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Invitrogen Launches Free Online Pathway Tool In Step Toward a Reimagined Reagent Catalog


Invitrogen released a new pathway informatics software package last week that differs a bit from the spate of other pathway tools that have emerged over the past few years.

For one thing, despite the fact that pathway informatics is so far proving to be a rare financial success for the commercial bioinformatics sector, Invitrogen is making the system freely available through its website. For another, the new software, called i-Path, serves as a critical component of Invitrogen's developing e-commerce strategy, which aims to restructure the traditional life science catalog in parallel with the rise in systems biology.

The launch delivers on a bioinformatics-based e-commerce initiative that Invitrogen has been working toward for some time. The company first said that bioinformatics would be part of its e-commerce strategy when it acquired InforMax in 2002 [BioInform, 10-21-02]. Last fall, the company delivered on this promise with the launch of Bioinformatics Central, a free version of InforMax's flagship Vector NTI clone-design software called VectorDesigner, which allows researchers to design primers and clones online, and then order them directly from Invitrogen's catalog [BioInform 09-13-04].

Siamak Baharloo, director of bioinformatics at Invitrogen, said that the company was "very encouraged" by the VectorDesigner test case to expand the bioinformatics-based e-commerce interface into several new areas. The first, pathway informatics, was a clear choice, he said, because the content "is so important, so critical, and in such high demand that if we provide a nice and user-friendly interface to the research community, people will come to it, people will read it, learn from it, experience it, and at the same time, if we make identifying the reagents easier for them, they will order through this mechanism."

"I think we have failed if people look at this only as a selling tool, because it is truly an informatics tool, and it has a lot of rich information that can be educational."

Baharloo said making the free version of Vector NTI available as an e-commerce tool had a positive effect on reagent sales to the point that they more than made up for the loss of software licensing revenues. He was unable to provide details.

"Looking at the number of subscribers to that version of Vector NTI, and the revenues [from reagents] on the click-throughs that were generated by it, we were convinced that this is a model that we need to implement and enhance," he said.

As researchers tackle more complex and higher-throughput experiments by using an increasing number of instruments and platforms and bioinformatics tools, it becomes harder for them to determine what reagents they need, Bahaloo said. To address that trend, the company's e-commerce framework aims to "provide products not like a catalog, but in the context of an application, in the context of the real biological question that a customer is asking," he said. "Our customers are not doing just DNA purification, or just RNA labeling, and they're not just running gels — they're asking biological questions, and they're answering them with a variety of different reagents."

Invitrogen's "application-centric" approach, Bahaloo said, enables the company and its customers to "make sure that these reagents actually match with each other [and] make sure we've positioned reagents that address a particular application."

Science or Salesmanship?

Despite the importance of the new pathway system to Invitrogen's marketing strategy — and the prominent shopping cart icons that identify Invitrogen products within i-Path's pathway maps — Barharloo said that the company took pains to ensure that the platform is as much an effective bioinformatics tool as it is an e-commerce interface.

"I think we have failed if people look at this only as a selling tool, because it is truly an informatics tool, and it has a lot of rich information that can be educational," he said.

The i-Path system is based on 225 pathways covering more than 2,500 genes that Invitrogen licensed from GeneGo as part of an agreement that the companies announced a year ago [BioInform 06-07-04]. The majority of the pathways — 171 — are signal transduction pathways, and the remaining 54 are metabolic pathways.

Baharloo said Invitrogen's bioinformatics group then did some work of its own to enhance the content. "What we've done is deconvoluted the relationship between various gene names, protein complexes, various IDs that are used, the synonyms, and normalized all of them to a specific set of reference sequence IDs, and then based on those we have identified corresponding reagents that map to a given gene on a pathway," he said.

The company plans to add more information to the system in collaboration with GeneGo. "We see this as the first step in our relationship with GeneGo, and we are already planning the expansion of this relationship," Baharloo said.

Researchers can browse the available pathways or search by keyword, SwissProt IDs, UniGene IDs, OMIM IDs, and the like, as well as by IDs from several microarray platforms. The user interface allows researchers to interrogate the molecules in each pathway and their relationship to each other. Additional biological information about each molecule appears separately on the right-hand side of the screen, along with specific Invitrogen products — such as clones, RNAi, antibodies, or assays — that match a particular molecule.

Baharloo said that the company designed the platform to ensure a clear separation between the research application and the e-commerce system. Rather than the "shopping cart" feature that most e-commerce systems use for compiling potential online purchases, the Invitrogen developers opted for the term "ice bucket" to appeal to molecular biologists used to storing test tubes of reagents in an ice bucket as they prepare their experiments. The idea, he said, is that "as you go from pathway to pathway, you don't have to go through an e-commerce environment. You can still stay in a research environment.

"We wanted to keep this as scientifically credible as possible," he said.

If the platform does prove as useful as a research tool as Invitrogen expects, should other pathway analysis vendors fear competition from the free resource? Not at all, according to Julie Bryant, vice president of business development and marketing at GeneGo.

While the threat of competition was something that GeneGo "had to consider" before deciding to license its pathways to Invitrogen, Bryant said that her firm's MetaCore platform is "more interactive" than the "static" maps available through i-Path, and that the agreement could actually increase the potential market for GeneGo's products, especially within the academic sector. Researchers could use i-Path as an entryway to pathway analysis, she said, and may eventually purchase a more sophisticated system like MetaCore that they wouldn't have even been aware of otherwise.

Bryant said that Invitrogen's launch of i-Path "is important to the market as a whole," and that it should be able to "move more biologists and bench scientist into using these kinds of tools."

Next Stop, Workflows

Invitrogen doesn't plan to limit its suite of free e-commerce informatics tools to pathways, however. The company also has plans to extend the framework into the areas of workflow, protocols, and search, Baharloo said.

These new capabilities are expected to be available some time this fall.

While Baharloo declined to provide much detail on the upcoming features, which are currently "in various stages of developing and prototyping," he said that the company is partnering with an undisclosed workflow software vendor to develop a tool that will "design and display research workflows and all the technologies and content and reagents associated with workflows."

In the area of protocols, "We are planning on licensing industry-leading protocols and content and presenting them along with Invitrogen protocols and other partner protocols on our website, and linking those protocols through to reagents," he said. Along similar lines, the company is developing new search capabilities "to provide access not just to Invitrogen reagents in the context of pathways, but all Invitrogen reagents that can be matched to a specific gene or protein sequence will be searchable and accessible."

But the initiative to release more free software through its website does not signal the end of Invitrogen's role as a commercial software provider. Baharloo said that the commercial version of Vector NTI is "fitting its revenue projections," and that the company plans to create a Vector NTI user group later this summer.

"I'm not saying that this is the end of developing software or the end of having enterprise applications," Baharloo said, "but for everyday bench scientists who need to design RNAi, who need to design peptides, who need to look at pathways, who need to look at workflows — there are ways to provide them with that information and content, make it simple, and then generate your sales and revenues through click-throughs to reagents."

— Bernadette Toner ([email protected])

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