In mid-April, the UK’s Medical Research Council discontinued its funding for further development of the Staden Package — a sequence analysis mainstay from Rodger Staden’s lab at the MRC Laboratory of Molecular Biology in Cambridge that was first developed in 1977.
The MRC’s decision not only impacts the five members of Staden’s group, who must now find positions elsewhere, but also affects an estimated 10,000 users of the software package, and raises a number of questions about the funding outlook for other publicly funded bioinformatics resources following the completion of the Human Genome Project.
Despite “excellent referee reports” for the project’s grant proposal, “MRC said that they had insufficient funds, even though I had suggested to them that it may cost them more in the long term if they did not fund us,” Staden told BioInform via e-mail.
An MRC spokeswoman noted, also via e-mail, that “MRC had many demands on its funds, which were insufficient to allow funding of all alpha-A-rated proposals. A number of other applications which were also highly rated also remained unfunded.”
In early April, when it became clear that funding for the project was in jeopardy, users of the package launched an e-mail campaign urging MRC’s chief executive, Sir George Radda, to overturn the decision. According to Staden, “hundreds” of researchers warned the agency that the funding cut would negatively impact other MRC-funded research projects. In spite of this outpouring of support, Staden posted a message to the BioNet software newsgroup last week that the decision would not be overturned.
Staden said that there are currently 2,500 license holders for the software worldwide, and an estimated total user base of 10,000. The suite of sequence assembly and analysis tools lies at the heart of many core bioinformatics labs and sequencing centers, and a skim through the comments of outraged users provided to BioInform by Staden indicates these groups will be strongly affected once support for the package is discontinued. “This decision is going to cause big problems for a large number of people who have incorporated components of the Staden package into their own software or websites,” wrote one user. As another noted, “many people cannot afford the commercial software packages and, more importantly, they cannot embed components of these commercial packages into their own software or dynamic websites.”
Several researchers questioned whether the MRC assumed, as one user wrote, “that since the world [human] genome project is about to be over, packages such as Staden’s will no longer be necessary.”
The MRC spokeswoman denied that the decision was connected to the completion of the HGP.
Users of the popular bioinformatics package are not the only critics of the MRC’s recent funding decisions. In late March, the UK Parliament’s Committee on Science and Technology issued a scorching report that criticized the MRC’s grant review process and budgeting policy. The MRC responded with a statement noting that its planning process “involves making difficult choices which are not always popular at the time.”
New License Model
Right now, Staden said, he is considering a number of options for keeping the software package updated and in researchers’ hands. For example, he said, he negotiated a change in the licensing structure through the MRC. Previously, the package required a license file that could restrict use to a particular machine, domain, or time frame. “As there would be nobody here to issue licenses ... I got MRC to agree to us supplying a license which allowed the package to work anywhere forever,” he said.
Staden said he has also looked into releasing the package under an open source license — an option that the MRC is willing to consider, but, as Staden noted, “it is unlikely that the package will become open source if there are insufficient people willing to work on it.” So far, he said, he has been in contact with the open source EMBOSS bioinformatics project “to see if some parts of our work, which provide an interface to EMBOSS, could be funded through them.” In addition, he said, several users suggested they would be interested in paying for the software in the future.
The Staden package is not the first bioinformatics resource to experience funding woes — SwissProt, for example, shifted to a fee-based model in 1998 when its public funding was threatened, and the GDB Human Genome Database found a new host at Toronto’s Hospital for Sick Children when the US Department of Energy cut its funding in 1998. Even a number of commercial bioinformatics packages have survived following the demise of their original vendors. Considering these precedents, it’s likely that the Staden package will also endure, provided there is sufficient demand. As Staden noted in his message to users, “There are enough of you to make it succeed, but it’s up to you.”
The MRC spokeswoman noted that “discussions are currently ongoing to look at other mechanisms for continued support for the Staden package, as well as how best to make the transition to a lower level of funding smoothly so that the community can continue to benefit from further development of the package, and so the Staden group can continue in its contributions.”