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[PRE REVIEW]: LTRpred: de novo annotation of intact retrotransposons #2129

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whedon opened this issue Mar 1, 2020 · 34 comments
Closed

[PRE REVIEW]: LTRpred: de novo annotation of intact retrotransposons #2129

whedon opened this issue Mar 1, 2020 · 34 comments
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@whedon
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whedon commented Mar 1, 2020

Submitting author: @HajkD (Hajk-Georg Drost)
Repository: https://github.com/HajkD/LTRpred
Version: v1.1.0
Editor: @lpantano
Reviewers: @dcassol
Managing EiC: Lorena A Barba

Author instructions

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

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

@HajkD 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
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whedon commented Mar 1, 2020

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
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whedon commented Mar 1, 2020

@labarba
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labarba commented Mar 1, 2020

👋 @karthik — The authors suggested you as editor for this submission. According to the README: "LTRpred will take any genome assembly file in fasta format as input and will generate a detailed annotation of functional and potentially mobile LTR retrotransposons." It's an R package. Can you handle it?

@HajkD
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HajkD commented Mar 2, 2020

Dear @labarba

Thank you so much for arranging the editorial assignment.

After going through the reviewer list, I think the following reviewers could be very suitable: rachelss and dcassol .

I very much look forward to receiving some feedback.

Many thanks!

@arfon
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arfon commented Mar 2, 2020

@whedon invite @karthik as editor

@whedon
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whedon commented Mar 2, 2020

@karthik has been invited to edit this submission.

@karthik
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karthik commented Mar 3, 2020

I'm unable to take this on. Is there another editor who can handle this?

@HajkD
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HajkD commented Mar 5, 2020

Dear @karthik
Many thanks for your prompt reply.

Dear @arfon and @labarba
Would it be possible to assign a different editor? There is no preference from my side
since all of them are very much suitable.

Thank you very much!

@arfon
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arfon commented Mar 5, 2020

@Kevin-Mattheus-Moerman is the EiC on rotation this week so will be handling this.

@Kevin-Mattheus-Moerman
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@lpantano @will-rowe @csoneson can one of you edit this submission?

@lpantano
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lpantano commented Mar 7, 2020

@whedon assign @lpantano as editor

@whedon
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whedon commented Mar 7, 2020

OK, the editor is @lpantano

@lpantano
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@dcassol, would you like to review this tool about LTRpred: de novo annotation of intact retrotransposons?

@lpantano
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@oushujun, would you like to review this tool about de novo annotation of intact retrotransposons?

@dcassol
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dcassol commented Mar 10, 2020

Sure!

@lpantano
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@whedon assign @dcassol as reviewer

@whedon whedon assigned dcassol and lpantano and unassigned lpantano Mar 10, 2020
@whedon
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whedon commented Mar 10, 2020

OK, @dcassol is now a reviewer

@oushujun
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oushujun commented Mar 10, 2020

@lpantano Hello I don't know what this is for but seems interesting. Unfortunately I don't have open times until Mar. 25.

@lpantano
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Thanks @oushujun, do you know somebody who could be a reviewer for this tool? JOSS makes its reviewing process through github, and it is a very nice experience in general.

@arfon
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arfon commented Mar 14, 2020

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.

@lpantano
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@whedon invite @MatthewHaas as reviewer

@whedon
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whedon commented Mar 18, 2020

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

@lpantano
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@whedon commands

@whedon
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whedon commented Mar 18, 2020

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a  dry run of accepting the paper and depositing with Crossref
@whedon accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true

@lpantano
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Hi @MatthewHaas, this tool may be interesting to you. Would you like to review this tool for Journal of Open Source Software? Cheers

@arfon
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arfon commented Mar 18, 2020

@whedon invite @MatthewHaas as reviewer

@lpantano - I'm afraid Whedon doesn't know how to do this yet for reviewers.

@lpantano
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@oushujun, since we didn't find any additional reviewer available, would you like to do it since we reached the date you may be free for this? Thanks!

@oushujun
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oushujun commented Mar 23, 2020 via email

@lpantano
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Hi @rachelss, would you like to review this tool?

@lpantano
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Hi @HajkD, I will start the review meanwhile looking for the second reviewer. Thanks!

@lpantano
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@whedon start review

@whedon
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whedon commented Mar 26, 2020

OK, I've started the review over in #2170.

@whedon whedon closed this as completed Mar 26, 2020
@HajkD
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HajkD commented Mar 26, 2020

Hi @lpantano

Thank you very much for arranging everything and for taking over the role of the second reviewer for now! I very much appreciate it!

@rachelss
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Sorry I just saw this notification by email. Looks from the other issue that you found a second reviewer.

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