to data management fails to meet the needs of high-throughput, next-generation genomics labs and does not recognize that critical research is being performed on alternative platforms across and among organizations,” said GenoLogics CEO Michael Ball. “The rollout of these significant enhancements to the GenoLogics LIMS — the immediate release of our Illumina pre-configured system and new GenoLogics Rapid Scripting APIs, with role-based user interfaces later this year — provides the industry’s most advanced, comprehensive information management system for next-generation genomics labs.”
It took more than a decade and an estimated cost of $3 billion to publish the first draft of the human genome in 2000. Just over 10 years later, businesses are competing to sequence an individual’s entire genome in a matter of weeks for about $10,000 (Genome sequences data: Management, storage, and visualization, BioTechniques 2009). With decreasing costs and incredible improvements in speed driving a projected 250 percent increase of NGS product sales between 2009 and 2014 (Scientia Advisors, August 2010), organizations are facing a deluge of critical genomic data. In fact, new instruments running at capacity could generate more information in a single year than the total deposited in GenBank at the beginning of 2008 (The new paradigm of flow cell sequencing, Genome Research 2010). In a J.P. Morgan survey published in 2010, lab directors cited data storage, data management and informatics as the biggest collective hurdle to expanding NGS operations.
A full-featured LIMS manages laboratory data from sample submission to delivery of data for analysis. However, the unprecedented throughput, experimental complexity and changeability associated with NGS create unique challenges for a LIMS. The rapid timescales associated with sequencing require systems that can be configured quickly and easily to accommodate the specific instrumentation chosen by a lab. Scientific programmers and bioinformaticians must be able to easily adapt the system themselves to support changing technologies and protocols. In addition, NGS requires iterative, collaborative work that is performed by many different types of scientists.
To spearhead the GenoLogics strategy that will guide the company’s LIMS from successful early adoption to mainstream market leadership, GenoLogics also announced today that it has appointed life sciences and technology product marketing veteran Bruce Pharr as vice president of product management and marketing. Pharr most recently served as vice president of marketing at Symyx Technologies.
“GenoLogics is producing a full-featured LIMS specifically for the next-generation genomics laboratory. By comparison, other companies have either modified a LIMS developed for another function or modified analysis or pipelining software to simulate some LIMS-like functions,” Pharr said. “GenoLogics is working closely with customers and partners to provide the genomics LIMS market with a complete product that is scalable, adaptable and easy to use.”
The GenoLogics LIMS 2011 Roadmap
Scalability – Meeting genomics lab information management needs now and in the future
Genomics laboratories adopting NGS technologies need to incorporate new instruments along with existing laboratory instrumentation and software quickly and easily.
GenoLogics has partnered with Illumina to develop and deliver a LIMS mapped to its NGS systems. Together, GenoLogics and Illumina can move labs into production faster so they can quickly realize the combined benefits and advantages of the leading sequencing and information management systems.
GenoLogics is working with other partners to speed installations that quickly and easily meet the end-to-end sample tracking and information management needs of the next-generation genomics lab. The GenoLogics LIMS not only handles the increasing volume of data produced by NGS instruments, but also data from QC, microarray and qPCR instruments. The GenoLogics LIMS can interface with upstream data sources, such as freezer management systems, and downstream data pipelining and analysis tools. GenoLogics is working closely with partners on new sequencing technologies to ensure the GenoLogics LIMS meets the needs of next-generation genomics labs now and in the future.
Adaptability - The GenoLogics Rapid Scripting™ Application Programming Interface
Next-generation genomics labs need the speed-to-production advantages of a pre-configured system, but also the flexibility to quickly and easily reconfigure or customize workflows as protocols change. The GenoLogics Rapid Scripting™ API empowers scientific programmers and bioinformaticians to adapt laboratory informatics and accelerate next-generation research.
The GenoLogics Rapid Scripting API provides control and flexibility so lab personnel can quickly and easily:
• Automate sample tracking to ensure quality results.
• Incorporate new analysis methods to extract full information from leading-edge technologies.
• Optimize laboratory research workflows to streamline operations.
According to Johanna Swanson, scientific programmer at the Northwest Genomics Center, University of Washington and an early access customer, “The GenoLogics Rapid Scripting APIs were critical to the successful scale-up of our Northwest Genomics Center. We have ever-changing protocols in our lab and they evolve daily. The nice thing about the GenoLogics LIMS and the Rapid Scripting API is that they allowed us to respond and adapt quite easily, so if someone changes a step in a process, we can pull it out, reconfigure another one and put it back in place. We don’t have to rework the entire workflow, or spend time struggling to figure out how we’re going to re-engineer a hard-coded LIMS.”
Usability – Role-Based User Interfaces
In a dynamic, leading-edge NGS lab, one user interface does not fit everyone’s needs. To work effectively, users require access to all the information, and only the information, relevant to their specific job. Scientists and technical staff require access to data that helps them track sample status, determine which samples can be prepared together, simplify creation of library pools for multiplexed sequencing runs and access and review past work. Laboratory managers need a high-level dashboard illustrating everything happening in the lab. And external collaborators want quick, timely access to relevant project data.
GenoLogics is creating role-based user interfaces that address the specific needs of laboratory managers, laboratory technicians and external collaborators. GenoLogics is working with customers, prospects and partners using goal-directed design and agile development, with a target of delivering the first role-based interface for lab technicians by the end of 2011.