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Almost 15 years ago, American computer programmer, writer and leading advocate of open source, Eric Steven Raymond, wrote an essay entitled The Cathedral and the Bazaar, referring to two different software development models. As the analogy implies, the cathedral model is a traditional, hierarchical, costly and time-consuming method of working where code only becomes available with each software release, restricted to an exclusive group of expert developers during interim phases. The bazaar model, by contrast, has code openly developed and available to public view online. Low barrier to entry, little start-up cost and a chaotic or self-organizing structure with fluid leadership among many motivated strangers are characteristic of the bazaar. Raymond’s work has not only had a lasting and substantial impact in the world of open source software (with the Linux operating system and the Firefox web browser being high profile examples which followed his lead), it has also significantly influenced several movements in open source science, recently named the Biobazaar in biotechnology circles.

Faculty Members Mario Pineda-Krch, Mark Lewis and Ferdinando Boero brought to our attention a comment piece by Woelfle et al. that appeared in Nature Chemistry, ‘Open science is a research accelerator’ ¹. The article highlights a case study in employing open source methodologies to solve a chemistry problem that would ultimately enable cheap and accessible delivery of a drug called praziquantel (PZQ) that is used to treat schistosomiasis, a neglected and serious parasitic disease, infecting 200 million people, with 400 million people at risk.

The chemistry predicament arose because the PZQ compound is a racemate, having two mirror-image forms, with one enantiomer being the active ingredient and the other simply causing side effects and a bitter taste. If, however, the pill could be produced in just its active enantiomer, it would be smaller, not bitter and much preferable to take in terms of providing optimal treatment and having limited negative effects. Unfortunately, the research and synthesis refinement it takes to do this is a costly endeavor rarely taken on in academia (too expensive and beyond the scope of graduate work) or industry (where profit margins in neglected disease R&D are too small).

The Synaptic Leap was started as a call to action to solve this problem via the biobazaar route. Online, interested researchers around the world, across industry and academia began to share an Electronic Lab Notebook collating data, results, successes, failures, analyses and manuscript drafts. The work on The Synaptic Leap gained substantial attention in 2010 after funding was secured and substantial traffic was generated through blog posts, LinkedIn forums, news articles and online videos. The chemistry problem was solved. In conclusion to their article, Woelfle et al. sum up a few key benefits of open science:

• Real world problems are solved much quicker when experts identify themselves and spontaneously contribute to mounting research data online; this is far preferable to the limits and costs of seeking out experts to research in a local area.
• Open science is transparent and therefore accountable; it can help to build the trust of public taxpayers who support science research.
• Projects live on and evolve much beyond the scope of the originators when experiments, data and analyses are available online.
• Open science provides the most rigorous means to peer review pre-, mid- and post-publication.

There are mounting sources of inspiration where scientific research communities are taking leaps into a biobazaar approach. If interested, you might take a look at the BiOS initiative (from Cambia) that uses internet communication to simplify proprietary struggles and forge links among open biology community members; also, the BioBricks Foundation and its associated Registry of Standard Biological Parts are key institutions that give undergraduate students the opportunity to use open source standard biological parts in order to learn synthetic biology fundamentals in the annual International Genetically Engineered Machine competition (iGEM); and the Tropical Disease Initiative (TDI) is providing a platform for open source drug discovery.

In case you missed it, just last week, we highlighted F1000’s own latest moves into the biobazaar with the new F1000 Research model in the development stages, which would offer transparent, immediate sharing of research data sets for analysis and enable open peer review.

¹ Woelfe et al. Nature Chemistry 2011, 3:745-8 [doi:10.1038/nchem.1149].