Tuesday, December 23, 2014

New version of the manuscript (2)

I have now made some significant changes in the arrangement of the simulation details part of the manuscript: the simulation details texts are now in the Supplementary section and references to the simulation files and details are added to the tables describing the simulated systems. There is also updated ToDo list. For these reasons I have now made a pdf with new file name:


You can still access the previous draft version using the links in previous post.

There are also some changes in the content (marked with bold) compared to the previous version.

The goal is to submit the manuscript to the arXiv server latest at 14.1.2015 due to the grant application deadline.

Important note:

I think that it would be very useful if we would share as much simulation files as possible. Since Zenodo allows 2 GB files, also the trajectory sharing is possible. I have created the nmrlipids community in the Zenodo where some simulation files with trajectories related to this project are already shared. The more we get trajectories and other files there the better. To exemplify the potential utility of this collection, I wrote a script which automatically dowloads simulation data from Zenodo and calculates the form factor (FFcomp.sh, see also discussion with Peter Heftberger). Note that Zenodo gives a doi indentification for your data, thus it can be cited. In the current version of the manuscript these citations are used in the simulation system tables to refer the location of files. If someone does not want or cannot share the files, we can just leave these table items empty.