[Vp-integration-subgroup] Recap from joint meeting regarding the white paper

[Jacob Barhak]

Greetings to all white paper contributors,

9 of 18 contributors approved the paper. I would ask that the rest will
take the time and read the paper and approve it. It is good to know what
your colleagues think anyway.

I am sending the file again:
https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing

If your name is marked in red, please answer the following questions:

1. Do you feel comfortable being listed as a contributor to the composed
version? There are no more changes expected other than minor grammar
corrections. I will need approval from all contributors to move forward and
since there are many of you, please send confirmation as soon as possible.

2. What is your affiliation so I can add it at the end.

3. If you have a conflict of interest, please report it so I can add it to
the paper. If you are unsure, please download the form from this link
http://icmje.org/downloads/coi_disclosure.zip and then fill in the
questions and press the generate button - it will create the COI disclosure
text for you.

4. If you have a target venue in mind for the paper, please suggest - we
will pick one with consensus that everyone is comfortable with.

Hopefully the remaining contributors can do this by the end of the week.

            Jacob

On Wed, Mar 10, 2021 at 3:15 PM Jacob Barhak <jacob.barhak at gmail.com> wrote:

> Greetings to all white paper contributors,
>
> You are getting this message as a reminder that you need to approve the
> current version of the paper. I am putting this task on the top of your
> mailbox.
>
> So far, only 4 of the 18 approved the paper in its current form - you will
> see the names of those still needing to approve in red in the contributors
> list. Here is the paper link again:
>
> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>
> If your name is in red, please send me an email answering the
> questions from my previous email.
>
> Hopefully we can get the approval process done quickly and move on to
> publish the paper.
>
>                   Jacob
>
>
> On Thu, Mar 4, 2021 at 3:46 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
>
>> Greetings to all the white paper contributors:
>>
>> Jonathan Karr
>> Rahuman Sheriff
>> James Osborne
>> Gilberto Gonzalez Parra
>> Eric Forgoston
>> Ruth Bowness
>> Yaling Liu
>> Robin Thompson
>> Winston Garira
>> Jacob Barhak
>> John Rice
>> Marcella Torres
>> John Gennari
>> Hana M. Dobrovolny
>> Tingting Tang
>> William Waites
>> James Glazier
>> James R Faeder
>>
>> If you contributed text to the white paper and not on this list, please
>> let me know as soon as possible - I did my best to assemble all
>> contributors and want to make sure no one was missed by mistake.
>>
>> Following the reopening, the white paper grew in size. It is now about 29
>> pages and 18 contributors. You will find it here:
>>
>> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>>
>> I suggest closing the paper and going again through the formal approval
>> process so that the paper can be submitted to some publisher.
>>
>> I will ask that all contributors approve the paper - so if you
>> contributed I expect an email from you with the following elements:
>>
>> 1. Do you feel comfortable being listed as a contributor to the composed
>> version? There are no more changes expected other than minor grammar
>> corrections or fixing issues listed with comments. I will need approval
>> from all contributors to move forward and since there are many of you,
>> please send confirmation as soon as possible.
>>
>> 2. What is your affiliation so I can add it at the end.
>>
>> 3. If you have a conflict of interest, please report it so I can add it
>> to the paper. If you are unsure, please download the form from this link
>> http://icmje.org/downloads/coi_disclosure.zip and then fill in the
>> questions and press the generate button - it will create the COI disclosure
>> text for you.
>>
>> 4. If you have a target venue in mind for the paper, please suggest - we
>> will pick one with consensus that everyone is comfortable with.
>>
>> I will ask those who approved the paper before to look at the changes
>> since the day of approval - we added around 4 pages of text and authors
>> should be aware of.
>>
>> For all those who wanted to add material and could not manage, I
>> apologize - yet at this point it seems we are refining the ideas and not
>> contributing new ones and it was open for a while and we need to move on.
>>
>> I look forward to your responses.
>>
>>                 Jacob
>>
>>
>>
>> On Thu, Feb 25, 2021 at 4:29 PM Jacob Barhak <jacob.barhak at gmail.com>
>> wrote:
>>
>>> Greetings subgroups,
>>>
>>> James Glazier the working group lead, indicated that the white paper
>>> deadline of tomorrow is flexible, so it is possible to get additional
>>> contributions to the white paper.
>>>
>>> Therefore I will ask anyone who wanted to contribute and did not have
>>> the chance to contribute to the paper until the end of the weekend.
>>> Please send me an email to gain access - I will redacted you to the
>>> correct draft. Here is again the link to the integrated version:
>>>
>>> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>>>
>>> Many of you contributed already and some even approved this assembled
>>> manuscript - I asked those who have not approved already to wait a few more
>>> days before reviewing the paper so that they can approve the final version
>>> next week.
>>>
>>>            Jacob
>>>
>>>
>>>
>>>
>>>
>>> On Sat, Feb 20, 2021 at 3:59 AM Jacob Barhak <jacob.barhak at gmail.com>
>>> wrote:
>>>
>>>> Greetings subgroups,
>>>>
>>>> As promised the merging of both papers have started.
>>>>
>>>> Here are some technicalities:
>>>>
>>>> The title of the jint white paper will be:
>>>> Model Integration in Computational Biology: the Role of
>>>> Reproducibility, Credibility and Utility
>>>>
>>>> The author of the paper will be:
>>>> Multiscale Modeling and Viral Pandemics Working Group
>>>>
>>>> I looked through all the edit list on the paper and found the following
>>>> contributors:
>>>> Jonathan Karr
>>>> Rahuman Sheriff
>>>> James Osborne
>>>> Gilberto Gonzalez Parra
>>>> Eric Forgoston
>>>> Ruth Bowness
>>>> Yaling Liu
>>>> Robin Thompson
>>>> Winston Garira
>>>> Anonymous contributor January 25, 2:13 PM
>>>> Jacob Barhak
>>>> John Rice
>>>>
>>>> The Anonymous contributor on January 25, 2:13 PM added the words: ".
>>>> There are also challenges in gaining testable insight. Are they truly
>>>> necessary? ". . However, unless the contributor identifies themselves, I
>>>> cannot add their name and may remove this sentence since it seems misplaced
>>>> and not attributed to any person.
>>>>
>>>> If I missed any contributor, please let me know so I can add the person
>>>> to the list of contributors. I just looked at the changes history on the
>>>> document and pulled names - if anyone added text using an account by
>>>> someone else, let me know.
>>>>
>>>> Also, I will wait for a couple of more days for any last minute
>>>> contributions. I will ask for anyone who wanted to contribute and did
>>>> not have a chance to edit the papers directly over the weekend. I will do
>>>> my best to integrate changes done over the weekend, yet I cannot guarantee
>>>> adding any more changes - we had enough time to make those edits and  we
>>>> need to wrap things up at some point.
>>>>
>>>> I will send the link to the combined draft paper once it is in good
>>>> shape for approval.
>>>>
>>>> I will try my best to harmonize all contributions and maintain flow.
>>>> Yet there are a lot of discussions and open end issues left, so I am not
>>>> sure how practical it is.
>>>>
>>>> If anyone wants to help editing, let me know.
>>>>
>>>> Hopefully you will find the final product in good shape.
>>>>
>>>>               Jacob
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Fri, Feb 12, 2021 at 10:26 AM Jacob Barhak <jacob.barhak at gmail.com>
>>>> wrote:
>>>>
>>>>> Greetings to the model reproducibility, credibility and
>>>>> standardization and integration subgroups
>>>>>
>>>>> In the joint meeting of the groups we discussed the papers and ideas
>>>>> behind the merge as well as their own contributions to the working group
>>>>> and paper.
>>>>>
>>>>> It was decided unanimously to merge the two white papers together.
>>>>>
>>>>> The white paper drafts are in good form currently and include a lot of
>>>>> information. You can find them in these links:
>>>>>
>>>>>
>>>>> https://docs.google.com/document/d/1voUSrSpv3AZlC1T-BLa3W4wzHQ5vEdJCVrBbwMUTDiQ/edit?usp=sharing
>>>>>
>>>>>
>>>>> https://docs.google.com/document/d/1cqwXAjBWEiJZ1tUBnf66QVHdHd2fKq_W0py7t4PNVLo/edit?usp=sharing
>>>>>
>>>>> The group did not reach a conclusion on the title of the joint paper.
>>>>> Suggestions for the title are welcome.
>>>>>
>>>>> Beyond what was discussed in the meeting I would like to add the
>>>>> following:
>>>>>
>>>>> Since the deadline for the white paper is Feb 26th - it is suggested
>>>>> that all contributors who want to join the author list of the white paper
>>>>> will make edits until Feb 19th in the respective papers. This will allow
>>>>> time to merge the papers together and send it to both lists.
>>>>>
>>>>> Unless someone else volunteers to help merge, I will personally start
>>>>> the merge on Feb 20th, so contributions to the text after that date may not
>>>>> be merged. Individuals who wish to be in the author list should contribute
>>>>> text before that date and preferably write their name near the contributed
>>>>> text.
>>>>>
>>>>> I personally look forward to more feedback and contributions.
>>>>>
>>>>>              Jacob
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
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