As Accelrys prepares to retire its GCG software package at the end of June, a petition has been circulating through the bioinformatics community calling for the company to release the GCG source code into the public domain to ensure continued support for a suite of tools that has been available for more than 25 years.
However, an Accelrys official told BioInform this week that the company is instead looking for a commercial partner to take over the package because it “legally cannot do what the petition is asking us to do” — a situation resulting from the patchwork of intellectual property surrounding the GCG suite, which was originally developed at the University of Wisconsin in the early 1980s and then sold through a series of commercial entities.
“We’re not ignoring it,” said Bill Stevens, vice president of life science marketing at Accelrys. “We’re aware that the petition … is out there and we’re trying to find an equitable solution for everybody that can work.”
The main challenge, Stevens said, is GCG’s tangled history. The software was first available from the University of Wisconsin, and then marketed through the UW spinout Genetics Computer Group, from which it gets its name. That company was acquired by Oxford Molecular in 1997, and three years later Oxford Molecular was itself acquired by Pharmacopeia. Pharmacopeia in 2004 spun out its software business as Accelrys.
GCG has “had a very long life and the code that is in it has evolved over time and it’s been put together from many different sources,” Stevens said. “While we have the right to sell the product, we do not actually own all the code outright, meaning that we could not release it without first gaining approval by all the owners of all the lines of code, and either reaching a financial agreement with them, or having them sign off on the release.”
Stevens said that there is a “substantial cost” involved in this option due to the time it would require and the legal expenses involved.
Instead, Accelrys is seeking a “suitable commercial partner” who would be willing to take over the package, Stevens said, though he stressed that any firm that agreed to do this would have the rights only to code that Accelrys has developed, “and they would then have to remediate to make the software work from that point forward.”
Rob Brown, senior director of informatics marketing at Accelrys, said that the most likely candidate to adopt the code would be a company “that has some existing expertise in these packages … and they would then be able to recreate the pieces that had been stripped out.”
“The reality of maintaining this product just wasn’t economically feasible for us anymore, but there are other companies that could create models around that that could work and we are trying to identify a proper partner that could possibly take that on.”
Stevens said that Accelrys has so far identified “a couple of potential partners” for this option, but stressed that the discussions are still in the very early stages.
He noted that the software would only be of interest to a partner with a “different financial situation” than Accelrys, which is a large company relative to most bioinformatics firms, and is also beholden to its shareholders as a publicly traded entity.
“The reality of maintaining this product just wasn’t economically feasible for us anymore, but there are other companies that could create models around that that could work and we are trying to identify a proper partner that could possibly take that on,” he said.
He explained that the total costs associated with supporting GCG became too much for Accelrys to maintain. “We have to have R&D staff constantly doing regression testing on software, we have to have customer support people trained and available on a reasonable schedule around the clock for our customers, and there’s the constant process of upgrading the product. When you look at that compared to the revenues that the product is providing, it’s not a viable situation for us,” he said.
However, “that doesn’t mean that the code is worthless,” he noted. “We do feel that there is still some value to this code and we would like to be able to realize that value for our shareholders, and we’re trying to reach an agreement that would allow us to do that.”
In the Lurch?
Some customers are concerned, however, that they will be left without support indefinitely once Accelrys officially retires GCG on June 30.
As of that date, “we will no longer offer new software development releases and hotline scientific application support,” Accelrys explained in a letter it sent to customers last July. The company is offering GCG customers the option to purchase a “perpetual license” that would give them the ability to use the software “as is” beyond the retirement date.
Steven Thompson, a faculty member at the Florida State University School of Computational Science and the author of the petition, said that his group opted for the perpetual license, but noted that “the problem is that without any active support, eventually the versions of Linux that people run will become incompatible with the GCG package — it’s just inevitable that that will happen.”
Thompson said that he is particularly concerned about GCG’s sequence-analysis interface and editor, SeqLab. While many of the individual programs in the GCG package are available from the open source EMBOSS suite and other freely available resources — a factor that actually drove Accelrys’ decision to discontinue the product — Thompson noted that none of the freely available interfaces he’s looked at are “anywhere near as powerful or comprehensive as SeqLab.”
Thompson’s petition — which has garnered nearly 170 signatures as of press time — requests that Accelrys release all the GCG source code to a “suitable repository,” but also poses a “compromise” in which Accelrys would release only the source code for the SeqLab module.
The petition notes that Steven Smith, the original author of SeqLab's predecessor, the Genetic Data Environment, and a member of the GCG team that built SeqLab, “has expressed interest in continuing to develop the GCG product,” and has also “offered to continue the development and support of the SeqLab [graphical user interface] in much the same fashion as the original GDE tool had been.”
The petition asks that Accelrys “release the GCG Package and/or SeqLab's license and code base to Steven Smith, so that he can continue to update and support this valuable bioinformatics resource.”
Smith declined to comment for this article.
Accelrys’ Stevens said that the company is considering the option proposed in the petition, noting that “one of the original developers might be interested in this code and we’re trying to reach a financial agreement with them that would make that feasible.”
He added that the developer, whom he did not name, is “possibly pushing this petition along in order to force a situation that would be as favorable to them as possible.”
Thompson said that he was surprised that the petition, which he first posted online about two weeks ago, has attracted as many signatures as it has. “I was hoping that it would be that well received, and the fact that it has been in less than two weeks time has really impressed me and driven home the point that I think there are a lot of people that have similar feelings to what I’m experiencing here,” he said.
Accelrys officials said they also were surprised at the number of signatures on the petition — particularly because the signees outnumber GCG customers in its records.
“This was a longstanding product for Accelrys, but it definitely wasn’t one of the biggest selling products for us,” Stevens said. “The number of people that have signed the petition exceeds the number of people who were active customers.”
Brown acknowledged that this discrepancy may be due to a number of GCG users who purchased perpetual licenses to the software “two companies ago and wouldn’t be in our system.” He noted, however, that “some of those signatures certainly aren’t current customers and may not even have been past customers.”
Stevens said that the customer response to the discontinuation of GCG has been “almost nonexistent” until now, and that the petition “hasn’t been what I would call the overwhelming voice of our customers telling us to reconsider our actions.”
Nevertheless, it’s clear that GCG’s potential disappearance has struck a chord with the bioinformatics community. It’s very likely that the strong response to the petition is related to GCG’s lengthy history and its legacy as one of the first bioinformatics packages on the market.
As Thompson notes in the petition, the GCG software has been cited in nearly 9,000 scientific articles since it was first published in 1984, according to PubMed, and more than 14,000 times according to ISI Web of Science — a number that places the paper in the top-ten most cited scientific papers of all time.
Thompson said that he’s been using the GCG package since 1982, when it was still a command-line program. “It just seems like such a shame to let a 25-year legacy just die,” he said.