Commit 0182839a authored by Jerome Mariette's avatar Jerome Mariette
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......@@ -47,7 +47,7 @@
% LETTER CONTENT
%----------------------------------------------------------------------------------------
The present cover letter is pertaining to the paper "Jflow: A JavaScript based
The present letter is pertaining to the paper "Jflow: A JavaScript based
workflow management system". After the review process, we were asked to solve
the concerns addressed about the paper. We made the requested modifications.
Hereafter are our answers to the reviewers.
......@@ -69,6 +69,12 @@ 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.
\textbf{Minor: \newline why is WEB written uppercase?}
WEB has been changed for web in the whole text.
......@@ -85,15 +91,21 @@ systems. E.g. section 1 describes other workflow systems and section 2
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.
\textbf{Also, it would help to provide a brief sketch of the scale (\# jobs, \#
machines, amount of time) at which JFlow has been used.}
The following sentence has been added to the text: ``[\ldots] NG6 (Mariette et
al., 2012), where it has been used to process more than 2 000 sequencing runs
on a 5 000 cores HPC.''.
\textbf{-- Reviewer 3 --}
\textbf{Comments to the Author\newline Jflow is a workflow management system
(WMS) that uses Python and JQuery to allow embedding of workflows with a web
application. The rationale is that biologists are used to use web interfaces to
......@@ -111,6 +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 ?!
\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
interfaces. I would say that this depends on the type on interface because
......@@ -118,6 +132,12 @@ Galaxy does provide a Galaxy Visualisation Plugin protocol that could be adapted
for the creation of WMS. Arguably this type of functionality could be used to
adapt the needs of NG6.}
To our knowledge, Galaxy does not provide any JavaScript libraries enabling its
integration in an existing web application. Galaxy provides a visualizations
registry and plugin framework to ease the creation of new, custom visualizations
for almost any data. This feature is available from the Galaxy application and
do not offer WMS features such as monitoring or running workflows.
\textbf{3. Not until the conclusion, it becomes a bit clearer to me that Jflow
allows embedding of WMS features within a web application. This is mentioned at
the beginning in the abstract, and given that this is the main feature, I would
......@@ -137,6 +157,9 @@ 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
generic web applications.
\textbf{5. General comment, the style of the article would help with a bit more
cohesion between different paragraphs. For example the paragraph "Jflow user
interface has been designed to allow an easy integration in mashup WEB
......@@ -144,6 +167,9 @@ 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.
\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
Bioinformatics, it is important to see the application to biology. I would have
......@@ -152,6 +178,10 @@ Jflow in action. You mention Jflow is working already embedded in NG6 and
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.
\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
example, hence it is difficult to ascertain how Jflow works without having to
......@@ -159,6 +189,12 @@ 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.''.
\textbf{Minor points\newline========\newline}
\textbf{1. p1 col1 line 50 misspelled intuitiveness.}
......
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