[Gepsc] Fwd: Re: Decision on your article submitted to PLOS Computational Biology (PCOMPBIOL-D-16-01660) [ ref:_00DU0Ifis._5000BaGFqj:ref ]

Karen Cranston karen.cranston at nescent.org
Wed Feb 15 10:26:32 CST 2017


I am working on the response to reviewers. Have already re-opened one
issue, and there may be more to come.

Karen


On Thu, Feb 9, 2017 at 6:31 PM Justin Kitzes <jkitzes at berkeley.edu> wrote:

> Hi Greg,
>
> Can you clarify what's left to do? It appears that there are two PR's to
> merge and then a decision to make on Tracy's comment #180, but that seems
> to be it. It would seem that you and Tracy could/should make the final call
> on these three remaining items at this point and then we can submit -
>
> Justin
>
>
> > On Feb 9, 2017, at 1:28 PM, Greg Wilson <gvwilson at third-bit.com> wrote:
> >
> > FYI, we have until Feb 17.  Anyone want to take lead on the next
> (hopefully final) revs?
> > - G
> >
> >
> > -------- Forwarded Message --------
> > Subject:      Re: Decision on your article submitted to PLOS
> Computational Biology (PCOMPBIOL-D-16-01660) [
> ref:_00DU0Ifis._5000BaGFqj:ref ]
> > Date: Thu, 9 Feb 2017 15:30:11 +0000 (GMT)
> > From: PLOS Computational Biology <ploscompbiol at plos.org>
> > To:   gvwilson at third-bit.com <gvwilson at third-bit.com>
> >
> > Dear Greg,
> >
> > Thank you for your email. That’s no problem – we try to allow our
> authors time to submit their best work. I have therefore altered your
> resubmission due date in our system February 17th, and we look forward to
> receiving your revised submission then.
> >
> > Please let me know if you require any assistance with submitting your
> manuscript.
> >
> > Best wishes,
> > Sheryl
> >
> > PLOS I OPEN FOR DISCOVERY
> > Sheryl Baptista I Publications Assistant, PLOS Computational Biology and
> PLOS Genetics
> > Carlyle House, Carlyle Road, Cambridge CB4 3DN | United Kingdom
> >
> > sbaptista at plos.org
> >  I Main +44 (0) 1223-442810 <+44%201223%20442810> I Direct +44 (0)
> 1223-446978 <+44%201223%20446978> I Fax +44 (0)1223-442833
> <+44%201223%20442833>
> > ploscompbiol.org | @PLOSCompBiol | plosgenetics.org | @PLOSGenetics
> > California (U.S.) corporation #C2354500, based in San Francisco
> >
> > Case Number: 05049883
> >
> >
> >
> >
> > --------------- Original Message ---------------
> > From: Greg Wilson [
> > gvwilson at third-bit.com
> > ]
> > Sent: 2/6/2017
> > To:
> > ploscompbiol at plos.org
> >
> > Subject: Re: Decision on your article submitted to PLOS Computational
> Biology (PCOMPBIOL-D-16-01660) - [EMID:bb81ad375bfbd1a8]
> >
> > Dear Francis,
> >
> > Please accept our apologies, but we will need at least another week (and
> > possibly until Feb 17) to finish revisions.  I hope that will not be an
> > inconvenience.
> >
> > Best regards,
> >
> > Greg
> >
> >
> > On 2017-01-05 9:16 AM, PLOS Computational Biology wrote:
> > > Dear Dr Wilson,
> > >
> > > Thank you very much for submitting your manuscript, 'Good Enough
> > > Practices in Scientific Computing', to PLOS Computational Biology. As
> > > with all papers submitted to the journal, yours was fully evaluated by
> > > the PLOS Computational Biology editorial team, and in this case, by
> > > independent peer reviewers. The reviewers appreciated the attention to
> > > an important topic but identified some aspects of the manuscript that
> > > should be improved.
> > >
> > > We would therefore like to ask you to modify the manuscript according
> > > to the review recommendations before we can consider your manuscript
> > > for acceptance. Your revisions should address the specific points made
> > > by each reviewer and we encourage you to respond to particular issues
> > > raised. Please take special care to address all of the reviewers' very
> > > useful comments.
> > >
> > > In addition, when you are ready to resubmit, please be prepared to
> > > provide the following:
> > > (1) A detailed list of your responses to the review comments and the
> > > changes you have made in the manuscript. We require a file of this
> > > nature before your manuscript is passed back to the editors.
> > > (2) A copy of your manuscript with the changes highlighted
> > > (encouraged). We encourage authors, if possible to show clearly where
> > > changes have been made to their manuscript e.g. by highlighting text.
> > > (3) PLOS offers a figure-checking tool, PACE
> > > (
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__pace.apexcovantage.com_&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=VX0iAmDFuTbk3uekcRA4BkyAO6JTnrjj8PkIVsil1JM&m=UN6vwajMwEIn-ZLiklfAjPSMCbyq5R3yNlXfQc5Ux_0&s=-dD-kCwrAxEf_VOBBK01-tdT0ydqwKf-Q0xybqbR_aU&e=
> > ), to help authors to ensure all
> > > figures meet PLOS requirements so that the quality of published
> > > figures is as high as possible. Please use this tool to help you
> > > format your figures.
> > > PACE is a digital diagnostic and conversion tool for figure files. It
> > > will provide information about any failed check(s) and, if able, will
> > > automatically convert the figure file into an acceptable file that
> > > passes quality checks. PACE requires you to register for an account to
> > > ensure your figure files are processed securely.
> > > (4) A striking still image to accompany your article (optional). If
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> > > on our website and might be chosen as the issue image for that month.
> > > These square, high-quality images should be accompanied by a short
> > > caption. Please note as well that there should be no copyright
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> > > attribution.
> > >
> > > Before you resubmit your manuscript, please consult our Submission
> > > Checklist to ensure your manuscript is formatted correctly for PLOS
> > > Computational Biology:
> > >
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ploscompbiol.org_static_checklist.action&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=VX0iAmDFuTbk3uekcRA4BkyAO6JTnrjj8PkIVsil1JM&m=UN6vwajMwEIn-ZLiklfAjPSMCbyq5R3yNlXfQc5Ux_0&s=y2aWw1KU8oVMXR3MwoQdwfMzIZbJoZro9inGP6i1T78&e=
> > . Some key points
> > > to remember are:
> > >
> > > - Figures uploaded separately as TIFF or EPS files (if you wish, your
> > > figures may remain in your main manuscript file in addition).
> > > - Supporting Information uploaded as separate files, titled 'Dataset',
> > > 'Figure', 'Table', 'Text', 'Protocol', 'Audio', or 'Video'.
> > > - Funding information in the 'Financial Disclosure' box in the online
> > > system.
> > >
> > > We hope to receive your revised manuscript within the next 30 days. If
> > > you anticipate any delay in its return, we ask that you let us know
> > > the expected resubmission date by email at
> > ploscompbiol at plos.org
> > .
> > >
> > > If you have any questions or concerns while you make these revisions,
> > > please let us know.
> > >
> > > Sincerely,
> > >
> > > Francis Ouellette
> > > Education Editor
> > > PLOS Computational Biology
> > >
> > > A link appears below if there are any accompanying review attachments.
> > > If you believe any reviews to be missing, please contact
> > >
> > ploscompbiol at plos.org
> >  immediately:
> > >
> > >
> > >
> > > Reviewer's Responses to Questions
> > >
> > > *Comments to the Authors:
> > > Please note here if the review is uploaded as an attachment.*
> > >
> > > Reviewer #1: 1) General Comments
> > >
> > > The manuscript summarizes a set of good practices for software
> > > engineering (for the life sciences communities, presumably). I
> > > cannot say I learnt anything new; and in various places the style
> > > is not particularly conducive for a novice to continue reading. I
> > > would recommend that certain passages are toned-down from a
> > > know-it-all style to something more modest. This will make a real
> > > difference for the better, and will engage your target audience.
> > >
> > > Another general comment that the authors might want to take
> > > into account and discuss a little more at the end of their text.
> > > Who will fund all these wonderful activities? Please discuss.
> > >
> > > 2a) Major comments
> > >
> > > 1/ "As a result, they take days or weeks to do things that could be
> > > done in minutes or hours, are often unable to reproduce their own
> > > work (much less the work of others), and have no idea how reliable
> > > their computational results are" -- this will need to be rewritten,
> > > from scratch. It 's not only offensive, but would not motivate any
> > > reasonable reader to continue. Defies purpose of 'Perspective'.
> > >
> > > 2/ In some sections, Software, Collaboration etc. it would also be
> > > good to maintain a more balanced view, so alternatives must also
> > > be provided along with their merits (their disadvantages are plainly
> > > obvious). Authors do not even attempt to give credit to any other
> > > option, and in that regard the whole perspective has a feel of a
> > > somewhat dogmatic position -- while this is not true, obviously.
> > > In fact, as good example of discussing alternatives is already given
> > > in the Data management section ("fold all data management...").
> > >
> > > 3/ The section 'Software' might be renamed? Up to the authors.
> > > Programming, scripting etc? Software is a very general term and
> > > means too many other things not covered here. Another qualifier
> > > must be that this section is NOT original as there are thousands
> > > of books and millions of articles on the subject, these are simple
> > > guidelines for the uninitiated. Lack fo any references is weird.
> > >
> > > 4/ Contributions in the Collaboration section: make clear that
> > > your underlying assumption refers to open source projects that
> > > invite co-developers to contribute.
> > >
> > > 5/ Figure is fine, but readers will expect something more. Can
> > > you think of another display, perhaps a visual guide of some
> > > of your recommendations, in a specific section?
> > >
> > > 2b) Minor comments
> > >
> > > 1/ in abstract: "can and should consider adopting".
> > >
> > > 2/ "regardless of their current level of technical skill" - lose
> > > 'technical' -- there are many technical skills that the authors do
> > > not possess. Better replace it with 'computational', or more
> > > precisely, 'programming'.
> > >
> > > 3/ Ditto for "collaborating with colleagues, organizing projects,
> > > tracking work, and writing manuscripts" -- perhaps stay within
> > > your expertise: organizing software projects, tracking versions,
> > > reporting (not writing manuscripts -- others might know better).
> > >
> > > 4/ page 2, line 9: should adopt. See Minor #1.
> > >
> > > 5/ "beyond emailing themselves a spreadsheet named" -- please
> > > consider rephrasing. Abrasive, with no reason. Not funny either.
> > >
> > > 6/ page 3, line 59: "pertinent info," -- information.
> > >
> > > 7/ page 3, line 76: NAs -> the "NA" value.
> > >
> > > 8/ page 4, line 99: "re-use data preparation logic in the future",
> > > re-write, clarify.
> > >
> > > 9/ page 5, line 153: what about -h ? Help not recommended?
> > >
> > > 10/ page 6, line 207: github, give URL for consistency with
> > > others (provided later in the manuscript of course).
> > >
> > > 11/ page 10, line 399: dropbox, give URL -- as above.
> > >
> > > 12 / page 11, line 437: "less than a latte", not everyone will get
> > > this, esp. people who have never ordered a latte.
> > >
> > > 13/ page 13, line 497: there's got to be some advantages!
> > >
> > > 14/ page 13, line 523: what are the disadvantages of Google
> > > Docs or similar?
> > >
> > > 15/ Need to include ® for Microsoft Word, I believe.
> > >
> > > Reviewer #2: I have attached the review as a MS Word docx.
> > >
> ------------------------------------------------------------------------
> > >
> > > *Reviewers who wish to reveal their identities to the authors and
> > > other reviewers should include their name here (optional). These names
> > > will not be published with the manuscript, should it be accepted.*
> > >
> > > Reviewer #1: (No Response)
> > >
> > > Reviewer #2: Todd Harris
> > >
> > >
> >
> > --
> > Nihil pro nobis sine nobis.
> > ref:_00DU0Ifis._5000BaGFqj:ref
> >
> > _______________________________________________
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> >
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