In step with the research community’s continued migration toward systems biology, Applied Biosystems has tweaked its online informatics tools to support what the company has dubbed “i-science,” or integrated science.
Last week, ABI released enhanced versions of its two online research environments — the free myScience e-commerce portal and the subscription-based Celera Discovery System — with new capabilities in each system for integrating the company’s instrument platforms, reagents, and other products. The two web-based interfaces enable researchers to analyze biological data, design experiments, and order ABI products all within a single framework, and “complete the concept that we have of integrated science,” said Tony Kerlavage, senior director of ABI’s online information business. To support integrated biology, Kerlavage said, “You need all the pieces — you need the information, you need the instrument platforms, and you need the reagents and other products — and all together we’re basically expanding out through the customer’s experimental workflow and providing the pieces that they need to complete their experiments.”
The strategy is in line with two emerging industry trends: vendors aligning themselves with the systems biology juggernaut, as well as the use of free, online informatics tools to add value to broader e-commerce environments. Invitrogen has recently taken steps to build out its own bioinformatics-enabled e-commerce portal [BioInform 03-08-04], and ABI’s plan has evolved out of a long history of online products, from Celera’s subscription-based genome database, to the “Knowledge Business” that once encompassed CDS and the web-based assays-on-demand service, to the latest incarnation of CDS and the MyScience portal.
ABI has officially retired the “Knowledge Business” name. Deborah Smeltzer, who led that business unit, is now VP and general manager of sequencing and applied markets, while responsibility for the MyScience portal falls under the company’s newly created Global Informatics, Software, and Professional Services Group, led by Bruce von Herrmann, with particular focus on supporting ABI’s gene expression, genotyping, and resequencing product lines.
MyScience is essentially a free subset of the tools and information available in CDS, Kerlavage said, which is directed toward the goal of “providing access to a growing set of genomics-based products.” As these products get more and more complex in line with researchers’ experimental needs, he said, “you can’t just use a product catalog to look them up. You really have to do your product selection in research mode, and you have to perform queries to get at the specific sets of reagents that are relevant to your experiment.”
MyScience and CDS share the “same framework,” Kerlavage said. “What you get with MyScience are all the features necessary to help you select your products for purchase, while CDS gives you much more of a scientific workflow.”
New and Improved
Both offerings have been upgraded to increase their integration with ABI’s instruments and consumables. In addition to the previously available Assays-on-Demand capability, the MyScience portal now enables researchers to access ABI’s recently released VariantSEQr resequencing primer set, as well as the company’s SNPlex assay design pipeline. Researchers can search for genes of interest by keyword, gene name, Panther protein classification, or chromosomal location using the MyScience graphical viewer. A results list based on LocusLink provides complete information on the gene or genes, along with links to relevant ABI products for gene expression, genotyping, or resequencing. Another click adds the product to an online shopping basket to complete the e-commerce experience.
On the CDS side of the fence, Kerlavage said that the rat genome has been added to the previously available human and mouse data, and the company has also mapped the syntenic regions and orthologs between human and mouse, human and rat, and mouse and rat. Users can also compare Celera’s human, mouse, and rat genomes with NCBI’s versions within CDS “so you can see additional annotations that we might have that aren’t available to the public,” Kerlavage said.
Another new feature, called MyData, allows users to map their own sequences onto the CDS map viewer, and there is also new capability based on Celera’s mouse SNP data that allows users to identify the genetic differences between any two strains of mice to help find causative mutations responsible for specific disease phenotypes.
ABI is also integrating CDS with its instrument platforms. For example, the company’s new whole-human-genome microarray platform contains genes that are only available in CDS, so subscribers will be able to view the location of those probes along the Celera genome. The company has also extended CDS into its proteomics instrumentation suite. “We created a set of protein sequence files that go through rigorous quality control, we removed the redundancy, and we now deliver those with all of our mass spec instruments,” Kerlavage said. “The instrument software can read in those protein data files and internally do the mapping of the results from the experiment onto known proteins.” This gives researchers the company’s Panther classification of all the proteins that were identified in the experiment, as well as a direct link into CDS for access to additional annotation and other data.
As in MyScience, CDS users are only a mouse click away from ordering reagents or other products in order to carry out wetlab experiments based on their in silico explorations.
Celera has reported steadily decreasing revenues for CDS over the last year and a half, but Kerlavage said that ABI still sees “an upsell opportunity” in the subscription-based product — both as a standalone source of revenue and as a driver for e-commerce-based product sales.
Kerlavage said that it’s not likely that the data and functionality available in CDS will be folded into the free MyScience portal any time in the near future. “For now, we see that there is significant extra value in the CDS product,” he said. “We do want to provide the baseline capabilities to let our customers select the right reagents, the right products for the experiments, but for those who need more background annotation or who have other scientific questions that they want to answer, we offer CDS.”
Kerlavage said that the company has had “a lot of positive response from the academic community” for a new pricing model it adopted a year ago that allowed academic users to subscribe to CDS for a flat rate of $2,000 per year. “There’s still a lot of interest out there in the academic community in this product,” he said.
In addition, the company intends to continue to invest in R&D to improve CDS, Kerlavage said. Data and annotations for the currently available genomes are updated “constantly,” he said, and the company is looking into pathway analysis and disease correlation for new content offerings.