Commit d0a55190 authored by Jerome Mariette's avatar Jerome Mariette
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add the cover letter for the answer to the reviewer

parent 07c77a7f
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\namefrom{Jerome Mariette} % Name
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\greetto{Alison Hutchins,} % Greeting text
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\begin{document}
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% LETTER CONTENT
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The present cover 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.
\textbf{-- Reviewer 1 --}
\textbf{Comments to the Author\newline General:\newline The authors describe a
jQuery based library for integration of WMS controls and monitoring into
existing web interfaces that is complemented by a Python based WMS
implementation that delegates execution of jobs to Makeflow and Weaver.}
\textbf{Major: \newline Clearly, the novelty of the presented approach is the
jQuery component, which is an interesting contribution. The method section
should be rewritten to properly reflect this and show the advantages of the
system. The authors should show at least one usage example of the jQuery
plugins. The Python API is of limited novelty and should not take that much
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.}
\textbf{Minor: \newline why is WEB written uppercase?}
WEB has been changed for web in the whole text.
\textbf{-- Reviewer 2 --}
\textbf{Comments to the Author\newline This short paper describes a new
web-based workflow system that interfaces to an existing workflow system in the
back end. The bulk of the (necessarily short) paper focuses on the operations
within the interface. The topic is worthwhile, but to attract interest, it must
clearly state how its design objective is clearly different from other workflow
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.}
\textbf{Also, it would help to provide a brief sketch of the scale (\# jobs, \#
machines, amount of time) at which JFlow has been used.}
\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
allow and analysis of their files. It is mentioned that WMS like Galaxy,
although widely used, do not provide the capability of integrating external
workflows.}
\textbf{In my opinion, the article needs major corrections to be accepted to
Bioinformatics as an application note. I write suggestions in order of
appearance, not importance.}
\textbf{Major points\newline========\newline}
\textbf{1. The title, “A JavaScript based workflow management system” does not
seem to fit Jflow, as, in my opinion, it is a python based WMS with a JavaScript
interface.}
\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
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.}
\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
recommend that you expand a lot more on that within the main body of text. I
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
plugins and their benefits. An integration example is also given in a new
section named ``Example''.
\textbf{4. "Providing users with a simple interface to load and process their
datasets is now a common need.” Seems to me that this statement needs to be
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.}
\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
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.}
\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
liked to see a much more applied, biologically meaningful example describing
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.}
\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
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?}
\textbf{Minor points\newline========\newline}
\textbf{1. p1 col1 line 50 misspelled intuitiveness.}
It has been corrected.
\textbf{2. Style: why do you capitalise “WEB” in page 1 col 1 line 53? page 1,
col 2 line 23, line 51, line 53, line 5, line 60; page 2 col 2, line 9.}
WEB has been changed for web in the whole text.
\textbf{3. Style: I have found that Jflow is capitalised at the beginning of a
sentence and “flow” when it is not makes it a bit confusing. I would recommend
that you stick to one form of capitalisation and maintaining it throughout
regardless of whether the word appears at the beginning of a sentence;e.g., page
2 col 1, line 17: “jflow”; line 24 “Jflow”.}
jflow has been changed for Jflow in the whole text.
This paper is unpublished and has not been submitted for publication elsewhere.
We would be grateful if you would consider it for publication in Bioinformatics.
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