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

[Jacob Barhak]

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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