TEANECK, N.J.—Cognizant and Eagle Genomics Ltd. are workingwith life-sciences company Pistoia Alliance Inc. to develop a cloud-basedplatform for streamlining sequence services.
According to Richard Holland, co-founder and operations anddelivery director at Eagle Genomics, Eagle and Cognizant have "demonstrated adeep understanding of the open-source bioinformatics world and how best toadapt and support these publicly available resources to meet the high standardsrequired by the leading pharmaceutical companies that are members of thePistoia Alliance."
Peter Sheppard, assistant vice president of life sciences atTeaneck, N.J.-based Cognizant, notes that Cognizant is an active member of andcontributor to Pistoia Alliance, and adds that in an increasingly virtualizedand globalized business environment, forward-thinking companies are looking forbetter ways to organize teams, cultivate innovation, allocate resources andreinvent knowledge processes.
"We call it the Future of Work," he explains. "Theobjectives of Pistoia Alliance are strongly aligned with this reality."
Pistoia Alliance is a nonprofit, precompetitive alliance oflife-science companies and vendors, and was engaged by this group to develop aconceptual cloud-based platform to facilitate access to public and proprietarysources of gene sequence data. Pistoia Alliance's sequencing services aim todefine and document a hosted service for storing and mining proprietary derivedgene information and public domain gene databases.
Nick Lynch, president at Pistoia Alliance, says the effortsupports the alliance's goal to inspire different ways of thinking in thelife-science industry and affect real change to benefit all of itsorganizations.
"With the combined strengths of Cognizant and Eagle Genomicsand the broader Pistoia community, we will build a platform to define standardsin sequence services, while overcoming the challenges of disparate data and tools,"he says.
This conceptual platform developed by Cognizant and EagleGenomics, as part of this piloting stage, will enable working group companiesto securely share their bioinformatics resources among simultaneous, registeredusers in a secure, encrypted environment, while leveraging the flexibility,scalability and cost efficiencies of a cloud-based Software as a Service (SaaS)platform. Francisco D'Souza, Cognizant's president and CEO, says the platformwill improve outcomes for each alliance member by creating a collaborativeenvironment to share pre-competitive information.
Sheppard explains that Cognizant and Eagle Genomics willcombine the best of their consulting, domain, technology and business processexpertise to effectively deliver the business solution. While Eagle Genomicswill contribute specialized bioinformatics knowledge, Cognizant will manage thedevelopment of the platform, oversee testing and security validation and helpstrengthen the initiative by managing relationships with existing and potentialmember organizations.
"Cognizant will leverage this collaboration platform todeliver its own services as well," Sheppard adds. "This platform will bedelivered as a Business Process as a Service (SaaS/BPaaS) solution to theindustry."
The platform will deploy a secure and scalable installationof Ensembl, a software system and supporting database developed jointly by theWellcome Trust Sanger Institute and the European Bioinformatics Institute toproduce and maintain automatic annotation on selected eukaryotic genomes. Thefounding members of Eagle have been part of Ensembl and have a very goodunderstanding of the sequence services landscape. The platform will deliver aPlasmapper and a gene alias service as part of the initial functional services.
The platform development will be an ongoing initiative andwill cater to any new demand/technology identified either by Pistoia or by theindustry in general.
The initial phase focused primarily on non-functionalaspects and was aimed at demonstrating a hosted solution (cloud model), andmore importantly, multilevel security.
"Pistoia has defined the focus for Phase II that will getdelivered in 2011," Sheppard notes. "The focus for 2011 is next-generationsequencing (NGS)."
Sheppard explains that with the viability of the cloudsolution and the ability to deliver solutions securely established in the firstphase, the focus now shifts to major functional challenges.
"Pistoia is still finalizing the scope of the second phase,"he adds. "The second phase would definitely address some of the key challengesof NGS around data storage, compute power and data privacy."
According to Sheppard, the alliance addresses a key unmetneed in the discovery research area.
"The focus of Pistoia Alliance is to identify potentialcommon challenges faced by the pharmaceutical and biotech industry andscientific researchers in the pre-competitive domains of research anddevelopment and address them through information-based solution pilots thatwill drive innovation and productivity that can eventually be owned, enhancedand delivered by the participating solution providers," he says. "The allianceprovides a forum for key thought leaders focused on addressing specificbusiness challenges in the various work streams."
Addressing ever-evolving sequence services provides its fairshare of challenges, and Sheppard says with the cost of sequencing coming downdramatically, the cost of sequencing may become cheaper than the cost ofstorage in the near future—a result of the evolution in rapidly changing domaintechnology.
"Someof the key challenges would be changing data types with evolving technology,the amount of data generated, the need to transfer the data, algorithms foranalysis and visualization and the associated compute power and data privacy,"he says. "The platform needs to be flexible to reflect the changes and reactquickly to the changing needs of the industry."