Next-generation sequence data analysis, translational research, and cloud computing were on the lips of researchers in the bioinformatics field during 2010 — a year that saw the rise of several new players in the space and shifting business strategies to accommodate the increasing demands of the life sciences community.
Whether it was a direct result of the economic recession and dwindling budgets or just good business strategy on the part of the companies involved, 2010 saw a number of new partnerships forged, older ones renewed, and a few high-profile acquisitions.
Undoubtedly, the largest and most expensive M&A activity in the sector during 2010 was Accelrys’ purchase of Symyx in July for approximately $180 million (BI 07/02/2010).
Accelrys first announced its plans to buy Symyx in April (BI 4/9/2010), but what should have been a relatively smooth process hit a snafu when Symyx began receiving competing offers from Certara, the parent company of Tripos International and Pharsight, which submitted a series of offers for the company that were all ultimately rejected (BI 06/25/2010).
After a few months of furious bidding and counter bidding, shareholders for Accelrys and Symyx approved the merger on June 30.
In other acquisition news, Thomson Reuters purchased GeneGo earlier this month to provide a pathway analysis complement to its life science offerings (BI 12/03/2010). Meanwhile, in August, IDBS bought Quantrix in an all-cash transaction to provide modeling and analytics tools as part of its life science portfolio (BI 08/27/2010). Financial terms were not disclosed for either transaction.
In addition, this year marked the rise of Microsoft Research as a formidable player in the bioinformatics arena with the summer launch of the open source Microsoft Biology Foundation suite of tools at the Intelligent Systems for Molecular Biology Conference (BI 07/16/2010).
The group is already gearing up for the release of version 2.0 of MBF next summer. Simon Mercer, director of Health and Wellbeing at Microsoft Research, told BioInform in October that the development team will focus on "scenario-based development," which involves asking current and potential users to submit scenarios that will help the team "better understand the needs of the scientist" and drive the development of a "rich repository" of features that will meet researchers' needs (BI 10/15/2010).
Other firms took steps to move into the informatics market during the year. For example, Nature Publishing Group's parent company Macmillan Publishers launched Digital Science, a new business focused on developing tools and services for scientists, manager, and funders that will provide "technology-based solutions for research rather than scientific content." (BI 12/10/2010).
So far, Macmillan is keeping mum about exactly what Digital Science's offerings will be but it did disclose that three firms — SureChem, BioData, and Symplectic — will provide resources to the new business and also that it has selected Timo Hannay, former publishing director of nature.com, to lead the new division.
Next-Gen Sequencing Marches on...
As in the past several years, rapid advances in the field of next-generation sequencing fostered a considerable amount of bioinformatics development, but one trend that set 2010 apart from prior years was the level of activity in the commercial sector. Many software companies launched new products in 2010 targeting the next-gen sequencing market, while others changed business strategies in hopes of gaining an edge in what is still one of the largest sectors in the bioinformatics space.
For example, Strand launched Avadis NGS 1.0, the first version of the company's software for analyzing next-generation sequence data from ChIP- and RNA-sequencing and DNA variation experiments (BI 10/09/2010).
GenomeQuest also set its sights on marketing its GQ-Engine to the whole-genome analysis market space (BI09/17/2010), as did San Francisco-based, Omicia, which has developed a set of platforms for use in clinical settings. (BI 06/25/2010)
Meanwhile, Integromics, a company that has historically focused on developing tools for microarray and qPCR analysis, rolled out a new next-generation sequence analysis software called SeqSolve earlier this month (BI12/03/2010). Similarly, Biobase launched GenomeTrax database, the company's first product geared toward the NGS market (BI10/15/2010), and Genedata, a company that has also focused on microarray analysis in the past, released Refiner Genome, a new NGS module for its Expressionist analysis platform (BI10/01/2010).
Moving into 2011, these firms stand to compete with players who have already established a strong foothold in the sequence analysis market, such as CLC Bio, Geospiza, DNAStar, and SoftGenetics.
Sequencing vendors also took steps to support the development of improved analysis tools during the year. In January, Life Technologies announced that it would dedicate approximately $100 million over the next three years to address bioinformatics challenges associated with whole-genome sequencing and at the same time launched Bioscope — a software package that is intended to decrease data analysis time by 80 percent, as well as to help researchers with SNP detection and transcriptome analysis (BI 01/27/2010).
Illumina, meantime, launched a competition in June called the Illumina Data Excellence Award, or iDEA, which is “designed to challenge the scientific community to develop creative visualization and data analysis techniques” for interpreting next-generation sequence data. The company is accepting entries through March 15, 2011 (BI 6/18/2010).
Internally, Illumina is exploring ways to enable whole-genome visualization on mobile devices, and demonstrated its prototype "MyGenome" app for the iPhone and iPad at several conferences during the year (BI 8/20/2010).
PacBio, which is slated to launch its single-molecule sequencer in the first half of 2011, kicked off its DevNet developers' network in June, with the goal of supporting third-party software development for its platform (BI7/9/2010). The site provides access to data sets, source code, application programming interfaces, conversion tools, and documentation related to SMRT sequencing.
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… as Translational Research Appears on the Horizon …
Progress in translational research and personalized medicine also drove informatics development in 2010, though the commercial payoff for applications in this area may be a bit longer-term than for next-gen sequencing tools.
In a discussion with BioInform in October, Harvard University and Beth Israel Deaconess Medical Center's Mark Boguski said that even though clinical genomics offers great promise, most bioinformatics firms "are not thinking about" that market because there isn’t a business model in place that takes into account factors like technical and economic feasibility, HIPAA compliance issues, and economic sustainability.
Boguski is currently partnering with GenomeQuest to use the company's software to analyze next generation sequencing data. The aim of the project is to enable clinicians to use genomic information to make personalized treatment decisions for their patients, and ultimately to test what could be a "viable business model" for the space, he said.
He added that while most sequencing vendors and bioinformatics companies have invested their resources in tools for the research market, the clinical diagnostics market is where the "real return on investment" lies (BI 10/22/2010).
Another company attempting to address clinical diagnostics' informatics needs is Finnish bioinformatics company MediSapiens, which is using a $1 million round of financing to reconfigure its research-based software for use in molecular diagnostics and personalized medicine (BI 06/18/2010).
Linking research to clinical care was a major focus at the sixth annual meeting of the National Cancer Institute Cancer Biomedical Informatics Grid Initiative held in Washington, DC. At the conference, participants were updated on several cancer research projects using the tools to collect biospecimens, manage clinical trials, and identify cancer mutations among other efforts.
During the conference, Kenneth Buetow, director of NCI's Center for Biomedical Informatics and Information Technology, noted that translational research in the current scientific and clinical climate is a "complex ecosystem" that requires scientists and clinicians to "seamlessly join multiple components," including information and tools for clinical research, a "rich" collection of biosamples and reagents for next-generation molecular analysis, as well as tools and infrastructure to capture and interpret terabytes and petabytes of genomic data (BI 09/17/2010).
One keynote speaker, Patrick Soon-Shiong, executive chairman of Abraxis Bioscience, noted that it takes 17 years for research findings to make their way into clinical care — a gap that Buetow called "intolerable." He added that to shorten the time from bench to bedside, the informatics community will have to "embrace new paradigms."
Across the Atlantic, the Finnish government pledged the equivalent of $2.6 million in February to help develop biomedical research infrastructure that would link bioinformatics, biobanking, and translational research.
The funds were earmarked to create, among other things; synergies between the European Life Sciences Infrastructure for Biological Innovation, ELIXIR; the Biobanking and Biomolecular Resources Research Infrastructure, BBMRI; and the European Advanced Translational Research Infrastructure in Medicine, EATRIS, which seeks to translate results for diagnostic and biomarker uses (BI02/04/2010).
… and the Cloud Gains Some Traction
While the bioinformatics community is in many ways still leery of cloud computing, the approach did move a bit more into the mainstream during 2010 as more evidence emerged that the cloud may be a cost-effective means for analyzing large genomic datasets.
Working under the translational bioinformatics umbrella, a Stanford research group published a paper in Genome Medicine during the summer that compared the cost of analyzing a large genomic dataset in Amazon's cloud to the cost of running the same dataset on a local compute cluster.
Although they found that the pay-as-you go pricing model of the cloud costs about three times more and takes 12 hours longer, by factoring in the costs of in-house hardware, software, and personnel to manage a local cluster, the team concluded that cloud computing is a cheaper and more sustainable method for clinical researchers who need to analyze large datasets sporadically (BI08/27/2010).
Two members from the Stanford group followed up with another paper published in Nature Biotechnology in the fall, in which they recommended cloud-based storage of "snapshots" of entire computational environments that are used to generate published research results. This approach, they argued, would make it easier for the scientific community to replicate and validate research findings from computational studies (BI 11/12/2010).
And while widespread adoption was not in the cards for 2010, cloud computing did gain some traction this year with Amazon's cloud keeping a firm grip on the life sciences market. Dana Farber Cancer Institute kicked off the year by announcing that the Cistrome project — an effort to compile a genome-wide database of protein binding sites along with corresponding analytical tools — would move its database and software tools to Amazon's Elastic Compute Cloud (BI02/19/2010).
On the commercial front, BioDiscovery selected Amazon's cloud to support a collaborative repository for genomic variation data that is linked with the company's Nexus Copy Number analysis software (BI 03/12/2010).
In addition, some companies seem to see a future for the cloud in the life sciences and are leveraging Amazon's resource to provide informatics-specific services. In March, Cycle Computing launched CycleCloud for Life Sciences, which offers researchers web-based access to cloud-based CPU clusters along with a suite of pre-installed bioinformatics, molecular modeling, and proteomics applications. (BI03/19/2010) A month later, DNANexus released its cloud-based data management and functional genomics analysis service targeted at next-gen sequencing datasets (BI 04/23/2010).
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