Open Science, Open Data, Open Access - Bio-IT World

"In two compelling presentations at the Bio-IT World Conference* last week, Atul Butte and Steven Salzberg provided formidable advocacy for the virtues of open data and open science.   Salzberg, a computer scientist at Johns Hopkins University, accepted the 2013 Benjamin Franklin Award for Open Access in the Life Sciences for his work promoting 'free and open access to the materials and methods used in the life sciences.'   Salzberg is perhaps best-known for developing a series of popular open-source software platforms, including Glimmer (a bacterial gene finder) and the Tuxedo software suite of next generation sequencing tools (see, 'Steven Salzberg on Microbial Genomes, Open Access, Flu Shots, and Gene Patents') . Salzberg insists the software stay open-source because 'free software gets used.'  Salzberg has also been a fervent advocate for a more open atmosphere in science for over a decade. In a 2003 letter to the editor of Nature, he asserted that 'genome data-collection projects should be freely available to the entire scientific community, immediately and with no restrictions or conditions.' In a paper last year on 'the perils of gene patents,' he argued that 'gene patents are antithetical to scientific process.'  After accepting the award from Jeff Bizzaro, president of Bioinformatics.org, Salzberg delivered a fast-paced talk on three components of open-science he feels are essential: free software, open data, and open access publication. He discussed some of his lab’s accomplishments in encouraging researchers to be more open with their experimental data. Salzberg’s talk echoed many of the themes in the preceding keynote from Stanford University’s Atul Butte, who highlighted how open access to experimental data could democratize science (see, 'Bits and SNPs: Atul Butte and Medicine in the Era of Big Data').   His talk came just two months after the White House’s Office of Science and Technology released a memorandum directing federal agencies with more than $100 million in R&D expenditures to develop plans for making their experimental data publicly available. With vast, publicly available data libraries, perhaps one day, Butte mused, students could create biotech startups “out of their garage,” the way many technology startups began in the past few decades.   'If you’re not going to do this, try and get your kids interested,' Butte challenged the packed audience. He sprinkled his talk with examples of commercial services such as Assay Depot, offering easy access to cell lines, animal models and so on, greatly expediting new experimental ideas.  While the plenary speakers suggested the halcyon days of open access in biomedical research are on the near horizon, the tone was a little different in the exhibit hall downstairs.    While many company representatives at the conference agreed that open-source software and open access to experimental data provide enormous benefits for researchers, they argue a 'pay for profit' model of resource distribution provides advantages that open-access platforms aren't prepared to address ..."