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New Players, Clinical Applications, and the Lure of Commercialization among 2012 Bioinformatics Trends

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Increasing activity from sequencing vendors and other new players, as well as a flurry of activity around clinical data analysis software and the commercialization of a number of open source tools were the key trends in the bioinformatics community in 2012.

Much of this activity spilled over from 2011, which was marked by an influx of newcomers into the next-generation sequence data analysis space and continued efforts to develop software tools for clinical data analysis and personalized medicine (BI 12/22/2011).

Sequencing vendors continued to encroach on the bioinformatics arena in 2012. The year had barely begun when Life Technologies subsidiary Ion Torrent unveiled plans to launch Ion Reporter, a commercial cloud-based variant analysis software package that it launched in November (BI 1/13/2012 and BI 11/9/2012).

Illumina took a more aggressive stance with the launch of BaseSpace Apps — a dedicated application store for BaseSpace, the genomics cloud computing platform that the company launched in 2011 (BI 4/27/2012).

Illumina secured the buy-in of bioinformatics companies like Golden Helix, Biomatters, Ingenuity, and newly minted firms like Station X and Spiral Genetics, all of whom signed on to develop apps for the store, which is slated for launch later this month. While these developers are willing to give the app-based model a try, several made it clear that they would keep a close eye on adoption rates when the store came online (BI 8/24/2012 and BI 11/2/2012).

Illumina has done its best to sweeten the deal for app developers by allowing them to set the price of their apps themselves. It has put in place a pricing structure for the core BaseSpace platform that offers users a terabyte of free space and relatively low-cost options for those that require additional storage or processing space (BI 7/27/2012).

Illumina is not the only company that finds the app-based approach promising. That list includes 23andMe, which released an application programming interface that will allow authorized third-party developers to build a broad range of apps for the web and mobile devices (BI 9/21/2012); and Portable Genomics, which develops applications for browsing personal genomic information on mobile devices such as iPhones and iPads (BI 2/17/2012).

Besides BaseSpace, Illumina also formed partnerships with companies like Diagnomics, Ingenuity, and Knome, who were all selected to provide analysis services for customers of the Illumina Genome Network, which links researchers conducting whole human genome sequencing projects with institutes that offer Illumina sequencing (BI 4/13/2012).

Other sequencing vendors also sought partnerships in the bioinformatics market this year. Accelrys and Oxford Nanopore Technologies continued to work on “nanopore-specific” workflows for the Pipeline Pilot workflow software that will enable higher-level data analysis for Oxford Nanopore’s sequencers (BI 2/24/2012). Also, Complete Genomics signed a deal with Ingenuity that allows the sequencing services provider to offer access to the Ingenuity Variant Analysis software (BI 7/27/2012).

Sequencing vendors weren't the only nontraditional players looking to grab a share of the bioinformatics market in 2012. Other new entrants into the genomics analysis space include Oracle, which released Omics Databank, a platform that provides tools to pull in data from -omics experiments and link this information with clinical data from electronic medical records (BI 1/30/2012).

Also, Qiagen and SAP announced a partnership that will focus on developing genomic sequence data alignment tools as well as variant identification software (BI 7/6/2012).

More broadly, telecommunications giant BT dipped its toe into the life science informatics market with partnerships with Accelrys and BioTeam that led to the launch of the cloud-based BT for Life Science R&D service and a Siri-based task management application (BI 4/27/2012).

The Commercial Alternative

2012 also saw some well-known open source tools go the commercial route.

In August, the Broad Institute signed an agreement with St. Louis-based cloud computing firm Appistry to distribute and support a commercial version of the Genome Analysis Toolkit. The Broad said at the time that the arrangement would allow it to provide better support for commercial users of its software and provide the resources needed to further develop the widely used toolkit (BI 8/3/2012 and BI 10/19/2012).

Then in December, Biobase signed a deal with University of Southern California and the Children’s Hospital of Philadelphia that allows it to commercialize Annotate Variation, or ANNOVAR, an open source software tool for annotating genomic variants (BI 12/14/2012).

Also this year, University of Washington partnered with Insilicos, a Seattle-based biomedical company, to market a cloud-based version of the university’s Rosetta protein and molecular modeling software (BI 9/7/2012).

Finally, the Joint BioEnergy Institute tapped startup TeselaGen Biotechnology to launch a cloud-based commercial version of the j5 software package, its automated DNA cloning tool (BI 10/26/2012).

Meanwhile, the Los Alamos National Laboratory is seeking industry partners to commercialize Sequedex, a software program developed at the lab for classifying short DNA sequence reads according to phylogeny and function (BI 10/19/2012).

In a related vein, several new startups spawned from academia moved into the limelight this year. A few examples include GenoSpace — started by researchers from the Dana-Farber Cancer Institute — which launched a cloud-based platform intended to provide access to a variety of 'omic and phenotype data (BI 6/29/2012).

And from the University of California, Santa Cruz, came companies like Maverix Biomics, which offers a cloud-based platform for next-generation sequence data management, exploration, and visualization (BI 11/9/2012); and Five3 Genomics, which began offering cloud-based cancer data processing and interpretation services using tools developed at UCSC (BI 10/26/2012).

Clinical Activity

With the rise of clinical applications for next-generation sequencing technology, there was a spike in informatics activity focused on this market.

Informatics efforts in this area included academic efforts such as Children's Hospital Boston's CLARITY (Children’s Leadership Award for the Reliable Interpretation and appropriate Transmission of Your genomic information) contest, which aimed to "advance standards for genomic analysis and interpretation and the reporting of clear, actionable results to clinicians and patients.” (BI 1/30/2012 and BI 8/24/2012).

The results of CLARITY indicated that the community largely agrees on the best informatics approaches for clinical genomic data analysis and interpretation, although there’s still room for improvement (BI 11/16/2012).

Meanwhile, PerkinElmer said that it was developing a custom bioinformatics platform to support a next-generation sequencing-based cancer genotyping assay that is under development at the Massachusetts General Hospital (BI 8/31/2012); and GenoLogics made changes to its laboratory informatics management system that will enable clinical laboratories to adhere to regulatory requirements (BI 10/12/2012). In addition, vendors such as GenomeQuest took steps to ensure that their software toes current federal regulatory lines (BI 8/10/2012).

Also, IBM and the Memorial Sloan-Kettering Cancer Center began prepping IBM’s Watson artificial intelligence technology to help with cancer diagnosis and therapy selection (BI 4/6/2012). IBM also began testing a prototype of an informatics platform that uses a combination of clinical knowledge with patients’ genomic information and electronic medical records to make treatment decisions (BI 3/16/2012).

NextBio, meantime, launched a clinical version of its life sciences platform in April (BI 4/27/2012) and then a few months later announced a partnership with the Cancer Care Institute that aimed to demonstrate NextBio Clinical’s ability to integrate and interpret genomic and clinical data from oncology patients in a medical setting (BI 6/29/2012).

In September, semantics-based software developer IO Informatics announced that it was working with the Center of Excellence for the Prevention of Organ Failure to build a web-based application that will be able to assess patients’ disease risk and make treatment recommendations (BI 9/14/2012). IO later launched a new business arm dubbed IO Healthcare that will focus on helping customers in the personalized medicine market use clinical information to enhance their research and development activities (BI 12/07/2012).

Other efforts focused on improving clinicians' treatment decisions include a partnership between bioinformatics firm Annai Systems and IT consultancy ThoughtWorks to develop a software system that extracts pertinent information from individuals’ molecular data and integrates it with information from the scientific literature and public databases (BI 11/30/2012); and one between MolecularHealth and SAP that will integrate MolecularHealth's oncology treatment decision support solution with the SAP Hana platform (BI 11/16/2012).

In November, Ingenuity said that it was working with two collaborators, including the Laboratory Corporation of America, to develop a new informatics solution that will address challenges associated with interpreting and analyzing sequence variants in the clinical setting (BI 11/9/2012).

Other activity in the clinical arena during 2012 included a grant that Integromics received from the European Regional Development Fund and the Spanish government to develop informatics solutions for analyzing next-generation sequence data in clinical laboratories (BI 2/10/2012). In addition, newbie N-of-One released its first product — an oncology informatics platform — and simultaneously announced a partnership with Foundation Medicine (BI 1/20/2012).

Buyers and Sellers

Acquisitions for the year included Accelrys’ $35 million purchase of VelQuest — a developer of software for federally regulated lab environments — an acquisition that extended the company’s product portfolio beyond research and development into late-stage product development and quality control (BI 1/6/2012).

Then in March, Certara bought Simcyp, a UK-based modeling and simulation software company, for $32 million in a bid to offer pharmaceutical customers a single informatics platform for drug discovery through preclinical and clinical development and clinical trials (BI 3/2/2012).

Meanwhile, Simulations Plus purchased software intellectual property from Enslein Research, a computational metabolism and toxicity prediction systems firm (BI 3/9/2012); and StarLIMS technologies, a subsidiary of Abbott Laboratories, purchased several distributors of its laboratory information management systems in an effort to improve services for its European customers (BI 3/9/2012).

In September, CLC Bio threw its hat into the drug discovery software ring with its acquisition of Molegro, a developer of molecular modeling software (BI 9/7/2012).

Finally, Life Technologies bought Compendia Bioscience, an Ann Arbor, Mich.-based cancer bioinformatics company, for an undisclosed sum (BI 10/12/2012).

Cloud Competition

While cloud computing continued to gain ground in the bioinformatics market during 2012, Amazon saw its position in the sector challenged by Google. In June, privately held Numerate said that it had integrated its computational drug design platform with Google Compute Engine — a new service launched by the search provider that bears more than a passing resemblance to Amazon’s Elastic Compute Cloud (BI 6/29/2012).

Google also worked with a bioinformatics team at the Institute for Systems Biology to evaluate Google Compute Engine’s ability to handle life science computing requirements.

A side-by-side comparison of the two platforms revealed some similarities and differences in terms of price, capabilities, and associated services and so those who have used both systems say the right cloud platform will vary from case to case. Google representatives would not comment on whether they intend to aggressively pursue life science clients (BI 7/20/2012).

Amazon responded quickly with the launch of Amazon Glacier, a new low-cost cloud storage solution for archiving rarely used data in August. At the time of the launch, an Amazon representative told BioInform that the company believed that the life sciences would be “a very big market” for Glacier.

The company said it expected to bag customers from several market segments including genomics and biomedicine. However, the new resource met with mixed reviews from the bioinformatics community, with some suggesting that Glacier would be “extremely useful” while others believed that life scientists would pass on the new infrastructure (BI 8/31/2012).

Also posing something of threat to Amazon’s dominance is Microsoft with its Windows Azure platform. Microsoft was able to woo customers such as TeraDiscoveries, which inked a deal that allows the company to run its Inverse Design computational modeling software on Azure (BI 4/27/2012).

Microsoft also partnered with UK-based drug discovery services firm Molplex, which is using its cloud infrastructure to build and support its computational compound screening business (BI 12/14/2012).

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