Commit 585ff3f2 authored by Jerome Mariette's avatar Jerome Mariette
Browse files

a start to the reviewer

parent 014f4271
......@@ -50,23 +50,23 @@ multiple services and analysis tools in an integrated manner for specific
experiments or data types. These applications require WMS features to manage
and execute their computational pipelines.
Generic WMS, such as Galaxy (Goecks et al., 2010), provide a user friendly
graphical interface easing workflow creation and execution. Today, Galaxy is
probably the most used WMS in the biologist community thanks to its
intuitiveness and large software package collection. Unfortunately, such
environments come with their own interface, complicating their integration
within already existing web tools. Other WMS such as weaver (Bui et al.,
2012) or Cosmos (Gafni et al., 2014) provide a framework or a domain-specific
language to developers wanting to build and run workflows. These software
packages offer the flexibility and power of a high level programming language,
but they do not provide a user interface, enable component and workflow
definition or check file formats.
Generic WMS, such as Galaxy (Goecks et al., 2010), Ergatis (Orvis et al., 2010)
or Mobyle (Wilkinson et al., 2009) provide a user friendly graphical interface
easing workflow creation and execution. Today, Galaxy is probably the most used
WMS in the biologist community thanks to its intuitiveness and large software
package collection. Unfortunately, such environments come with their own
interface, complicating their integration within already existing web tools.
Other WMS such as weaver (Bui et al., 2012), Snakemake (Koster et al., 2012),
Ruffus (Goodstadt, 2010) or Cosmos (Gafni et al., 2014) provide a framework or a
domain-specific language to developers wanting to build and run workflows. These
software packages offer the flexibility and power of a high level programming
language, but they do not provide a user interface, enable component and
workflow definition or check file formats.
To our knowledge, Jflow, presented in this article, is the only WMS designed to
be embedded in any web application, thanks to its organization as jQuery
(http://jquery.com/) plug-ins.
\section{Methods}
Jflow user interface gathers five jQuery plug-ins providing user oriented views.
......@@ -94,7 +94,7 @@ step. Adding a component to the system requires to write a Python
\textit{Component} subclass. In Jflow, different solutions are available to ease
component creation. To wrap a single command line, the developer can give a
position or a flag for each parameter. Jflow also embeds an XML parser which
allows to run genuine Mobyle (Neron et al., 2009) components. Finally, to
allows to run genuine Mobyle (Wilkinson et al., 2009) components. Finally, to
allow developers to integrate components from other WMS, Jflow provides a
skeleton class. This class only requires to implement the parsing step. A
workflow chains several components. A Jflow workflow is built as a
......@@ -173,7 +173,7 @@ and outputs.
NG6 was first implemented using the Ergatis (Orvis et al., 2010) WMS, which had
a separate user interface. With Jflow, all actions are now available from the
same application, which makes it really user friendly.
same application, which makes it user friendly.
\section{Conclusion}
......@@ -181,53 +181,68 @@ Jflow is a simple and efficient solution to embed WMS features within a web
application. It is, to our knowledge, the only WMS designed with this purpose.
It is already embedded in RNAbrowse (Mariette et al., 2014) and NG6 (Mariette et
al., 2012), where it has been used to process more than 2 000 sequencing runs
on a 5 000 cores HPC.
on a 5 000 cores HPC environment.
\paragraph{Conflict of Interest\textcolon} none declared.
\begin{thebibliography}{}
\bibitem[Albrecht {\it et~al}., 2012]{Albrecht} Albrecht M, et al. (2012)
Makeflow: A Portable Abstraction for Data Intensive Computing on Clusters,
Clouds, and Grids. {\it SWEET at ACM SIGMOD}, {\bf20}.
\bibitem[Albrecht {\it et~al}., 2012]{Albrecht} Albrecht M, Donnelly P, Bui P
and Thain D. (2012) Makeflow: A Portable Abstraction for Data Intensive
Computing on Clusters, Clouds, and Grids. {\it SWEET at ACM SIGMOD}, {\bf20}.
\bibitem[Bui, 2012]{Bui} Bui P, (2012) Compiler Toolchain For Data Intensive
Scientific Workflows. {\it Ph.D. Thesis, University of Notre Dame}.
\bibitem[Gafni {\it et~al}., 2014]{Gafni} Gafni E, et al. (2014) COSMOS: Python
\bibitem[Gafni {\it et~al}., 2014]{Gafni} Gafni E, Luquette L, Lancaster A,
Hawkins J, Jung J-Y, Souilmi Y, Wall D and Tonellato P. (2014) COSMOS: Python
library for massively parallel workflows. {\it Bioinformatics}, {\bf30},
2956-2958.
\bibitem[Goecks {\it et~al}., 2010]{Goecks} Goecks J, et al. (2010) Galaxy: a
comprehensive approach for supporting accessible, reproducible, and transparent
computational research in the life sciences, {\it Genome Biology}, {\bf 11},
R86.
\bibitem[Goecks {\it et~al}., 2010]{Goecks} Goecks J, Nekrutenko A, Taylor J and
The Galaxy Team. (2010) Galaxy: a comprehensive approach for supporting
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SL, Morris Q and Bader GD. (2010) Cytoscape Web: an interactive web-based
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\bibitem[Mariette {\it et~al}., 2012]{Mariette} Mariette J, et al. (2012)
NG6: Integrated next generation sequencing storage and processing environment.
{\it BMC Genomics}, 13:462.
\bibitem[Mariette {\it et~al}., 2012]{Mariette} Mariette J, Escudie F, Allias
N, Salin G, Noirot C, Thomas S and Klopp C. (2012) NG6: Integrated next
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\bibitem[Mariette {\it et~al}., 2014]{Mariette} Mariette J, et al. (2014)
\bibitem[Mariette {\it et~al}., 2014]{Mariette} Mariette J, Noirot C,
Nabihoudine I, Bardou P, Hoede C, Djari A, Cabau C and Klopp C. (2014)
RNAbrowse: RNA-Seq De Novo Assembly Results Browser. {\it PLoS ONE}, 9(5).
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R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J
and Edwards RA. (2008) The metagenomics RAST server – a public resource for the
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Bioinformatics}, {\bf 9:386}.
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3005-3011.
\bibitem[Orvis {\it et~al}., 2010] Orvis J, Crabtree J, Galens K, Gussman A,
Inman JM, Lee E, Nampally S, Riley D, Sundaram JP, Felix V, Whitty B, Mahurkar
A, Wortman J, White O, Angiuoli SV. (2010) Ergatis: A web interface and scalable
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Bioinformatics}, 15;26(12).
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\end{thebibliography}
\end{document}
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\namefrom{Jerome Mariette} % Name
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\greetto{Alison Hutchins,} % Greeting text
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The present letter is pertaining to the paper "Jflow: a workflow management
system for web applications". 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}
\textbf{The paper is improved over the original submission and does a better job
of placing JFlow in context and explaining what it does. The figure on page two
is much superior to the previous version.}
\textbf{The introduction still needs work to focus the argument. To paraphrase,
the introduction as written says: Galaxy (and similar things) are easy to use,
but not programmable; Weaver (and similar things) are programmable, but not
easy to use; JFlow can be embedded in a web application.}
\textbf{These three statements do not hang together. Clearly, you meant to
compare JFlow to two other categories of previous work. Did you mean to argue
that JFlow combines the usability of Galaxy with the programmability of Weaver?
If so, say that clearly. If not, take care to make a parallel construction in
each sentence, so that the third statement is a clear reaction to the first
two.}
\textbf{Reviewer: 2}
\textbf{Comments to the Author}
\textbf{# Review 2}
\textbf{With the rewriting, my major comment about centering the paper about the
jQuery API has been addressed. I still think that the paper presents a
potentially relevant idea. I would like to point to some important issues that I
discovered, though.}
\textbf{Major comments:}
\textbf{- The authors say that a workflow chains components. This is quite
unspecific. Typicially workflows are seen as directed graphs or directed acyclic
graphs. The figure shows that this is the case for Jflow as well. I think, a few
sentences about what theoretical workflow model is supported by Jflow and its
server component should be added.}
\textbf{- The references should list all authors, not only the first.}
All authors of the references have been added.
\textbf{- The server part of Jflow is implemented in Python. Although mentioned
in the docs that it runs with Python 2.7 or higher, it does not run with Python
3. Given that Python 3 is more than 8 years old, in my opinion this is not
acceptable for newly released software. Also, I would like to propose to package
and distribute Jflow properly as a Pypi or even a Conda package to simplify
installation and upgrades.}
\textbf{Minor comments:}
\textbf{- The introduction should try to give a broader overview over available
workflow management systems. Only citing three representatives is not a
sufficient assessment of the state of the art.}
Tools such as Ergatis (Orvis et al., 2010), Mobyle (Wilkinson et al., 2009),
Snakemake (Koster et al., 2012) and Ruffus (Goodstadt, 2010) have been added in
the state of the art.
\textbf{- you should remove the "really" in the last sentence of the example
section.}
The word ``really'' has been removed as suggested.
\textbf{- if HPC is the abbreviation for high performance computing, you should
add the word "environment" to the last sentence of the conclusion.}
The word ``environment'' has been added as suggested.
\textbf{Reviewer: 3}
\textbf{Comments to the Author}
\textbf{In p1 col2 line29 add “The".}
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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