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communication/Bioinformatics/jflow_BIOINF.tex

@@ -5,7 +5,7 @@
 \begin{document}
 \firstpage{1}
 
-\title[short Title]{Jflow: A JavaScript based workflow management system}
+\title[short Title]{Jflow: a workflow management system for web applications}
 \author[Mariette \textit{et~al}]{J\'{e}r\^{o}me Mariette\,$^{1,*}$,
 Fr\'{e}d\'{e}ric Escudi\'{e}\,$^{1}$, Philippe Bardou\,$^2$, Ibouniyamine
 Nabihoudine\,$^1$, C\'{e}line Noirot\,$^1$, Marie-St\'{e}phane Trotard\,$^1$,
@@ -29,8 +29,7 @@ tools requires to mask the complexity induced by the needed High Performance
 Computing (HPC) environment. The connexion between interface and computing
 infrastructure is usually specific to each portal. With Jflow, we introduce
 a Workflow Management System (WMS), composed of jQuery plug-ins which can easily
-be
-embedded in any web application and a Python library providing all requested
+be embedded in any web application and a Python library providing all requested
 features to setup, run and monitor workflows.
 
 \section{Availability:}

communication/Bioinformatics/jflow_coverletter_bis.tex

@@ -69,10 +69,10 @@ space, especially since it only seems to wrap Makeflow and weaver. While the
 english is acceptable, the article contains some grammatical errors and should
 be checked for correct english.}
 
-The ``Methode'' section has been fully rewritten to fucus on the Jquery
-plugins and their benefits. An integration example is also described in a new
-section named ``Example''. The article has been checked by a native engish
-speaker.
+The ``Method'' section has been fully rewritten to focus on the Jquery
+plugins and their benefits. An integration example description is also provided
+in a new section named ``Example''. The article has also been checked by a
+native engish speaker.
 
 
 \textbf{Minor: \newline why is WEB written uppercase?}
@@ -92,9 +92,9 @@ describes the key operations, but in between those two needs to be a clear
 statement of what makes JFlow itself unique.}
 
 The introduction has been rewritten, to first introduce the benefits of WMS,
-then to describe existing WMS and finally introduce jflow and its originality.
-A section ``Example'' as also been added to explain and focus on jflow main
-features which are its five jQuery plugins.
+then to describe existing WMS and finally to introduce jflow and its
+originality. An ``Example'' section as also been added to explain and focus on
+jflow main features which are its five jQuery plugins.
 
 \textbf{Also, it would help to provide a brief sketch of the scale (\# jobs, \#
 machines, amount of time) at which JFlow has been used.}         
@@ -123,7 +123,8 @@ appearance, not importance.}
 seem to fit Jflow, as, in my opinion, it is a python based WMS with a JavaScript
 interface.}
 
-La je pense qu'il faut changer de titre non ?!
+Title has been changed for ``Jflow: a workflow management system for web
+applications''.
 
 \textbf{2. The justification for the article hinges on the fact that using WMS
 such as Galaxy does not enable an easy integration with already existing
@@ -146,7 +147,7 @@ think this is even more relevant than the Jflow API section. Perhaps you might
 want to reduce that section and include some text on the embedding of WMS
 features more explicitly —I leave this to the authors’s discretion.}
 
-The ``Methode'' section has been fully rewritten to fucus on the Jquery
+The ``Method'' section has been fully rewritten to focus on the Jquery
 plugins and their benefits. An integration example is also given in a new
 section named ``Example''.
 
@@ -157,7 +158,7 @@ substantiated further. It would help if it was further contextualised giving
 specific examples and/or references. to me this need is not so clear and/or
 common.}
 
-This sentence has been deleted from the introduction in order to focus more on
+This sentence has been removed from the introduction in order to focus more on
 generic web applications.
 
 \textbf{5. General comment, the style of the article would help with a bit more
@@ -167,8 +168,8 @@ applications.” Why is this a paragraph? It seems that it does not follow nor
 precedes any idea; it does not seem to flow. It seems like this paragraph lies
 in isolation, reducing the readability of the article.}
 
-The article was taken up in its entirety and in order to add cohesion between
-the different paragraphs the text has been checked by a native engish speaker. 
+The article was reorganized in order to add cohesion between the different
+paragraphs. The text has also been checked by a native engish speaker.
 
 \textbf{6. I find figure 1 does not add too much to the article. It would make
 sense in a software-oriented type of journal but I think that for
@@ -179,8 +180,7 @@ RNAbrowse. An example like that where I can see Jflow working would make this
 article a lot more attractive and compelling.}
 
 A full section describing jflow integration within NG6 has been added to the
-text. The previous figure has been substituted by a figure illustrating this
-example.
+text. The figure represents now this example.
 
 \textbf{7. I tried to look further into the documentation, which is extensive
 (e.g., Quick start) and went to Example1. Example1 is a template, not a running
@@ -189,10 +189,10 @@ install it. I have tried to install it in my laptop and failed miserably
 downloading and installing Makeflow. Perhaps it might be good to have an
 installation package that could already include the required dependencies?}
 
-Example1 is not a template but a running example of jflow. To avoid the
-confusion, the page describtion has been changed to ``This is a running example
-for a simple workflow manager website. Use it as a starting point to create
-something more unique.''.
+Example1 is not a template but a running example of jflow. To avoid confusion,
+the page description has been changed to ``This is a running example for a
+simple workflow manager website. Use it as a starting point to create something
+more unique.''. 
 
 
 \textbf{Minor points\newline========\newline}