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Tropical Disease Initiative

moskito.jpgThe "Free/Open Source" model could be as revolutionary in the world of biological science as it has been in the world of software. We've the notion of open source biomedical research a number of times here, and expect the idea to be of increasing importance in the coming years. An open source approach to biological research offers significant leapfrog potential, as scientists in the developing world could participate in the research and get unrestricted access to what has been learned, and local companies and governments could produce the resulting medicines. And just as free/open source software fills niches ignored or awkwardly approached by proprietary software, a distributed, collaborative, transparent process of biomedical development can take on health challenges that pharmaceutical corporations have determined to be unprofitable. Perhaps the most glaring example of this category of medical research is the realm of tropical diseases: malaria, dengue fever, African sleeping sickness -- fatal diseases, rampant in the developing world, but for which cures offer little profit.

The Tropical Disease Initiative seeks cures for these "orphan" illnesses using an open source research and development model. Started by Dr. Andrej Sali, professor of Biopharmaceutical Sciences and Pharmaceutical Chemistry at UC San Francisco, TDI will combine the efforts of hundreds of volunteer researchers from around the globe, focusing on the application of computational biology and chemistry on drug discovery (see the extended entry for a graph illustrating the TDI process). Dr. Sali, along with Stephen M. Maurer (professor of Public Policy at UC Berkeley) and Arti Rai (from the School of Law at Duke University), details the open source research process in a new article entitled "Finding Cures for Tropical Diseases: Is Open Source an Answer?", freely available at PLoS Medicine, a peer-reviewed open access medical journal:

What would open-source drug discovery look like? As with current software collaborations, we propose a Web site where volunteers use a variety of computer programs, databases, and computing hardware (Figure 1) [Image Below]. Individual pages would host tasks like searching for new protein targets, finding chemicals to attack known targets, and posting data from related chemistry and biology experiments. Volunteers could use chat rooms and bulletin boards to announce discoveries and debate future research directions. Over time, the most dedicated and proficient volunteers would become leaders.

Ten years ago, TDI would not have been feasible. The difference today is the vastly greater size and variety of chemical, biological, and medical databases; new software; and more powerful computers. Researchers can now identify promising protein targets and small sets of chemicals, including good lead compounds, using computation alone. For example, a SARS protein similar to mRNA cap-1 methyltransferases—a class of proteins with available inhibitors—was recently identified by scanning proteins encoded by the SARS genome against proteins of known structure. This discovery provides an important new target for future experimental validation and iterative lead optimization. More generally, existing projects such as the University of California at San Francisco's Tropical Disease Research Unit (San Francisco, California, United States) show that even relatively modest computing, chemistry, and biology resources can deliver compounds suitable for clinical trials. Increases in computing power and improved computational tools will make these methods even more powerful in the future.

Discoveries resulting from this research would not be patented; instead, they would be made available to so-called "virtual pharma" such as the Institute for OneWorld Health and the Drugs for Neglected Diseases Initiative for development and production, and (as possible) to the affected nations themselves for local production. TDI has not yet finalized the details of its intellectual property model; the PLoS article lists some of the options TDI is considering:

  • A public-domain license that permits anyone to use the information for any purpose.
  • Licenses similar to the Creative Commons Attribution License that permit anyone to use the information for any purpose, provided proper attribution is given.
  • Licenses such as the General Public License that prohibit users from seeking intellectual property rights.
  • Licenses that permit commercial companies to obtain and exploit patents outside the developing world. These would allow Virtual Pharma to stretch its own R&D funds by letting corporate partners sell patented products to ecotourists, governments, and other consumers living in the industrialized world.
  • (The last sounds similar to the Creative Commons Developing Nations License.)

    TDI is still in its very early stages; the site has little detail as of yet, although it does offer a discussion forum for those interested in participating. Given its emphasis on computational biology, it seems to be an ideal partner for distributed computing projects (such as Folding@Home). The need for greater research emphasis on neglected tropical diseases is clear, and the approach TDI is taking holds much promise. We'll be watching TDI closely over the coming months -- it could be the first significant success of the open source model in biomedicine.

    The TDI Process


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    Oh, crap. I've written a really long article about Open Source and it's relation to Research Projects. I wasn't able to save it (timeout), now it is gone. Still, here a  link to the issue. I think it is an interesting idea.And I will save every text in lo [Read More]


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