Levels used are from 1000mb to 100mb. Input winds are available 4 times daily(0,6,12 and 18z). The trajectory model does not know about the surface and calculations can result in air moving down through the surface. Interpolated model output is used below the surface.
The bug that impacted trajectories drawn over 360 has been fixed when we updated our NCL version. Let us know if you notice other trajectory plot issues, and if so, what options you selected.
Referencing Trajectory Code: The parcel trajectory software (traj3d) was obtained from the University of Melbourne Parcel Trajectory Software web page (http://www.cycstats.org/trajectories/trajhome.htm). A discussion of the algorithm is given by Noone and Simmonds (1999) and Barras and Simmonds (2009). Noone, D., and I. Simmonds, 1999: A three-dimensional spherical trajectory algorithm. Research Activities in Atmospheric and Oceanic Modelling, Report No. 28, WMO/TD-No. 942. H. Ritchie, Ed., World Meteorological Organization, 3.26-3.27. Barras, V., and I. Simmonds, 2009: Observation and modeling of stable water isotopes as diagnostics of rainfall dynamics over southeastern Australia Journal of Geophysical Research, 114, D23308, doi:10.1029/2009JD012132, 2009.
If you use plots or data from the page, we would also appreciate a reference: "Image provided by the NOAA-ESRL Physical Sciences Division, Boulder Colorado from their Web site at http://www.esrl.noaa.gov/psd/". Finally, you should reference the dataset that is used in the plot.