Joss-reviews: [PRE REVIEW]: Bacting: a next generation, command line version of Bioclipse

[whedon]

Submitting author: @egonw (Egon Willighagen)
Repository: https://github.com/egonw/bacting
Version: 0.0.11
Editor: @majensen
Reviewers: @Zethson, @arcuri82
Managing EiC: Kevin M. Moerman

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Author instructions

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

The author's suggestion for the handling editor is @trallard.

@egonw 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]

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

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.18 s (209.5 files/s, 23737.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Java                            19            360            982           1969
Maven                           15             85              0            732
Markdown                         2             57              0             97
YAML                             1              4              0             11
Groovy                           1              3              0              6
-------------------------------------------------------------------------------
SUM:                            38            509            982           2815
-------------------------------------------------------------------------------


Statistical information for the repository '2510' was gathered on 2020/07/23.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Egon Willighagen                64          6474           3163          100.00

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
Egon Willighagen           3311           51.1          7.5               29.66

[whedon]

PDF failed to compile for issue #2510 with the following error:

Can't find any papers to compile :-(

[Kevin-Mattheus-Moerman]

@whedon generate pdf from branch devel/0.0.13

[whedon]

Attempting PDF compilation from custom branch devel/0.0.13. Reticulating splines etc...

[whedon]

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

[Kevin-Mattheus-Moerman]

@egonw thanks for this submission. I am reviewing the suitability of this submission for JOSS and will also look for editors to handle it.
In the mean time can you please describe, for the record, the difference between the current submission and this paper to clarify this is not a duplicate publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-397

[Kevin-Mattheus-Moerman]

@trallard @majensen @will-rowe @csoneson is one of you able to handle this submission? Thanks!

[egonw]

Potential reviewers: zethson, reality (collaborators on a EU project, so probably not), 7omasz, arcuri82

[Kevin-Mattheus-Moerman]

@egonw thanks for those suggestions. Which ones exactly are collaborators?

[egonw]

In the mean time can you please describe, for the record, the difference between the current submission and this paper to clarify this is not a duplicate publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-397

The Bioclipse 2 paper is still about the Eclipse-based version, not about the command line version and suffers from the limitations outlined in the "Statement of Need" section.

[egonw]

@egonw thanks for those suggestions. Which ones exactly are collaborators?

reality, whom I work together with in the NanoCommons project on ontologies.

[Kevin-Mattheus-Moerman]

@galessiorob is this submission something you could handle?

[egonw]

I would also not mind having someone of the original Bioclipse team look at it, e.g. jonalv, as they know the ins and outs of the technology. They have not contributed to this adaption of it, but obviously have an academic CoI.

[majensen]

@Kevin-Mattheus-Moerman I can backstop for this submission, if others are unable.

[Kevin-Mattheus-Moerman]

@whedon assign @majensen as editor

[whedon]

OK, the editor is @majensen

[Kevin-Mattheus-Moerman]

@majensen note the various reviewers recommended :point_up: in a couple of comments.

[majensen]

@Zethson - would you be willing to share your expertise in a review of this package for the Journal of Open Source Software ? It is meant to improve Bioeclipse build management and command line usability, among other things. Please have a look at these reviewer steps and let us know here whether you would have an interest.
Thanks for your consideration --@majensen

[egonw]

@majensen, can you please email me asap on my first.lastname @ gmail? thanks.

[Zethson]

Yes, I would do it. ETA 14 days is fine? Saturday, 25 July 2020, 08:29PM +02:00 from Mark Jensen [email protected] :

@Zethson - would you be willing to share your expertise in a review of this package for the Journal of Open Source Software ? It is meant to improve Bioeclipse build management and command line usability, among other things. Please have a look at these reviewer steps and let us know here whether you would have an interest.
Thanks for your consideration -- @majensen
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub , or unsubscribe .

[majensen]

@Zethson that would be great. Thanks very much

[majensen]

@whedon add @Zethson as reviewer

[whedon]

OK, @Zethson is now a reviewer

[majensen]

All, will be getting additional review invites out over next couple days. Thanks for yr patience

[majensen]

@jonalv - Would you be willing to review this work for the Journal of Open Source Software? Your expertise in Bioeclipse would be extremely valuable here. An overview of reviewing for the journal (performed openly on Github) is here. I appreciate your consideration very much --@majensen

[jonalv]

Hi I can not get your link to work but from the title I see this is about
Bacting, since I know Egon Willighagen is behind a project with that name I
am hesitant as to whether I really am impartial. I have worked closely with
him, co-authoring a book with him and helped him move twice :)

// Jonathan

On Thu, 6 Aug 2020 at 04:50, Mark Jensen [e-mail] wrote:

@jonalv https://github.com/jonalv - Would you be willing to review this
work <#m_1586595749754460526_2510> for the Journal of Open Source Software
https://joss.theoj.org? Your expertise in Bioeclipse would be extremely
valuable here. An overview of reviewing for the journal (performed openly
on Github) is here
https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. I
appreciate your consideration very much --@majensen
https://github.com/majensen

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/2510#issuecomment-669651863,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AAAIITLLMZ6RLZHQI2BWTSDR7ILAVANCNFSM4PF3JILQ
.

[majensen]

@jonalv - I understand, having helped @egonw move might bias your review negatively 😄
For me, your expertise is very important since it deals very directly with the application, and you have not directly contributed code to Bacting. Since you have declared possible conflict, I can take that into account.

@Kevin-Mattheus-Moerman - can you please comment here from the AIC point of view?

[danielskatz]

If the co-authoring has been recent (last 4 years), that's another conflict. My impression is that we should find alternative reviewers unless there is no other choice, or if @jonalv does review, then have at least 2 other reviewers.

[majensen]

Ok @danielskatz .

Thanks for your consideration @jonalv - If you or @egonw can possibly recommend someone with Bioeclipse experience but without close collaboration, that would great. Difficult I'm sure.

[egonw]

@majensen, reviewers do not need Bioclipse experience. The build system is a regular Maven installation. Anyone with Maven experience can build, test, and use this adaption of Bioclipse.

Please see also my original list at https://github.com/openjournals/joss-reviews/issues/2510#issuecomment-663096346 (but plz exclude Luke).

[majensen]

Thanks @egonw - that makes sense.

[majensen]

@arcuri82, would you consider reviewing this work (https://github.com/openjournals/joss-reviews/issues/2510) for the Journal of Open Source Software? Your java expertise would be greatly appreciated. Guidelines for reviewing are here.
Thanks very much for considering! --@majensen

[arcuri82]

@majensen: Hi, yes, I can review it. Busy period (start of teaching semester)... so I do not think I ll have time to start the review before at least 2 weeks, but should be able to complete within the given 6 weeks

[majensen]

@arcuri82 thanks so much; that will be fine. Very much appreciated

[majensen]

@whedon add @arcuri82 as reviewer

[whedon]

OK, @arcuri82 is now a reviewer

[majensen]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2558.

[majensen]

@egonw @arcuri82 @Zethson we will perform the review over in #2558 - thanks!