In the six years since SciTegic opened its doors, its Pipeline Pilot software has emerged as the de facto standard for data pipelining in cheminformatics. This week, the company will debut a new product line that it hopes will give it a similar position in the bioinformatics world.
JR Tozer, vice president of marketing for SciTegic, said it expects the new offering, called the Sequence Analysis Collection, to address a number of technological and cultural differences between the bioinformatics and cheminformatics communities. The company has been developing the suite of wrappers for its workflow management software for 18 months, Tozer said, with an eye toward the particular needs of the bioinformatics community.
"There's a lot more commercial software in cheminformatics than in bioinformatics," Tozer said. In addition, he said, "Perl is now a much bigger element of our sales process."
Acknowledging that the company is moving into a market where most customers are heavily biased toward "build" as opposed to "buy," Tozer said that SciTegic does not want to be considered as "another bioinformatics vendor trying to sell a suite of tools to replace what customers already have installed."
With this in mind, the company has added a number of new options for wrapping internal and third-party code so that it can plug into Pipeline Pilot, including Perl- and Java-scripting components so that users can execute BioPerl or BioJava modules or their own scripts directly through the software. In addition, Tozer said, the software has a SOAP layer so that users can integrate the system with their own web services architectures.
Tozer said that Pipeline Pilot can enhance existing in-house bioinformatics pipelines built with scripts and web services because it adds a user-friendly graphical interface that provides access for bench scientists unaccustomed to command-line interfaces. In addition, he said, because Pipeline Pilot allows users to save application workflows, or "protocols," as the company calls them, bioinformatics groups can easily store, manage, modify, and deploy these protocols across a broad user base.
SciTegic, a subsidiary of Accelrys, has written several hundred components for Pipeline Pilot to handle common cheminformatics tasks, like chemical searching and clustering, but Tozer said that the company decided to allow for more end-user modification when it entered the bioinformatics arena because so many basic capabilities are available in the public domain.
In its first release of the Sequence Analysis Collection, SciTegic has integrated around 50 bioinformatics tools, including Blast, ClustalW, the NCBI Toolkit, Accelrys' GCG Wisconsin Package, and some components of EMBOSS. Tozer said that in the case of EMBOSS and some other publicly available tools, SciTegic provided wrappers for a few modules that customers can use as a "template" to write their own.
Tozer noted that the company began developing the bioinformatics side of Pipeline Pilot well before it was acquired by Accelrys last September, but said that the additional bioinformatics expertise from Accelrys "allowed us to accelerate the process."
He stressed that the company's relationship with Accelrys hasn't changed SciTegic's goal of providing customers "complete choice." GCG is integrated with the system, but Pipeline Pilot customers don't have to purchase it if they don't want to. "We're not making that decision for our customers," he said.
While SciTegic was able to claim first-mover advantage for data pipelining in cheminformatics, the company is actually a relative latecomer in this market on the bioinformatics side of the fence. A number of companies, including InforSense, Incogen, and TurboWorx, and several open-source projects such as Taverna and Wildfire, offer workflow solutions targeted at the bioinformatics community.
But Tozer said that the company is so far "not encountering these companies" when approaching potential customers with the new offering. One reason for this, he surmised, is the reputation — and customer base — that the company already has in cheminformatics. Customers who are already using Pipeline Pilot for cheminformatics are more likely to extend the software to bioinformatics rather than shop around for a new vendor, and Tozer said that many of the company's cheminformatics customers have already adapted the software to work with some bioinformatics algorithms on their own.
Michael Pear, director of research informatics at Isis Pharmaceuticals, may be a typical case. Isis was already using Pipeline Pilot to integrate its cheminformatics applications, so Pear said that he didn't even consider other workflow options. "It's something we already had in house, so rather than look for a solution externally, it was good timing that the sequence collection came to pass at the time that I was starting to look at this," he said.
Isis has had access to the Sequence Analysis Collection as a beta customer, and Pear said that it has been an effective interface for the company's existing bioinformatics integration system, which he described as a "slew of things," including Visual Basic, command-line code, and Perl and Java scripts.
But it's likely that SciTegic will see more competition — and more customer resistance — as it takes steps to expand its bioinformatics presence beyond its core cheminformatics base in biotech and pharma into the academic and government markets. Tozer said that SciTegic is offering "price incentives" for academic labs developing bioinformatics software, and has also targeted several potential collaborators in the public sector "where we see good synergies."
Pear said that the software should be of interest to most bioinformatics groups, however. "Even if they think they have it all together in terms of integration, this is worth looking at," he said.
As for future development plans, Tozer said the company is staying flexible. While the first bioinformatics release focuses on sequence analysis, he said that the company has already developed prototypes for gene-expression analysis, proteomics, and other bioinformatics areas. The rollout of these new options will be "driven by customer feedback" he said.