Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data

Background: Single-molecule techniques have emerged as incisive approaches for addressing a wide range of questions arising in contemporary biological research [Trends Biochem Sci 38: 30-37, 2013; Nat Rev Genet 14: 9-22, 2013; Curr Opin Struct Biol 2014, 28C: 112-121; Annu Rev Biophys 43: 19-39, 2014]. The analysis and interpretation of raw single-molecule data benefits greatly from the ongoing development of sophisticated statistical analysis tools that enable accurate inference at the low signal-to-noise ratios frequently associated with these measurements. While a number of groups have released analysis toolkits as open source software [J Phys Chem B 114: 5386-5403, 2010; Biophys J 79: 1915-1927, 2000; Biophys J 91: 1941-1951, 2006; Biophys J 79: 1928-1944, 2000; Biophys J 86: 4015-4029, 2004; Biophys J 97: 3196-3205, 2009; PLoS One 7: e30024, 2012; BMC Bioinformatics 288 11(8): S2, 2010; Biophys J 106: 1327-1337, 2014; Proc Int Conf Mach Learn 28: 361-369, 2013], it remains difficult to compare analysis for experiments performed in different labs due to a lack of standardization. Results: Here we propose a standardized single-molecule dataset (SMD) file format. SMD is designed to accommodate a wide variety of computer programming languages, single-molecule techniques, and analysis strategies. To facilitate adoption of this format we have made two existing data analysis packages that are used for single-molecule analysis compatible with this format. Conclusion: Adoption of a common, standard data file format for sharing raw single-molecule data and analysis outcomes is a critical step for the emerging and powerful single-molecule field, which will benefit both sophisticated users and non-specialists by allowing standardized, transparent, and reproducible analysis practices.