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[PRE REVIEW]: MASTR-Quant: An Open-Source Web-based Software Tool for the Quantitive Analysis of Mass Spectrometry-based Data #2144

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @MetabolomicsAustralia-Bioinformatics (Vinod Narayana) Repository: https://github.com/MetabolomicsAustralia-Bioinformatics/metabio Version: 1.0 Editor: @csoneson Reviewers: @lgatto, @bovee Managing EiC: Kevin M. Moerman

Author instructions

Thanks for submitting your paper to JOSS @MetabolomicsAustralia-Bioinformatics. Currently, there isn't an JOSS editor assigned to your paper.

@MetabolomicsAustralia-Bioinformatics if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands
whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
whedon commented 4 years ago 
Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1038/nrg3575 may be missing for title: Systems genetics approaches to understand complex traits

INVALID DOIs

- None
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 4 years ago

@whedon check repository

whedon commented 4 years ago 

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=34.10 s (126.4 files/s, 56961.0 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
JSON                            352            118              0         552238
Python                         2491         155080         199581         548569
PO File                        1109          71710           9717         216767
JavaScript                       97          20453          29412          85504
CSS                              47           2503            644          15088
HTML                             94           2139            228          14902
C/C++ Header                     26            936           1338           5865
reStructuredText                 29           1680            501           3978
SQL                               3              0              0           1103
C                                 3            102             92           1091
Fortran 90                       15             69             35            252
SVG                              25              0              0            129
Markdown                          3             35              0            114
TeX                               4              1             16             55
Fish Shell                        1             16             13             47
XML                               5              1              1             44
INI                               2              5              0             27
YAML                              1              0              0             18
C Shell                           1             12              7             17
Fortran 77                        2              1              1             14
Bourne Again Shell                1              1              0              9
--------------------------------------------------------------------------------
SUM:                           4311         254862         241586        1445831
--------------------------------------------------------------------------------
Kevin-Mattheus-Moerman commented 4 years ago

@lpantano @will-rowe @csoneson @lorenanicole could on of you edit this submission?

whedon commented 4 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=36.05 s (119.5 files/s, 53873.2 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
JSON                            352            118              0         552238
Python                         2491         155080         199581         548569
PO File                        1109          71710           9717         216767
JavaScript                       97          20453          29412          85504
CSS                              47           2503            644          15088
HTML                             94           2139            228          14902
C/C++ Header                     26            936           1338           5865
reStructuredText                 29           1680            501           3978
SQL                               3              0              0           1103
C                                 3            102             92           1091
Fortran 90                       15             69             35            252
SVG                              25              0              0            129
Markdown                          3             35              0            114
TeX                               4              1             16             55
Fish Shell                        1             16             13             47
XML                               5              1              1             44
INI                               2              5              0             27
C Shell                           1             12              7             17
Fortran 77                        2              1              1             14
Bourne Again Shell                1              1              0              9
--------------------------------------------------------------------------------
SUM:                           4310         254862         241586        1445813
--------------------------------------------------------------------------------

Statistical information for the repository '2144' was gathered on 2020/03/04.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
MetabolomicsAustrali             5            60         109381            8.84
shushu-leng                     27       1128299            677           91.16

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
MetabolomicsAustrali         57           95.0          1.0                8.77
shushu-leng             1075686           95.3         10.8               11.49
csoneson commented 4 years ago

@lpantano @will-rowe @csoneson @lorenanicole could on of you edit this submission?

I can take this one

csoneson commented 4 years ago

@whedon assign @csoneson as editor

whedon commented 4 years ago

OK, the editor is @csoneson

csoneson commented 4 years ago

👋 @MetabolomicsAustralia-Bioinformatics - I'll handle your submission, and start by looking for suitable reviewers.

Looking at your submission, I noticed that your paper is a bit too short for JOSS standards (see https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain). Could you add a bit more context?

csoneson commented 4 years ago

👋 @bovee, @lgatto, @jorainer - would (two of) you be willing to review this submission for the Journal of Open Source Software (JOSS)?

MASTR-Quant: An Open-Source Web-based Software Tool for the Quantitive Analysis of Mass Spectrometry-based Data

software: https://github.com/MetabolomicsAustralia-Bioinformatics/metabio accompanying paper: https://github.com/openjournals/joss-papers/blob/joss.02144/joss.02144/10.21105.joss.02144.pdf

instructions on reviewing for JOSS: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

csoneson commented 4 years ago

ping @bovee, @lgatto, @jorainer

👋 @bovee, @lgatto, @jorainer - would (two of) you be willing to review this submission for the Journal of Open Source Software (JOSS)?

MASTR-Quant: An Open-Source Web-based Software Tool for the Quantitive Analysis of Mass Spectrometry-based Data

software: https://github.com/MetabolomicsAustralia-Bioinformatics/metabio accompanying paper: https://github.com/openjournals/joss-papers/blob/joss.02144/joss.02144/10.21105.joss.02144.pdf

instructions on reviewing for JOSS: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

lgatto commented 4 years ago

Here are my comments regarding this submission:

I confirm that I have read the JOSS conflict of interest policy and that I have no COIs with reviewing this work.

csoneson commented 4 years ago

Thanks @lgatto (that was super fast 😃)! Once one more reviewer confirms their interest, I will close this issue and open the actual review issue that contains the checklist for each reviewer. I will then transfer your comments above over there so that we have everything in one place.

jorainer commented 4 years ago

Dear @csoneson - I'm quite busy at present with other reviews - so I would only want to accept to review yet another one when it's absolutely necessary. Would be happy if another reviewer would accept to review...

csoneson commented 4 years ago

@jorainer - no problem! If you happen to have a suggestion for someone that I might reach out to, that would be awesome :)

jorainer commented 4 years ago

@sgibb eventually - but I'm not sure if he's available.

csoneson commented 4 years ago

@sgibb - would you be interested in reviewing this submission for the Journal of Open Source Software?

MASTR-Quant: An Open-Source Web-based Software Tool for the Quantitive Analysis of Mass Spectrometry-based Data

software: https://github.com/MetabolomicsAustralia-Bioinformatics/metabio accompanying paper: https://github.com/openjournals/joss-papers/blob/joss.02144/joss.02144/10.21105.joss.02144.pdf

instructions on reviewing for JOSS: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

sgibb commented 4 years ago

@csoneson I am sorry but I am currently not able to review anything.

arfon commented 4 years ago

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

bovee commented 4 years ago

@csoneson Sorry about the delay! I'm a little stretched right now, but happy to review.

csoneson commented 4 years ago

@bovee - brilliant, thanks so much! I'll add you too as a reviewer and open the actual review issue.

csoneson commented 4 years ago

@whedon assign @lgatto as reviewer

whedon commented 4 years ago

OK, @lgatto is now a reviewer

csoneson commented 4 years ago

@whedon add @bovee as reviewer

whedon commented 4 years ago

OK, @bovee is now a reviewer

csoneson commented 4 years ago

@whedon start review

whedon commented 4 years ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2163.

MetabolomicsAustralia-Bioinformatics commented 4 years ago

Hi all,

Thanks for your time and effort in reviewing so far. Only about manuscript submission:

  1. We actually have a larger, 2 page, manuscript written, as a pdf. I’ve restructured (in particular, cut down) this larger paper to the approximate size and formatting as recommended here: https://joss.theoj.org/papers/10.21105/joss.00388, where it looked like only a summary was needed. Should I be submitting the full manuscript instead?
  2. As for lack of references: I’ve actually included references in paper.bib (https://github.com/MetabolomicsAustralia-Bioinformatics/metabio/blob/master/paper/paper.bib), as per the submission instructions.  Unfortunately, this won’t actually compile. In fact, the Whedon paper preview service provided won’t compile its own example either to contain References (the gala paper). An attempt as of a few minutes ago has received a 404 error.

Just to address the manuscript issues, any advice to get around these technical issues would be greatly appreciated.

Many thanks and regards, Don Teng Bioinformatician Metabolomics Australia University of Melbourne, Parkville, Melbourne, Victoria On 11 Mar 2020, 8:23 AM +1100, Laurent Gatto notifications@github.com, wrote:

Here are my comments regarding this submission:

• The submission contains a repository (but see below) and a valid OSI approved license. • I find the manuscript to be extremely short. In particular, I miss some citation/comparison with existing alternatives in general, and a description of this software compares to other commonly-used packages in this research area. • There are no references. • The documentation on the README page only contains installation instructions (which I have not tested). There is no information about the underlying implementations or core functionality. In particular, it seems the user is let to decide what regression type and parameters are best suited based on visual inspection of the fit, being also allowed to manually define outliers. More rigorous approaches such (standardised) residuals, leverage and/or Cook's distance might be applicable. • The application is available at mastr-quant.bio21.unimelb.edu.au, which contains some basic documentation of how to use the web interface. I tried it twice but the application froze and became unresponsive. The web application contains test data for user to try the interface out, but there is no description of these test data. • I managed to download result files, which seem to contain various forms of the data (raw, normalised, ...), at time poorly formatted (multiple table per sheet) and I could find any documentation describing the output file or how to use the results for downstream analyses. • It is confusion that the repo to be reviewed is itself a for of uncle-leng/metabio. There are only two contributors to either of the fork or original repository. It would be useful to document the contributions of the 9 authors.

I confirm that I have read the JOSS conflict of interest policy and that I have no COIs with reviewing this work. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.