Merge pull request #181 from EDiLD/dev_ms

reformat output.
Merge pull request #182 from EDiLD/dev_ms

Dev ms
Merge pull request #184 from EDiLD/dev_ms

Dev ms
Merge pull request #185 from EDiLD/dev_ms

Dev ms
added a few changes to the main ms, #178
a few slight changes to manuscript, added detailed response to reviewers for the f1000 website, 2nd version just submitted