fixed long URL bug

manuscript/manuscript.md

@@ -660,7 +660,7 @@ the Life Sciences Research Foundation. PB was funded by the Natural Sciences &
 Engineering Research Council of Canada and the Academic Development Fund of the
 University of Western Ontario. SM would like to thank Dr. Laurence Tratt for
 reviewing an early draft of this paper. TP was funded by an NSERC Discovery Grant,
-and a Start-Up grant from the Université de Montréal. 
+and a Start-Up grant from the Université de Montréal.
 
 \newpage
 
@@ -687,17 +687,8 @@ and length), information about "where", "when", and "what" animals were
 measured can be considered meta-data. Using the tidy format makes this
 distinction clearer.
 
-# Figures {-}
-
-\begin{figure}[h!]
-\centering
-\includegraphics[width=\columnwidth]{resources/tidy_data.eps}
-\caption{}
-\label{fig:tidy-data}
-\end{figure}
-
-\nolinenumbers
 \newpage
 
+
 # References {-}
 \bibdata{resources/manuscript.bib}

manuscript/resources/manuscript.bib

@@ -1,16 +1,16 @@
 @proceedings{higgins2002,
-  author = {Higgins, D. and Berkley, C. and Jones, M.B.}, 
-  editor = {}, 
-  title = {Managing heterogeneous ecological data using Morpho}, 
-  booktitle = {Managing heterogeneous ecological data using Morpho}, 
-  volume = {14th International Conference on Scientific and Statistical Database Management}, 
-  publisher = {IEEE Comput. Soc}, 
-  address = {}, 
-  pages = {69-76}, 
-  year = {2002}, 
-  abstract = {}, 
-  keywords = {}, 
-  doi = {10.1109/SSDM.2002.1029707}, 
+  author = {Higgins, D. and Berkley, C. and Jones, M.B.},
+  editor = {},
+  title = {Managing heterogeneous ecological data using Morpho},
+  booktitle = {Managing heterogeneous ecological data using Morpho},
+  volume = {14th International Conference on Scientific and Statistical Database Management},
+  publisher = {IEEE Comput. Soc},
+  address = {},
+  pages = {69-76},
+  year = {2002},
+  abstract = {},
+  keywords = {},
+  doi = {10.1109/SSDM.2002.1029707},
   url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=1029707}
 }
 

manuscript/resources/plos_template.tex

@@ -12,18 +12,18 @@
 %
 % -- IMPORTANT NOTE
 %
-% This template contains comments intended 
-% to minimize problems and delays during our production 
+% This template contains comments intended
+% to minimize problems and delays during our production
 % process. Please follow the template instructions
 % whenever possible.
 %
-% % % % % % % % % % % % % % % % % % % % % % % 
+% % % % % % % % % % % % % % % % % % % % % % %
 %
-% Once your paper is accepted for publication, 
+% Once your paper is accepted for publication,
 % PLEASE REMOVE ALL TRACKED CHANGES in this file and leave only
 % the final text of your manuscript.
 %
-% There are no restrictions on package use within the LaTeX files except that 
+% There are no restrictions on package use within the LaTeX files except that
 % no packages listed in the template may be deleted.
 %
 % Please do not include colors or graphics in the text.
@@ -37,8 +37,8 @@
 % Please include tables/figure captions directly after the paragraph where they are first cited in the text.
 %
 % DO NOT INCLUDE GRAPHICS IN YOUR MANUSCRIPT
-% - Figures should be uploaded separately from your manuscript file. 
-% - Figures generated using LaTeX should be extracted and removed from the PDF before submission. 
+% - Figures should be uploaded separately from your manuscript file.
+% - Figures generated using LaTeX should be extracted and removed from the PDF before submission.
 % - Figures containing multiple panels/subfigures must be combined into one image file before submission.
 % For figure citations, please use "Fig." instead of "Figure".
 % See http://www.plosone.org/static/figureGuidelines for PLOS figure guidelines.
@@ -62,11 +62,11 @@
 %
 % Do not include text that is not math in the math environment. For example, CO2 will be CO\textsubscript{2}.
 %
-% Please add line breaks to long display equations when possible in order to fit size of the column. 
+% Please add line breaks to long display equations when possible in order to fit size of the column.
 %
 % For inline equations, please do not include punctuation (commas, etc) within the math environment unless this is part of the equation.
 %
-% % % % % % % % % % % % % % % % % % % % % % % % 
+% % % % % % % % % % % % % % % % % % % % % % % %
 %
 % Please contact [email protected] with any questions.
 %
@@ -94,7 +94,7 @@
 \usepackage{cite}
 
 % Use nameref to cite supporting information files (see Supporting Information section for more info)
-\usepackage{nameref,hyperref}
+\usepackage{nameref}
 
 % line numbers
 \usepackage[right]{lineno}
@@ -107,13 +107,18 @@
 \usepackage{rotating}
 
 % Remove comment for double spacing
-%\usepackage{setspace} 
+%\usepackage{setspace}
 %\doublespacing
 
+%to handle url breaks in references
+\usepackage{url}
+\usepackage{hyperref}
+\usepackage{breakurl}
+
 % Text layout
 \raggedright
 \setlength{\parindent}{0.5cm}
-\textwidth 5.25in 
+\textwidth 5.25in
 \textheight 8.75in
 
 % Bold the 'Figure #' in the caption and separate it from the title/caption with a period
@@ -190,8 +195,8 @@
 % Please keep the abstract below 300 words
 
 % Please keep the Author Summary between 150 and 200 words
-% Use first person. PLOS ONE authors please skip this step. 
-% Author Summary not valid for PLOS ONE submissions.   
+% Use first person. PLOS ONE authors please skip this step.
+% Author Summary not valid for PLOS ONE submissions.
 
 % For figure citations, please use "Fig." instead of "Figure".
 
@@ -209,7 +214,6 @@
 % Compile your BiBTeX database using our plos2015.bst
 % style file and paste the contents of your .bbl file
 % here.
-% 
+%
 
 \end{document}
-

resubmission_materials/Revised_cover_letter.md

@@ -0,0 +1,10 @@
+                                                            July 5, 2016
+
+Dear Dr. Markel,
+
+Thank you for reviewing our manuscript "Ten Simple Rules for Digital
+Data Storage" and considering our resubmission. We have thoroughly considered the reviewer responses and taken almost all of their suggestions into account in our revived manuscript.  We believe this has made our submission even stronger.  Thank you again for your time in helping us improve our manuscript.
+
+Sincerely,
+
+Dr. Edmund Hart

resubmission_materials/reviewer_response.md

@@ -1,10 +1,6 @@
 Dear Dr. Markel,
 
-Thank you for reviewing our manuscript "Ten Simple Rules for Digital
-Data Storage" and considering our resubmission. We appreciate the
-thoughtful feedback reviewers have provided and incorporated their
-comments into our revised manuscript. Below is a detailed accounting
-of our changes, with reviewer submissions highlighted in bold.
+Below is a detailed accounting of our changes, with reviewer submissions highlighted in bold.
 
 
 **_Reviewer #1:_** _The manuscript enumerates a set of "rules" that
@@ -97,9 +93,9 @@ situation in reality can become very complicated, these ten simple
 rules can still provide good and useful guidance for researchers to
 develop data storage and management systems. Actually, we have pretty
 much followed these rules in our own practices. The manuscript was
-concise and well written.
+concise and well written._
 
-Minor suggestions:_
+_Minor suggestions:_
 
 **Page 2, Line 50: "can help" -> "can help to"**
 
@@ -129,10 +125,10 @@ We have added several examples in our rules that are specific to
 biomedical data to address this concern. In particular:
 
 Line 24-26: We suggest GenBank as an example place to archive sequence
-data 
+data
 
 Line 64-66: We suggest using community tools for formatting
-sequence data and ecological metadata 
+sequence data and ecological metadata
 
 Line 177-178: We give an example of version numbers
 that are specific to NCBI repositories