Silicon Genetics has announced it will offer ArrayMiner, a clustering algorithm developed by Optimal Design of Brussels, Belgium, as an optional add-on with its GeneSpring software.
Separately, the company defended itself against a flurry of online criticism by customers upset at its policy of charging them at the end of each year a renewal fee for the license to GeneSpring that is equivalent to the purchase price.
ArrayMiner is a non-hierarchical clustering algorithm that provides a more reliable alternative to the commonly used k-means algorithm, according to Emanuel Falkenauer, managing director of Optimal Design.
“K-means is an extremely unreliable technique,” Falkenauer said. “Given a dataset of expression profiles, the clustering solution supplied by k-means crucially depends on the way the k-means algorithm was initialized. Unfortunately, nobody knows what is the best initialization for a given dataset.”
Optimal Design has posted a demo on its website that illustrates these ostensible flaws, at http://www. optimaldesign.com/BioOD/ArrayMiner/ kmeans.html#drawbacks. The company designed ArrayMiner to avoid the pitfalls of the k-means, Falkenauer said.
Silicon Genetics decided to add ArrayMiner to the array of algorithms available with GeneSpring after Optimal Design approached company executives with a version designed to fit seamlessly into GeneSpring.
“A whole lot of people have come up with other algorithms, and every one of course believes their algorithm is the best,” said Andrew Conway, CEO of Silicon Genetics. “Our approach at SGI is to say that we’ve included the ones we consider most important. However, we can’t say that everyone else is utterly wrong so we’ve got a facility that lets third parties like Optimal Design make their own algorithms that plug into GeneSpring.”
Silicon Genetics will offer ArrayMiner for $2,000 per single copy per year, and $1,000 per customer per year for academics. This price will be discounted if an organization buys five copies or more, the company said.
Company Defends Renewal Fees Against Critics
SGI meanwhile defended its general policy of charging customers the full amount of the purchase price every year they renew GeneSpring version 4.1.
In recent weeks, customers have been complaining about this pricing policy in posts to the Gene-Arrays listserv. (GENE-ARRAYS @ITSSRV1.UCSF.EDU). In particular, they have objected to the feature that makes the analysis software freeze exactly 366 days after a customer buys it, if the customer does not renew at the original price. One customer said he had only learned of this renewal policy in reading the details of the purchase agreement for the software, and that it had not been included in a quote. Others opined that it is unfair to “sell” a product that they must renew to continue to own.
“I understand the need to recover development costs in a small market, but SGI’s approach of renting software is not the solution (no matter what they call it, it is renting),” said Robert Gross, director of the Center for Biological and Biomedical Computing at Dartmouth College. “What if I’m working on a grant proposal and come in on a Saturday night to finish up some array analysis ... but find that GeneSpring has expired? I am at a loss when I need the software the most.”
SGI responded to the criticism, stating that this seemingly high renewal fee just represents an overall restructuring of the price of the software. The initial one-year purchase fee is a little more than one-third of the perpetual license fee the company charged for versions 1.0, 2.0, and 3.0, the company said.
The company restructured the pricing on GeneSpring from a perpetual license to a renewal model in order to reduce the barriers to entry for small labs, said Deepak Thakkar, SGI’s director of marketing. “The company felt it was important to address the needs of individual researchers and those working off of grants in large companies, as well as those working on a limited budget for analysis,” he said.
The other criticism levied against the software — that it goes totally dead after a year if not renewed — is not completely true, Thakkar added. While customers do lose their visualization and analysis tools when the software expires, they can still export their data files, which are stored as HTML files that can be opened by any web browser, he said. “You can take the data and plug it into any other product at that point.”
Thakkar also said SGI would be responding to this criticism by developing, within the next few weeks, certain visualization tools in the product that will remain active in perpetuity.
Nevertheless, for disgruntled customers like Gross, this new feature could prove too little, too late. “I am seriously considering going to a competitor and am likely to do so if SGI does not change its policy,” Gross said.
SGI is not too worried, Thakkar said, noting that these criticisms come from “just a handful of people” among the company’s 4,000 customers. “But those 10 or so are important to us, and we are going to call each one individually so they know we’re in this for the long run,” he added.