Beta blockers? : proprietary data formats may be legally defensible but open standards can be a better spur for innovation
"Thomson [Thomson Reuters] makes the proprietary bibliography software EndNote, and claims that Zotero is causing its commercial business 'irreparable harm' and is wilfully and intentionally destroying Thomson's customer base. In particular, Thomson is demanding that GMU stop distributing the newer beta-version of Zotero that allegedly allows EndNote's proprietary data format for storing journal citation styles to be converted into an open-standard format readable by Zotero and other software. Thomson claims that Zotero 'reverse engineered or decompiled' not only the format, but also the EndNote software itself. ...
Litigation, which may go to a jury trial, is pending, so judging this case on its legal merits would be premature. But on a more general level, the virtues of interoperability and easy data-sharing among researchers are worth restating. Imagine if Microsoft Word or Excel files could be opened and saved only in these proprietary formats, for example. It would be impossible for OpenOffice and other such software to read and save these files using open standards - as they can legally do.
Competition between open-source and proprietary software is long-running, as personified by the struggle between Windows and Linux for desktop and server operating systems, but also in many branches of software used by scientists. Researchers tend to lean towards open sharing, but they will also pay for added-value features, and it's important that the playing field is level. Ultimately, the customer is king."
(Nature, p.708)
Nature Volume 455, p.708 (9 October 2008) | doi:10.1038/455708a; Published online 8 October 2008, Nature Publishing Group, a division of Macmillan Publishers Limited.
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Simon PerkinsSHARE
Citizen science: predicting protein structures with a multiplayer online game
"People exert large amounts of problem-solving effort playing computer games. Simple image- and text-recognition tasks have been successfully ‘crowd-sourced’ through games, but it is not clear if more complex scientific problems can be solved with human-directed computing. Protein structure prediction is one such problem: locating the biologically relevant native conformation of a protein is a formidable computational challenge given the very large size of the search space. Here we describe Foldit, a multiplayer online game that engages non-scientists in solving hard prediction problems. Foldit players interact with protein structures using direct manipulation tools and user-friendly versions of algorithms from the Rosetta structure prediction methodology, while they compete and collaborate to optimize the computed energy. We show that top-ranked Foldit players excel at solving challenging structure refinement problems in which substantial backbone rearrangements are necessary to achieve the burial of hydrophobic residues. Players working collaboratively develop a rich assortment of new strategies and algorithms; unlike computational approaches, they explore not only the conformational space but also the space of possible search strategies. The integration of human visual problem-solving and strategy development capabilities with traditional computational algorithms through interactive multiplayer games is a powerful new approach to solving computationally-limited scientific problems."
(Seth Cooper, Firas Khatib, Adrien Treuille, Janos Barbero, Jeehyung Lee, Michael Beenen, Andrew Leaver-Fay, David Baker, Zoran Popović & Foldit players)
Nature 466, 756–760 (05 August 2010) doi:10.1038/nature09304 Received 22 January 2010 Accepted 30 June 2010
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Simon PerkinsSHARE
