MetaPathways v2.5: quantitative functional, taxonomic and usability improvements.

UNLABELLED: Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation. We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure. Additionally, we improve LAST homology searches through BLAST-equivalent E-values and output formats that are natively compatible with prevailing software applications. Finally, an updated graphical user interface allows for keyword annotation query and projection onto user-defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database. AVAILABILITY AND IMPLEMENTATION: MetaPathways v2.5 is available on GitHub: http://github.com/hallamlab/metapathways2. CONTACT: shallam@mail.ubc.ca SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Are we missing the sitting? Agreement between accelerometer non-wear time validation methods used with older adults' data.

We used Bland Altman plots to compare agreement between a self-report diary and five different non-wear time algorithms [an algorithm that uses ≥60 min of consecutive zeroes (Troiano) and four variations of an algorithm that uses ≥90 min of consecutive zeroes to define a non-wear period] for estimating community-dwelling older adults' (n = 106) sedentary behaviour and wear time (min/day) as measured by accelerometry. We found that the Troiano algorithm may overestimate sedentary behaviour and wear time by ≥30 min/day. Algorithms that use ≥90 min of continuous zeroes more closely approximate participants' sedentary behaviour and wear time. Across the self-report diary vs. ≥90 min algorithm comparisons, mean differences ranged between -4.4 to 8.1 min/day for estimates of sedentary behaviour and between -10.8 to 1.0 min/day for estimates of wear time; all 95% confidence intervals for mean differences crossed zero. We also found that 95% limits of agreement were wide for all comparisons, highlighting the large variation in estimates of sedentary behaviour and wear time. Given the importance of reducing sedentary behaviour and encouraging physical activity for older adult health, we conclude that it is critical to establish accurate approaches for measurement.