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3rd Millennium Opts for Open Source Licensing Model in New Role as Software Provider


Bioinformatics consulting firm 3rd Millennium has cited its customized approach to technology development — rather than shrink-wrapped software solutions — as the reason for its continued success in the otherwise struggling commercial bioinformatics market. So when it came time to consider making some of its software available on a standalone basis, the company saw only one logical licensing option: Make it freely available under the General Public License.

“We’ve really thought about this a lot,” said Richard Dweck, 3rd Millennium CEO. “We looked at all the companies in this space and we said, ‘Okay, there used to be about 150; there’s about 15 now –— what went wrong with them and why are we doing well? And we realized that over the course of all these engagements, we’ve been able to iterate the basic structures that most companies need … These are things we’ve been giving away as part of our consulting on a one-by-one basis, but now we really want to put it out there for the whole world.”

On Dec. 15, 3rd Millennium will make the first of several “foundation technologies” that it has developed during five years of consulting work freely available through its website ( The first release is what the company calls a “data-centric knowledge management system” that allows researchers to organize and share knowledge about biological and chemical entities within or across organizations. The system — which was developed to handle information about genes, targets, compounds, leads, and assays, and offers data-mining functionality as well as automated sequence analysis and patent searching — is available under the GPL for all users. Because the “real value” of its offering is in customization, Dweck said, it just made sense to make the software components freely available.

“We realized that there are probably a lot of companies and academic labs and research institutions that wouldn’t come to us anyway, so we’re going to give it away to them so that at least they can get going and then spend whatever money and effort they have tweaking it and customizing it to their needs,” Dweck said. But the company is also planning to use this free software as a means to lure in consulting customers: Some users will download the software and eventually bring in 3rd Millennium to customize it by adding interfaces or specialized modules; and still others will like what they see and consider the company’s services when they’re in the market for another custom project or system. “We think there will be a significant amount of work that we’ll get from this,” Dweck said.

Eric Meyers, 3rd Millennium’s COO, said that some of the company’s current clients have already expressed interest in maintenance and support contracts on top of the open source software offering. “Where this goes is not certain,” he acknowledged, “but having looked in other industries at how this [strategy] has evolved in a very positive way, we think it’s going to be very positive for this industry, and for 3rd Millennium.”

In Good Company

Bioinformatics is an open-source-friendly discipline. Linux is the operating system of choice for many labs, and it’s standard practice for academic and government bioinformatics groups to share their work with the community. In the past few years, other bioinformatics firms — such as Electric Genetics, Iobion, and Sequence Bioinformatics — have built commercial products on top of publicly available open source tools, but 3rd Millennium is among the first to make available software that it developed for its own consulting engagements under an open source license.

Tania Hide, CEO of Electric Genetics, said that 3rd Millennium’s decision makes good business sense. “There’s very little potential downside in what they’re doing, and a lot of potential upside for the community and for them,” she said. Electric Genetics has found a successful model in the combination of open source software and consulting services, and is seeing a great deal of interest in its support services for Bioperl and other open source packages, she said. “You have the open source tools, so you get a bit more standardization and acceptance in the industry, while at the same time the service organization provides the really valuable validation, support, and integration,” she said.

Electric Genetics decided to follow an open source model around two years ago, and Hide said she’s seen “a lot more acceptance of open source tools” since that time,“so that means more work for people like 3rd Millennium.” Many companies are turning away from commercial enterprise-wide informatics systems and adopting “selective outsourcing,” she said, in which they build their own informatics systems using best-of-breed commercial or public domain tools, but bring in experts to fill in the gaps where they don’t have manpower or expertise. “Open source fits into that perfectly,” Hide said, “because you need an integrator or an outside person to help you validate the open source software and ensure that it’s going to do what it says it’s supposed to do.”

Open Source Options

Meyers said that the benefits of releasing 3rd Millennium’s software under an open source license weren’t obvious at first. The option first came up a year ago when someone from another industry “challenged” the company to do it. At first, he said, 3rd Millennium was skeptical, “but the more we thought about it and we looked at how the software industry was developing in other industries, and what some of the real problems were that confronted software product companies, we said it absolutely makes a tremendous amount of sense.” After floating the idea by several clients, Meyers said, “We were somewhat caught off guard by how much more enthusiastic they were than we expected them to be.”

Next came licensing options. As anyone who has navigated the Open Source Initiative’s list of approved licenses ( can attest, the number of available licenses is dizzying. “I had to get reading glasses after reading all of them,” Meyers said. After careful consideration, the company decided that the GPL would be “perfectly fine” for most people, but it is also offering an option for some companies to pay a “nominal fee” for a commercial license to redistribute it without modifications. “You may not want [a] collaborator to have access to certain parts of the system that you modified, but under the GPL you would be required to do so,” Meyers said. In those cases, the company will offer “a commercial license where to them it’s open source, but not governed by the GPL.”

Meyers said he envisions users taking advantage of the open source license in three primary ways. In the first scenario, he said, biotech and pharma users will modify the software, but keep it in house. In this case, the GPL stipulates that “only if you distribute it to someone else do you have to make what you’ve added to it open source,” Meyers said. In the second user scenario, developers will release their modifications into the open source community when there is no reason to keep them confidential or treat them as proprietary. In the third case, Meyers said, users are free to commercialize any add-ons or modules they develop that work with the foundation software — an option that 3rd Millennium is also considering, Dweck said.

The company expects to release at least two more sets of open source technologies, Dweck said: a large LIMS system with a data repository and analysis features, and a workflow system.

Acknowledging that some users have had bad experiences with poorly documented or buggy open source packages from academia, Dweck said the professional quality of 3rd Millennium’s software should set it apart from the rest of the open source pack. “We’re hoping to start a movement here,” he said, “and continue to be the leader in the field of informatics development.”

— BT


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