It's been a very busy week for Strand Life Sciences.
This week, the company launched a new US-based subsidiary, released the first version of its next-generation sequence analysis software, and announced an extension of an existing partnership with Agilent Technologies to create a version of GeneSpring that will integrate multiple types of –omics data.
The new multi-year agreement builds on a partnership between Strand and Agilent that dates back to 2007, when Agilent hired the Bangalore, India-based software company to merge ArrayAssist, a microarray analysis package it picked up as part of its acquisition of Stratagene, with GeneSpring, the array analysis software from its earlier purchase of Silicon Genetics. As part of that integration project, Strand migrated GeneSpring its Avadis platform, which has served as the foundation for the GeneSpring suite ever since.
The renewed partnership is between Agilent and Strand Scientific Intelligence, a Bay Area subsidiary that Strand created in order to expand its presence in the US market, as well as to identify "new product spaces" for the company, Francois Mandeville, Strand's executive vice president for marketing, technology, and strategy, told BioInform.
Financial details of the renewed partnership with Agilent were not disclosed.
According to the partners, the latest addition to the GeneSpring family, which will be released in December, will let users analyze and visualize genomic, metabolomic, and proteomic data together in the same interface, and will also provide integrated next-generation sequence analysis capabilities.
In the meantime, Strand launched Avadis NGS 1.0, a new software application for analyzing next-generation sequence data from ChIP- and RNA-sequencing and DNA variation experiments. Earlier this year, the company issued a call for researchers to beta-test its newest offering and provide feedback, which it planned to incorporate in the release. (BI 09/03/2010)
Gustavo Salem, Agilent's vice president and general manager of the company's biological systems division, told BioInform that the new GeneSpring tool will be designed to meet the needs of customers who want to integrate different types of data.
"The marketplace has really been our guide here," Salem said, noting that the company has received requests from customers who want to be able to visualize their metabolomic, proteomic, and genomic datasets within the same application, a move that he said reflects the current direction of the systems biology arena.
"What we are seeing happening in the marketplace is a real interest in taking [a] systems biology approach and truly applying it in translational research," he said. "We are really starting to see a functional need for a common researcher to actually be able to work with multiple datasets."
When it is developed, the new tool, which will be built on Avadis, will let users integrate data from GeneSpring GX, Agilent's software application for analyzing and visualizing gene expression data, with data from Agilent's Mass Profile Professional software, which is used to analyze and visualize mass spectrometry data.
Because all three software applications are built on Avadis, the data integration process should be straightforward for customers, Salem said, since the tools are all "handled by common software logic."
Although Agilent hasn’t selected a name for the software, it will be "trade named" under the GeneSpring brand due to the "very positive equity that’s been established in the marketplace" for that product line, Salem said. The company is considering names like GeneSpring Multi-Omics or Poly-Omics suite.
He said that Agilent expects to see "significant continued growth" in both the microarray and mass spectrometry fields and as such he expects that the market for tools like Mass Profiler, GeneSpring GX, and the upcoming data integration tool will continue to grow over time.
As part of the partnership, Strand and Agilent are developing a new "transactional model" for delivering GeneSpring products that will involve the development of "a fully integrated portal for licensing, upgrading and supporting the GeneSpring family of bioinformatics systems."
Although Salem could not provide specifics about the revised business model, he hinted that Strand will be playing a much larger role in terms of customer service and support.
One of the reasons that Agilent has "assertively" identified Strand as a partner is "to encourage our customer base to know that a lot of the customer support that they require in terms of modification or customization of the software or training for the correct use of the software is a service that will be provided primarily through Strand," he said.
"Agilent's not a software company, and … as the number of customers … continues to increase, we [need] to improve our ability to really deliver product to customers … [and] provide them with more robust support and service," Salem said.
He also declined to provide specifics on the kinds of NGS capabilities that Strand is developing in the new software but he did say that there would be "some unique capabilities" when the tool is complete.
Salem said that the partners expect that the data integration tool will be adopted by research groups at translational research institutes and in university research centers, particularly in clinical settings. Customers who only need to analyze microarray or mass spec data can buy the standalone GeneSpring GX and Mass Profiler products, he said, but "for a customer who needs the ability to integrate these things there will be a new product … that would allow them to integrate the multiple datasets."
Strand's Mandeville said that the company launched Strand Scientific Intelligence in order to expand its "worldwide commercialization activities."
He defined "scientific intelligence" as software products and services that let users aggregate data from multiple sources, visualize the data and put it in a scientific context, and create predictive models based on the data.
According to Mandeville, Strand wants to form partnerships with other "large instrument manufacturers" much like it has with Agilent, where both companies are creating IP and "marketing responsibilities can take place in both directions." He said that Strand felt that creating "a full-blown corporation in the US" would make it "easier to enter these new breakthrough relationships with some of our partners."
Tools like the newly released Avadis NGS software and the new data integration tool show that Strand has "built a platform that can be applied to very different spaces" — a feature that the company plans to use to expand its influence to other areas in the life science space, Mandeville said.
Strand created Avadis NGS 1.0 for ChIP-seq, RNA-seq, and genetic variation data analysis. The software also includes a genome browser that lets users visualize their data and perform downstream analyses such as gene ontology analysis, pathway analysis, and gene set enrichment analysis.
Mandeville said he expects Avadis NGS to be "commercially appealing," and cited the oft-suggested point that many of the tools in the NGS market space are geared towards bioinformaticians and information technology specialists as a key differentiator of his company's software.
"What we are doing with Avadis NGS is really shifting to a tool that the biologist can use effectively — you can go from the sequencer to the biologist without intermediaries," he said. "I think that this means the population of users that it serves is much wider … [T]he more you empower biologists to be able to derive value out of what they have measured … the faster you allow for science to evolve."
The company is currently offering biologists and NGS researchers a 20-day free trial of Avadis NGS.
Furthermore, Mandeville said that Strand plans to release additional products that aren’t focused on the NGS space. For example, the company will release a tool in December geared towards the microscopy market called Avadis Microscopy.
The tool, which will go into beta-testing next month, will enable users to manage microscopy images and compare and exchange images generated on multiple microscopes, he said.
A final reason Mandeville cited for creating a US subsidiary is that Strand wants to ensure that its customers have access to support and services for these new products. To meet that need, he said that the company is rolling out an "iTunes-like platform that allows scientists to download new applications, obtain support, and renew licenses."
Strand plans to use the platform to provide customer support for both its NGS and microscopy offerings and Agilent has also licensed the tool to provide similar support services for its GeneSpring users. Agilent is also marketing Avadis NGS to its GeneSpring users as "a natural extension and accessory module for the GeneSpring portfolio" he said.
Mandeville also said that the company plans to hire additional staff later in the year, especially as it gets ready to release new products like Avadis Microscopy.
Furthermore, Strand plans to move into other areas in the life sciences in the months to come and is currently trying to make inroads into the health informatics space.
Although this will be a new focus area for Strand, Mandeville said that over the last decade, the company has been involved in several projects in the field that involve analyzing and assessing clinical data, but declined to provide further details about the company's current efforts in this area.