Open Source Science: A Revolution From Within
Nov 20, 2009 4:00 AM PT
Ask anyone in the open source science movement what it's all about, and you're likely to come back to the word that's right there in its name: "open." Open source science is all about open access. To research methods. To data. To scholarly publications. And supporters feel that it's vital to the continued growth and evolution of science itself.
"Open source science is a collaborative and transparent approach to science," said Walter Jessen, a bioinformatician and cancer biologist at Cincinnati Children's Hospital and the founder of Highlight HEALTH and Next Generation Science.
Just as open source software allows programmers to access the code in order to create new and improved versions of software, open source science gives the scientific community open and easy access to fundamental experiments, methods and data in order to facilitate more research. The goal, ultimately, is better science.
"There are many benefits to open source science: speed, efficiency, quality, increased communication, worldwide participation, [and] accelerated progress towards understanding and eradicating disease," Jessen told LinuxInsider.
One of the main tenets of the open source science movement is access. Traditional scientific publishing is a slow, cumbersome process, and it can be expensive and difficult for both the public and scientists to access the information.
The Public Library of Science (PLoS) is one example of the open access spirit at work. In 2003, it started two open access journals, and now it has seven.
"Each PLoS journal provides a suite of metrics for every article, including measures of online usage, citations from the scholarly literature, social bookmarks, blog coverage, and the Comments, Notes and 'Star' ratings," explained Jessen. "Its most recent journal, PLoSOne, has experienced substantial growth since it was launched in 2006. It's already the largest open access journal in the world and is projected to become the third-largest journal in the world by the end of the year."
Open source science also seeks to provide access to the methodology and data, so that researchers can reproduce the results of a study without having to jump through unnecessary hoops, such as having to purchase proprietary software.
"It all comes down to allowing researchers the ability to access what other people have done so they can see what was done and reproduce the results," Jeff Bizarro, the president of Bioinformatics Organization, told LinuxInsider. "Open source and open access movements argue that information shouldn't be held as proprietary, but should be disclosed."
Open Source at Work
Many of the cutting-edge examples of open source science are based on the wiki model. Project Polymath, for instance, uses blogs and wikis to allow people to collaboratively work on an unsolved mathematical problem.
"In less than two months, it was announced that the Polymath participants had worked out an elementary proof, and a manuscript describing the proof is currently being written," said Jessen. "The project demonstrated that many people could work together to solve difficult mathematical problems."
Another example of a wiki-based open source science project is Bizarro's Bioinformatics Organization, which started as a collaborative project in 1998. At the intersection of biology and computer science, the Bioinformatics Organization uses wiki software to let researchers post their models, questions, experiments and discoveries.
"We found there were people looking for a central location for their open source projects," said Bizarro. "We decided to create something that was a bit of a utopian environment, where everyone who was involved shared everything with everyone else."
Today, the organization has 27,000 members from all around the world, using the organization's wiki site to post projects in bioinformatics subfields such as DNA and RNA sequence analysis, protein analysis and drug discovery. Increasingly, scientists are using the site for social and professional networking, as well.
"In more recent years, it's become more of an online community like Facebook," said Bizarro.
Google Research is another new project that is based on open source science models, and many other such ventures are on the horizon.
Openness vs. Intellectual Property
All this openness does raise some questions about intellectual property, however. Certainly, science is fundamentally about sharing data and information, but how can scientists share information while at the same time protect their ideas and discoveries?
The Open Source Science Project, which is developing a research-based, openly accessible scientific curriculum, addresses this issue by allowing scientists to document their process of discovery all along the way.
"Our project was designed so that researchers willing to conduct open research would be protected from this form of theft by their ability to maintain an openly available paper trail from the time they submit their project proposal until the time they publish their final report," Priyan Weerappuli, executive director of The Open Source Science Project, told LinuxInsider. "It's worth noting that while the risk of intellectual theft is real, the ability for researchers to work off of one another is an invaluable tool for furthering any given field of study. We seek to ensure is that researchers are properly credited for any such property they produce."
Creative Commons-type licensing is another option for scientists, publications, and institutions that want to allow open access to data, methods and discoveries, while at the same time give some measure of protection to those who produce this information. Science Commons, a project of Creative Commons, for instance, provides licensing for scientific content; over a thousand scholarly journals worldwide are making use of Science Commons' licenses. It is also involved in patent licensing for companies such as Nike, Best Buy and Yahoo.
"What we do at Creative Commons in the sciences is try to intervene and change the fundamentals," John Wilbanks, vice president of Science Commons, told LinuxInsider. "More access to information and tools means more people can take a shot at science. More freedom to operate means it's easier to be an entrepreneur. It's all about democratizing access to the information and tools enough to allow that distributed innovation to occur."
Everyone -- scientists, the general public, and even taxpayers -- stands to benefit from a new scientific model, argued Wilbanks, who prefers the term "distributed science" to "open source science" to describe this process.
"If we can lower the cost of failure and increase the interconnection and discoverability of the things we actually know, it's one of the only non-miraculous ways to systematically increase the odds in our favor to discover drugs, understand climate change, and generally make good choices in a complex world," explained Wilbanks.
"Distributed approaches have a tendency to scale better, at lower costs, than closed ones," he maintained, "so it's also a better return on investment for the funders of science -- who, overwhelmingly, are the taxpayers."