Geschickten, a Bangalore, India-based bioinformatics service provider, is readying to launch in India this quarter an on-demand analytical platform called the GenomicsCloud and plans to expand the offering into the US and Europe before the end of the year.
The company, which took its name from the German word for "skillful," was founded in 2008 by IT industry veterans Prahalad Achutharao, CEO, and Asoke Talukder, CSO, with the goal of applying high-performance computing to life-science analysis.
Geschickten currently employs eight staffers in its Bangalore office and provides analytical services for microarray and next-generation sequencing data. It relies primarily on established open-source tools, but has integrated these algorithms into streamlined pipelines that it has designed for a number of analytical workflows.
"Our approach is to provide proven tools with our own pipelines that have been designed for analysis," Achutharao told BioInform. "We guarantee to the scientific community that our results are publishable."
In addition, Achutharao said, "we reengineer those open source tools to make sure they are more efficient in terms of resources and time." In particular, the company has parallelized a number of algorithms, including MAQ, Velvet, Euler, Erange, Bowtie, BFAST, MPI-Blast, InGap, ChIPSeq Peak Finder, and others.
To date, Geschickten has focused on the Indian research market. While it could not disclose the names of any customers due to confidentiality agreements, Taluker said it is currently working on three de novo sequencing projects — "one for a nitrogen-fixing bacteria, one for a domesticated animal, and one for an insect" — and is also developing a pipeline for miRNA analysis for a crop genome and is performing transcriptome analysis for a domesticated mammal.
The company has also partnered with Premas Biotech, a distributor of Illumina products in India, which recommends that its customers use Geschickten for any next-gen sequencing bioinformatics services.
"Most labs in India do not have the wherewithal to analyze NGS data," Praveen Gupta, vice president of business development for Premas, told BioInform via e-mail. He said that Geschickten provides "flexibility and low-cost solutions for data analysis," as well as a "strong statistical team."
He added that he expects the upcoming cloud-based option to be "the biggest advantage to Illumina users as they don’t need to invest in high performance computing infrastructure."
Gupta noted that demand for Illumina sequencers in India is quite high. "Sales have been growing quite steadily and we have a funnel of more then 10 NGS platforms this year," he said. In particular, "we are getting a lot of traction from providers of NGS services and this would boost our usage even higher."
Geschickten is also working with partners to expand its reach worldwide. The company has formed a strategic partnership with Santa Clara, Calif.-based IT services firm US Interactive, which serves as its US business-development arm and provides some programming manpower in India through a Mumbai subsidiary.
"We represent all of Geschickten's interests in the United States," said Sunil Mathur, president and CEO of US Interactive. He said that his team has been talking to prospective US customers for around three months, "and the response has been good," though he stressed that the effort is still in the "early stages."
US Interactive doesn't have a presence in the life-science market, but offers a range of general-purpose IT offerings for other verticals. "What we are doing is combining our strengths — our IT development and Geschickten's specific technology for high-performance computing and bioinformatics," Mathur said.
He added that the partnership between the firms is "not just for sales," but also involves co-development. In particular, US Interactive's Mumbai subsidiary works with Geschickten on tool development.
Achutharao said that the agreement with US Interactive enables Geschickten to "share our resources," which gives the firm the equivalent of around 100 staffers.
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Cloud on the Horizon
Gesechickten plans to launch the GenomicsCloud some time this quarter, Achutharao said. The pay-as-you-go platform will offer a range of tools for pre-processing, reference mapping, SNP and structural variant analysis, and miRNA detection and analysis.
Achutharao said that there are several options for customers who use the cloud-based offering, which will serve as "the first entry into all of our services." The company plans to provide its parallelized software solutions through the cloud infrastructure so that researchers can access the tools from anywhere and do the analysis themselves.
In addition to that, "[w]e'll also offer a GenomicsCloud workbench or dashboard where the scientists can request a customized pipeline, and we do the pipeline for them but they do the analysis."
Finally, the cloud model could serve as an interface through which researchers can upload their data so that Geschickten performs the analysis as a service.
The company is not the only one looking to make cloud computing accessible for next-gen sequence analysis. In April, Stanford University spinout DNAnexus launched a cloud-based data-management and -analysis service for users of Illumina and SOLiD sequencers (BioInform 4/23/2010).
The platform, which runs on Amazon's Elastic Compute Cloud, is priced at $95 per Illumina GA lane, or $30 per gigabase. The price covers data transfer, analysis, visualization, export, sharing, and indefinite storage.
Earlier this year, IT vendor Cycle Computing debuted CycleCloud for Life Sciences, which offers web-based access to cloud-based CPU clusters along with a suite of pre-configured life-science algorithms, including Blast, GMAP, HMMer, MAQ, Bowtie, RMAP, MrBayes, OMSSA, X! Tandem, Gromacs, and Schrodinger's molecular-modeling stack (BioInform 3/19/2010).
Achutharao acknowledged that Geschickten is not the first mover in the market, but noted that "competition is good for us. We can learn from each other and see what it is that we do best."
Even so, he said that the company's roots in high-performance computing should give it an advantage. "Understanding the cloud is not rocket science. A lot of people do that," he said. "But we know how the computing works, the underlying architecture. The pipeline we developed is so unique that it's probably hard for people to compete at that level."
Pricing for the GenomicsCloud has not yet been finalized. While "hardware will be pay as you go and will depend on the cloud vendors," Achutharao said that the company is still determining what it will charge for storage and software subscriptions.
Talukder added that the company is also proceeding cautiously regarding its expansion into the international market via the cloud computing model. "If we deal with patient data there will be a number of regulatory requirements that we need to respect, so we need to study all those things, and after we are confident that we respect all the regulatory requirements, only then will it be possible to launch these services outside of India," he said.