[REVIEW]: Finch: MinHashing for Sequencing Data with Abundance Calculation and Adaptive Filtering #505

whedon · 2017-12-13T11:51:55Z

Submitting author: @bovee (Roderick Boveee)
Repository: https://github.com/onecodex/finch-rs
Version: v0.1.4
Editor: @biorelated
Reviewer: @HadrienG
Archive: 10.5281/zenodo.1164259

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Software paper

Authors: Does the paper.md file include a list of authors with their affiliations?
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References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

The text was updated successfully, but these errors were encountered:

whedon · 2017-12-13T11:51:57Z

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @HadrienG it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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@whedon commands

whedon · 2017-12-13T11:51:58Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2017-12-13T11:52:10Z

https://github.com/openjournals/joss-papers/blob/joss.00505/joss.00505/10.21105.joss.00505.pdf

HadrienG · 2017-12-13T12:46:10Z

@whedon commands

whedon · 2017-12-13T12:46:13Z

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

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

# Open the review issue
@whedon start review

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper
@whedon generate pdf

HadrienG · 2017-12-15T10:37:00Z

The version in this review doesn't correspond to the latest version of the software. Unsure how to fix that here @biorelated. Can I simply edit the Whedon comment?

I will carry the review with the latest version 0.1.4 in the meantime

arfon · 2017-12-15T11:40:52Z

I will carry the review with the latest version 0.1.4 in the meantime

I've updated the comment at the top of the issue.

arfon · 2018-01-16T01:32:09Z

@HadrienG - how are you getting along here?

HadrienG · 2018-01-19T08:57:59Z

@arfon It's going pretty well thanks for checking!

Vacations have slowed things a little but my last issue is now closed. I'll test the new release and if everything goes fine I fell comfortable recommending for publication

HadrienG · 2018-01-19T08:58:44Z

@whedon generate pdf

whedon · 2018-01-19T08:58:46Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-01-19T08:59:00Z

https://github.com/openjournals/joss-papers/blob/joss.00505/joss.00505/10.21105.joss.00505.pdf

HadrienG · 2018-01-23T19:08:43Z

@arfon - all my comments have been addressed! What's the next steps for acceptance?

george-githinji · 2018-01-24T16:47:17Z

@arfon Kindly review this for any final checks before consideration and publication. Many thanks @HadrienG for taking your time to review and @bovee for the submission.

arfon · 2018-01-25T02:46:59Z

@arfon Kindly review this for any final checks before consideration and publication.

Mostly this looks fine. I would encourage the authors to consider adding a little more detail to their paper as per our submission guidelines:

A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience

A clear statement of need that illustrates the purpose of the software

A list of key references including a link to the software archive

Mentions (if applicable) of any ongoing research projects using the software or recent scholarly publications enabled by it

george-githinji · 2018-01-25T06:21:24Z

@bovee, Kindly address the concerns highlighted by @arfon.

bovee · 2018-01-30T19:04:13Z

@arfon Thanks for the suggestions; we've expanded the paper.md to address those concerns.

@biorelated Please let me know if there are any remaining concerns or if there's anything else to do. Thanks!

More detailed notes:

A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience

The opening paragraph has been expanded to describe what MinHashing is used for and what Finch adds to traditional MinHashing schemes.

A clear statement of need that illustrates the purpose of the software

The second paragraph contains an expanded description of how MinHash works that motivates a discussion of the problems that Finch solves in the third paragraph.

A list of key references including a link to the software archive

We've added a link to the GitHub software repository.

Mentions (if applicable) of any ongoing research projects using the software or recent scholarly publications enabled by it

The last paragraph now contains a description of how we are using Finch in our web platform.

george-githinji · 2018-01-31T18:32:52Z

@bovee: Thank you for the submission and for addressing all the issues and concerns
@arfon: Could we kindly consider this work for publication?

arfon · 2018-02-01T00:02:49Z

@whedon generate pdf

whedon · 2018-02-01T00:02:51Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-02-01T00:03:10Z

https://github.com/openjournals/joss-papers/blob/joss.00505/joss.00505/10.21105.joss.00505.pdf

arfon · 2018-02-01T00:06:12Z

@bovee - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

bovee · 2018-02-01T19:09:10Z

@arfon - I just submitted the repo to Zenodo and the record's at https://zenodo.org/record/1164259 and the DOI should be 10.5281/zenodo.1164259 (once it's propagated). Thanks!

arfon · 2018-02-01T19:13:09Z

@whedon set 10.5281/zenodo.1164259 as archive

whedon · 2018-02-01T19:13:12Z

OK. 10.5281/zenodo.1164259 is the archive.

arfon · 2018-02-01T19:31:42Z

@HadrienG - many thanks for your review here and to @biorelated for editing this submission ✨

@bovee - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00505 ⚡️ 🚀 💥

whedon · 2018-02-01T19:31:57Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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whedon assigned george-githinji Dec 13, 2017

whedon added the review label Dec 13, 2017

whedon mentioned this issue Dec 13, 2017

[PRE REVIEW]: Finch: MinHashing for Sequencing Data with Abundance Calculation and Adaptive Filtering #378

Closed

HadrienG mentioned this issue Dec 15, 2017

Linux executable onecodex/finch-rs#9

Closed

This was referenced Dec 15, 2017

finch dist fails on non-suffixed sketches onecodex/finch-rs#10

Open

Documentation onecodex/finch-rs#11

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JOSS paper onecodex/finch-rs#12

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bovee mentioned this issue Jan 19, 2018

Submit to JOSS onecodex/finch-rs#3

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3 tasks

bovee mentioned this issue Jan 30, 2018

Updates to address remaining reviewer comments onecodex/finch-rs#16

Merged

arfon closed this as completed Feb 1, 2018

arfon reopened this Feb 1, 2018

arfon added the accepted label Feb 1, 2018

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[PRE REVIEW]: Fasten with Pipes #6000

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[PRE REVIEW]: Binette: a fast and accurate bin refinement tool to construct high quality Metagenome Assembled Genomes. #6333

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[REVIEW]: Finch: MinHashing for Sequencing Data with Abundance Calculation and Adaptive Filtering #505

[REVIEW]: Finch: MinHashing for Sequencing Data with Abundance Calculation and Adaptive Filtering #505

whedon commented Dec 13, 2017 •

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[REVIEW]: Finch: MinHashing for Sequencing Data with Abundance Calculation and Adaptive Filtering #505

[REVIEW]: Finch: MinHashing for Sequencing Data with Abundance Calculation and Adaptive Filtering #505

Comments

whedon commented Dec 13, 2017 • edited

Status

Reviewer instructions & questions

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Dec 13, 2017

whedon commented Dec 13, 2017

whedon commented Dec 13, 2017

HadrienG commented Dec 13, 2017

whedon commented Dec 13, 2017

HadrienG commented Dec 15, 2017

arfon commented Dec 15, 2017

arfon commented Jan 16, 2018

HadrienG commented Jan 19, 2018 • edited

HadrienG commented Jan 19, 2018

whedon commented Jan 19, 2018

whedon commented Jan 19, 2018

HadrienG commented Jan 23, 2018

george-githinji commented Jan 24, 2018 • edited

arfon commented Jan 25, 2018 • edited

george-githinji commented Jan 25, 2018

bovee commented Jan 30, 2018

george-githinji commented Jan 31, 2018

arfon commented Feb 1, 2018

whedon commented Feb 1, 2018

whedon commented Feb 1, 2018

arfon commented Feb 1, 2018

bovee commented Feb 1, 2018

arfon commented Feb 1, 2018

whedon commented Feb 1, 2018

arfon commented Feb 1, 2018

whedon commented Feb 1, 2018

whedon commented Dec 13, 2017 •

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HadrienG commented Jan 19, 2018 •

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george-githinji commented Jan 24, 2018 •

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arfon commented Jan 25, 2018 •

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