<div dir="ltr">Hi Gilberto,<div><br></div><div>Your message must get some response from me. </div><div><br></div><div>The self citations the editor wrote about are mine - yet many contributors have self cited - and self citation is not really an issue. It expresses the opinion of the persons signed on the paper. I did not see any objections to those references and please note that my references are partially to patented technology - so if anyone else does similar work in the US - they better communicate with me beforehand. And please note that I did declare conflict of interest multiple times including in the paper - and once declared publicly this should not be an issue. In fact there are multiple leads for these subgroups partially at my request to allow proper function in case of a conflict of interest. </div><div><br></div><div>Therefore unless you know how to rewrite the paper without my references, or convince me to remove those there is no simple way we can address this editor's comments to his satisfaction. </div><div><br></div><div>Specifically the video the editor pinpointed is:</div><div>
<ul><li><p class="gmail-western" style="margin-bottom:0in;line-height:100%;font-family:Calibri,serif;font-size:11pt;direction:ltr;color:rgb(0,0,10);background:transparent">
<font face="Times New Roman, serif"><font style="font-size:11pt">Jacob.
Barhak, Open Source and Sustainability, COMBINE 2020 October 5-9.
Video:
</font></font><font color="#0000ff"><u><a href="https://drive.google.com/drive/folders/1actGnx6FwvoCcPrrF3qbnO0AmHt10WN6" style="color:rgb(0,0,255)"><font face="Times New Roman, serif"><font style="font-size:11pt">https://drive.google.com/drive/folders/1actGnx6FwvoCcPrrF3qbnO0AmHt10WN6</font></font></a></u></font><font face="Times New Roman, serif"><font style="font-size:11pt">
starting from minute 13:10. Presentation:
</font></font><font color="#0000ff"><u><a href="https://jacob-barhak.github.io/COMBINE2020_OpenSource_upload_2020_10_04.odp" style="color:rgb(0,0,255)"><font face="Times New Roman, serif"><font style="font-size:11pt">https://jacob-barhak.github.io/COMBINE2020_OpenSource_upload_2020_10_04.odp</font></font></a></u></font></p>
</li></ul></div><div>If please check out my arguments in this talk and decide for yourself if this is not worth as a citable reference. If you want to open the discussion on licenses, I can add that I personally have been negatively affected due to licensing issues and my conclusion is that CC0 is a good solution to share code and data to some cases and there is an increasing number of entities realizing it - at least one cited in the paper. We can explore this issue deeper, yet I think the version in the paper is good enough and the editor rejected the paper due to style issues and not due to substance and accuracy issues - I think the editor made a bad decision and in fact my communication with the editor in chief did change the response, meaning that there was an issue on the side of the Journal - not our group. This is my personal opinion, yet it is more important for the group to decide here since we are many people that need to reach unanimous consensus.</div><div><br></div><div>Note, however, that I do ask that whoever wants to introduce the changes will do the hard work of making sure that:</div><div>1. They make the edits - I did enough - if you want a change you need to do the leg work. </div><div>2. They comply with the target journal format - this means also making sure references are properly ordered and cited and do this properly coordinated amongst all the changes flowing in. </div><div>3. Unanimous consensus is established before submission - this is actually a legal requirement - without that we cannot submit to a 3rd party that will ask for copyright transfer. </div><div>4. We do this in a timely manner and finish in about 4 weeks from now. </div><div><br></div><div> So all those who voted, will actually have to act to make your vote materialize. The sooner you start, the better. </div><div><br></div><div>I hope my response is clear enough to understand some of the difficulties and that we can clear those. </div><div><br></div><div> Jacob</div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, May 2, 2021 at 9:47 AM Gilberto Gonzalez-Parra <<a href="mailto:gilberto.gonzalezparra@nmt.edu">gilberto.gonzalezparra@nmt.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>I agree with option 13. We should focus on the comments of the editor of Cureus. Very briefly and seen the big picture. These are the main aspects that she/he commented:</div><div><br></div><div><b>Abstract:</b> Emphasize the reproducibility issue (the editor said he knew about it but not everyone knows). Explain methodology (review, discussions, seminars, etc), key findings, and proposed ideas to solve the reproducibility issues.</div><div><br></div><div><div><b>Structure and message</b>: Take into account the editor's comment <b>"The authors propose that ensuring reproducibility, credibility and utility will lead to easier integration, which seems correct and would make a nice paper if those aspects were discussed in that order."</b>. I think a diagram would help to organize the ideas for us and readers. Maybe the open discussion issues section can be renamed just to Discussions and try to put the ideas more organized with some particular purpose based on the previous sections. In the conclusions, send a more clear message about the purpose of the paper. For instance
key findings, and proposed ideas to solve the reproducibility issues. </div><div><br></div><div><b>References</b>: Try to support the claims with at least one or two references. Some things in life are subjective (even sometimes seem obvious), so giving references from previous authors helps to the credibility of the paper. The editor (cureus) raised some issues regarding references and video of a conference talk. Usually it is better to support the paper with references that have been already peer-reviewed to give a more solid base. This is how the paper review process and journal works.</div><div><br></div><div><br></div><div>Best regards, </div></div><div><br></div><div><br></div><div><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">***************************************************************************</div><div dir="ltr">Gilberto C. Gonzalez-Parra, <span style="color:rgb(0,0,0);font-family:"Helvetica Neue",Helvetica,Arial,"Lucida Grande",sans-serif,serif,EmojiFont;font-size:13px">Ph.D in Applied Mathematics.</span></div><div dir="ltr"><font color="#000000" face="Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif, serif, EmojiFont"><span style="font-size:13px">Faculty of the </span></font>Mathematics Department<div><div>New Mexico Tech, NM, USA.</div></div><div>****************************************************************************</div></div></div></div></div></div></div></div></div></div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, May 1, 2021 at 10:36 PM Winston Garira <<a href="mailto:Winston.Garira@univen.ac.za" target="_blank">Winston.Garira@univen.ac.za</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div dir="ltr">
<div>
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<div dir="ltr">
<div dir="ltr" style="color:rgb(0,0,0);background-color:rgb(255,255,255)">I agree with making revisions- 13! </div>
<div dir="ltr" style="color:rgb(0,0,0);background-color:rgb(255,255,255)"><br>
</div>
<div dir="ltr" style="color:rgb(0,0,0);background-color:rgb(255,255,255)"><span id="gmail-m_5737793992451594791gmail-m_-2924975225885522573current-cursor-0ec0d479-062f-4e16-afa4-1419a6e03b88"></span>WIinston</div>
</div>
</div>
<div><br>
</div>
<div>Get <a href="https://aka.ms/o0ukef" target="_blank">Outlook for iOS</a></div>
</div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_5737793992451594791gmail-m_-2924975225885522573divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Dr. Rahuman Sheriff <<a href="mailto:sheriff@ebi.ac.uk" target="_blank">sheriff@ebi.ac.uk</a>><br>
<b>Sent:</b> Saturday, May 1, 2021 11:42:11 PM<br>
<b>To:</b> James Glazier <<a href="mailto:jaglazier@gmail.com" target="_blank">jaglazier@gmail.com</a>><br>
<b>Cc:</b> William Waites <<a href="mailto:wwaites@ieee.org" target="_blank">wwaites@ieee.org</a>>; <a href="mailto:vp-reproduce-subgroup@lists.simtk.org" target="_blank">vp-reproduce-subgroup@lists.simtk.org</a> <<a href="mailto:vp-reproduce-subgroup@lists.simtk.org" target="_blank">vp-reproduce-subgroup@lists.simtk.org</a>>; <a href="mailto:vp-integration-subgroup@lists.simtk.org" target="_blank">vp-integration-subgroup@lists.simtk.org</a> <<a href="mailto:vp-integration-subgroup@lists.simtk.org" target="_blank">vp-integration-subgroup@lists.simtk.org</a>>; Jonathan Karr <<a href="mailto:jonrkarr@gmail.com" target="_blank">jonrkarr@gmail.com</a>>; John Gennari
<<a href="mailto:gennari@uw.edu" target="_blank">gennari@uw.edu</a>>; Winston Garira <<a href="mailto:Winston.Garira@univen.ac.za" target="_blank">Winston.Garira@univen.ac.za</a>><br>
<b>Subject:</b> Re: [Vp-integration-subgroup] [Vp-reproduce-subgroup] White paper submission - vote for venue</font>
<div> </div>
</div>
<div dir="auto">I agree with 13 - revision.
<div>Sheriff<br>
<div>
<div dir="ltr">Sent from my iPhone</div>
<div dir="ltr"><br>
<blockquote type="cite">On 2 May 2021, at 02:34, James Glazier <<a href="mailto:jaglazier@gmail.com" target="_blank">jaglazier@gmail.com</a>> wrote:<br>
<br>
</blockquote>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">I believe the manuscript must be revised before submission. As presented now it does not do justice to the great ideas provided by the many contributors.
<div>I am indifferent to the venue of publication. RS Interface or Bioinformatics are both fine, but I am happy to see it published anywhere (as long as it is cleaned up). Bulletin of Mathematical Biology had Reinhard as chief editor, so you would at least
get a review....</div>
<div><br>
</div>
<div>JAG</div>
</div>
<br>
<div>
<div dir="ltr">On Sat, May 1, 2021 at 4:22 PM William Waites <<a href="mailto:wwaites@ieee.org" target="_blank">wwaites@ieee.org</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Agree on 13 revision, though I am severely time-constrained for the next few weeks.<br>
<br>
No strong preference on venue but it’s good to have an idea of the audience we’re writing for. I like RS Interface or Bioinformatics. If this gets done before my MRC funding runs out, they will pay OA fees.<br>
<br>
Cheers,<br>
-w<br>
<br>
<br>
> On 1 May 2021, at 20:38, Eric Forgoston <<a href="mailto:eric.forgoston@montclair.edu" target="_blank">eric.forgoston@montclair.edu</a>> wrote:<br>
> <br>
> 13 - open for revision; no preference on venue.<br>
> ---------------------<br>
> Dr. Eric Forgoston<br>
> Professor of Applied Mathematics<br>
> Chair, Department of Applied Mathematics and Statistics<br>
> Montclair State University<br>
> Montclair, NJ 07043 USA<br>
> +1 973 655-7242 <br>
> <a href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Feric-forgoston.github.io%2F&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C66fc4261f4fb459414d708d90ce9fee3%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637555021414684464%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6PTWhvVbSOhetbZypl2z4dICfg1WIZ5gvtIwQ1HhKos%3D&reserved=0" rel="noreferrer" target="_blank">
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> <br>
> <br>
> On Sat, May 1, 2021 at 1:32 PM Jonathan Karr <<a href="mailto:jonrkarr@gmail.com" target="_blank">jonrkarr@gmail.com</a>> wrote:<br>
> #13 -- revise<br>
> <br>
> On Sat, May 1, 2021 at 1:18 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>> wrote:<br>
> Greetings white paper contributors,<br>
> <br>
> It is time to vote again for the target venue. Here are the options again. <br>
> • Cureus - resubmission after addressing editor comments<br>
> • Nature - if you vote for this venue please specify flavour such as Nature Scientific Reports<br>
> • Science<br>
> • Briefings in Bioinformatics<br>
> • Trends in Biotechnology - requires distilling the paper<br>
> • Journal of The Royal Society Interface<br>
> • Annual Review of Public Health<br>
> • BMJ<br>
> • Annual Review of Biomedical Engineering<br>
> • F1000research - if you vote for this this venue please specify Gateway / Collection
<br>
> • bulletin of mathematical biology<br>
> • Bioinformatics.<br>
> • Do not submit now - instead open for revisions for 2 weeks and then submit. If you choose this option also vote for the target venue after revisions so that we will not have to delay further.
<br>
> <br>
> I will ask that contributors pick one journal from that list - I ask that you REPLY ALL so votes will be transparent and time of vote will be registered since first to vote will break ties.<br>
> <br>
> The voting period will be until Tuesday 11-May 1am CDT <br>
> <br>
> Again, if a journal costs for open publication, whoever voted, will split publication costs. If anyone on this list is funded for this, please vote.
<br>
> <br>
> I urge contributors to vote - just so that we will have a preference order to follow in case of rejection.<br>
> <br>
> Looking forward to your votes. <br>
> <br>
> Jacob<br>
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<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">
<div dir="ltr">James A. Glazier, PhD
<div>Professor of Intelligent Systems Engineering, Adjunct Professor of Physics</div>
<div>Director Biocomplexity Institute<br>
<div>
<div>Indiana University, Bloomington</div>
</div>
</div>
<div>(812) 391-2159</div>
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