As such stories tend to be, this one is complicated, but it's crucially important, so bear with my attempt at a concise summary. Dr. Shaffer, an associate professor of medicine and pathology at Stanford University, established the HIV Drug Resistance Database (HIVdb) (wikipedia link) in 1998. As the article reports,
Since then, the database has built a following among HIV researchers and practitioners around the world, attracting some 50,000 unique visitors a month. Those who use it generally fall into three categories: academic researchers, commercial and noncommercial laboratories, and doctors. ... The database allows users to enter genetic information for viruses from individual patients or groups of patients, and to retrieve drug resistance information, which can then be used to help devise treatment regimens. Such information is critical to HIV research and drug development, as well as to treating individual patients. HIVdb is especially popular in the developing world not least because it's freely available to anyone with an Internet connection. In some developing countries, medical practitioners have heard of Stanford University mainly through their interactions with HIVdb.
This is quite obviously a heroic, important, noble and benevolent effort. As the article notes, it's "a highly regarded free resource that he developed, Stanford hosts, and doctors and scientists around the world rely on."
However, in January 2007, ABL, a medical software company based in Luxembourg, claimed that the database infringed its patents. Read the article for more details, but in short: Stanford first moved to invalidate ABL's patents by filing a declaratory judgment suit in California in October 2007; but then later settled with ABL, where ABL agreed not to sue Stanford for patent infringement and Stanford agreed to put a prominent disclaimer on the HIVdb, informing those who used it that, depending on the nature of their work, they might need a patent license from ABL. However, Shafer wasn't required to sign the agreement with ABL and was not told him about the settlement's terms until after it was reached.
Shafer at first refused to post the notice, and bully for him. He was afraid it would lead doctors to think they owe money to ABL, "and that the database built mostly with taxpayer-funded National Institutes of Health grants is no longer free." Finally, under pressure, he did post a notice but he appended his own language arguing the patents are overbroad and invalid. See about halfway down on this page, where Dr. Shafer bravely challenges the validity of these patents. He also launched the site Harmful Patents, where he defiantly and courageously challenges the use of these patents to claim "a monopoly on the very concept of developing software to help physicians make treatment decisions"--absurdly, the patent gives ABL a monopoly on "the science of using computers to enhance medical treatment and decision making." As one of Shafer's colleagues notes, "If you read [ABL's patents] literally, anyone who is providing therapeutic options based on the sequence of a pathogen violates their patent, and that goes on in hundreds of contexts. It's truly a dangerous precedent."
Although ABL already settled with Stanford, its suit against Sahfer for breach of contract and defamation is ongoing. According to Mullin's report, Shafer has racked up more than $100,000 in legal bills and his career is in jeopardy, since he's fighting ABL and refused to cravenly give in, as his employer, Stanford University, arguably did.
I do not know if Shafer seeks or needs or welcomes help, or how it might be done. But I am all in favor of helping this man fight these people, and fight for the principle of "free access to published data" as "an intrinsic part of science and medicine." Good for Shafer, and for Mullin for bringing this to light.