Merge pull request #185 from brookehus/changes-bh-th

some edits/consistency changes, and TODOs

Author: cwehmeyer

manuscript/literature.bib

@@ -774,4 +774,5 @@ @Misc{mdtutorial
   year =      {2018},
   url = "https://github.com/MobleyLab/basic_simulation_training",
   note = "Accessed November 15, 2018."
+  DOI = {10.33011/livecoms.1.1.5957}
 }