[Vp-integration-subgroup] [EXT] Re: White paper revision
Jacob Barhak
jacob.barhak at gmail.com
Tue May 18 07:27:25 PDT 2021
So Tomas,
Before starting editing, to save time it is important that we establish
what is going to be edited - I voiced my concern over the large deletions
in Johns version more than once - there is a real problem there - many
authors may be completely eliminated in the name of style - I don't like it
- so John has to decide how he spends his time - first just define what
sections you want to contribute in - this will help John comprehend the
magnitude of the task - he promised editorial services for two weeks - so
before we start wasting time with edits, lets see the entire picture.
Tomas, what you like may be something I dislike or something I do not care
about, and eventually we all have to agree - and there are about 20 of us -
this is a legal requirement for copyright transfer. The task here is time
consuming and I do not envy John and it is important we all help him
realize the task before he spends time on it.
And please reply to all - there are some contributors that are listed in
only one list and some that may not have signed up - they all need to be
aware of what we are doing.
Hopefully you identified the sections you want to contribute to - please
state those to move this forward quicker.
Jacob
On Tue, May 18, 2021 at 9:08 AM Tomas Helikar <thelikar2 at unl.edu> wrote:
> I suggest we use John's version - the flow has begun to improve there and
> he'll be bringing the content over from the submitted version.
>
> At the top of each of the other version, there should be big red "DO NOT
> EDIT THIS VERSION" and a link to John's version that will be the running
> draft where our efforts should focus.
>
> Best,
> Tomas Helikar, Ph.D.
> Susan J. Rosowski Associate Professor
> Department of Biochemistry | University of Nebraska-Lincoln
> m: 402-547-8904 <callto:402-547-8904> | o: 402-472-3530
> <callto:402-472-3530>
> www.helikarlab.org <http://www.postbox-inc.com> | cellcollective.org
> <http://helikarlab.org>
> twitter: @helikarlab <http://twitter.com/helikarlab>, @biocollective
> <http://twitter.com/biocollective>
> On 5/18/21 9:05 AM, Jacob Barhak wrote:
>
> Non-NU Email
> ------------------------------
> Yes Sheriff,
>
> You have a good point. Here are the versions of the paper that I recall.
>
> 1. The version we all approved - I suggest we use this:
> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1IMEgmdNkx-2DEsnOjGuegpenSIMmKIkK00Lc8Gred3QxM_edit-3Fusp-3Dsharing&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=FanQUPp95Lqx2G9Ojb6SLVQzkZS6mrqBIt_W-zgW8_Q&e=>
> 2. John Gennari version:
> https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?ts=60a294c2
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1VvyP3YZQdQYjj8DFKOpQ4pn-5F0pdDGgiT_edit-3Fts-3D60a294c2&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=7h_7qlaNYzcnYViiFjrrVhBADdtnSQ8eh_Wg_vxmY4I&e=>
> 3. Rahuman Sheriff version:
> https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh_edit&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=yaBZO6lyEXDKmMXfrDPDqy10sDgl0FQgkFFMO3_iShg&e=>
> 4. Alexander Kulesza version
> https://drive.google.com/file/d/1U_lTHrV6STXWNT3GiCepvsLk1WdYgzN5/view
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1U-5FlTHrV6STXWNT3GiCepvsLk1WdYgzN5_view&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=6gQoAQCH7F2WOy92A0xjfWmCMUjW7onPku8BYcIsY9Y&e=>
> 5. Original Model Reproducibility, Credibility, Standardization subgroup
> version
> https://docs.google.com/document/d/1cqwXAjBWEiJZ1tUBnf66QVHdHd2fKq_W0py7t4PNVLo/edit?usp=sharing
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1cqwXAjBWEiJZ1tUBnf66QVHdHd2fKq-5FW0py7t4PNVLo_edit-3Fusp-3Dsharing&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=QH6Rgy4why7ib2YGE2T5AA61L68xDE1K-ySoCdKV9ew&e=>
> 6. Original Integration subgroup version:
> https://docs.google.com/document/d/1voUSrSpv3AZlC1T-BLa3W4wzHQ5vEdJCVrBbwMUTDiQ/edit?usp=sharing
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1voUSrSpv3AZlC1T-2DBLa3W4wzHQ5vEdJCVrBbwMUTDiQ_edit-3Fusp-3Dsharing&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=WPFW1D-ECFULPKl8uijQsNA58J5V7TNynIc9OeqCiBE&e=>
>
> The last two versions hold the original discussions before the merge to
> the version on top. The history of those contain most contributions -
> however it will take hours to figure out where each text portion is located
> in the new version. Yet the new version also includes many modifications.
> And I believe Hana has another version of proofs that were never made
> public - we did this revision and proof process before, yet I think she
> sent me her version privately. I may be mistaken - it was a long time ago.
>
> Hopefully this list will help understand the undertaking and save time.
>
> Jacob
>
>
>
>
>
>
>
> On Tue, May 18, 2021 at 8:34 AM Rahuman Sheriff <sheriff at ebi.ac.uk> wrote:
>
>> Dear John G,
>> Many thanks for the update.
>> I like the new ordering :)
>>
>> @Jacob, as you mentioned you have 6 versions, could you please add the
>> link to those versions in John G document, so they are all inked.
>> I give consent to to rephrase my contribution or even remove part or all
>> of my contribution to the white paper and present the ideas in other
>> sections if required to make the paper coherent and flow well.
>>
>> The white paper has a great collections of ideas, I hope we can get it
>> into a good shape soon for submission and benefit the scientific community.
>>
>> Best regards
>> Sheriff
>>
>>
>> On 18 May 2021, at 13:28, James Osborne <jmosborne at unimelb.edu.au> wrote:
>>
>> Sorry I wasn't on the call Yesterday (it was 1 am for me so not really
>> achievable). Looking at the emails looks like it was useful.
>>
>> Happy to help how I can, in terms of areas as someone on the
>> multicellular side of life i'm probably most use on 3 but happy to support
>> others.
>>
>> James
>>
>> On Tue, May 18, 2021 at 3:12 PM John Gennari <gennari at uw.edu> wrote:
>>
>>> * External email: Please exercise caution *
>>> ------------------------------
>>>
>>>
>>> All: About 9 of us had a lively Zoom meeting today to chat about the
>>> manuscript. By the end, it was a productive meeting, and I'm hoping that
>>> this email will capture some key outputs from the meeting. I apologize if I
>>> said some things that were a bit "inflammatory". Obviously 2 years would be
>>> much too long to get this paper out-the door.
>>>
>>> I saw two outcomes. First, we had some nice ideas and discussion about
>>> re-ordering (initiated by Tomas Helikar). In the below, I'm going to
>>> propose one possible ordering, but this is certainly a work-in-progress.
>>> The reason that I think ordering is important is that it will give us a
>>> much better ability to write a strong concluding section, where we talk
>>> about themes and the larger arc of our ideas.
>>>
>>> Second, we agreed that we should nominate "point persons" who would be
>>> in charge of at least the initial cut of each of the subsections. As Jacob
>>> pointed out, this information should be easy to get from older email and
>>> history of the development of the paper. During the zoom meeting, we
>>> associated some co-authors with some sections, but our coverage wasn't
>>> perfect (see challenge #12). Hopefully people will "stand up" and admit
>>> that some section of text is theirs.
>>>
>>> So in the below, I include the original title of the section, a few
>>> words about the content of that section, and then a name (or several names)
>>> of co-authors who will be the "point person" to make sure that the
>>> appropriate content is included. Obviously, all co-authors can and should
>>> chime in on any part of the text, but the point person should make sure
>>> that the key ideas are included.
>>>
>>> The basic ordering idea for the dozen challenges was to follow the
>>> life-cycle of model development, execution, sharing and integration, and
>>> eventually implementation. So...
>>>
>>> *********************************************
>>>
>>> *(1) "**Data** and measurement definitions*". Before you can build a
>>> model, you must have data. So data availability and measurement standards
>>> is the place to start.
>>>
>>> *People: *Hana D, Jacob B
>>>
>>> *(2) "**The variety of modeling languages*" This is about the choice of
>>> modeling languages, such as using SBML, CellML, or Matlab. As I said on the
>>> phone call, this is sort of about "syntax"--how do you write down your
>>> model?
>>>
>>> *People:* John G, Jon K, Rahuman S.
>>>
>>> *(3) "**The variety of modeling paradigms and scales"* Separately from
>>> modeling syntax, we must acknowledge modeling paradigms with very different
>>> semantics. Some clear examples are PDEs versus ODEs versus rule-based
>>> systems (and obviously one can combine these). Certainly semantics might
>>> impact syntax (the prior challenge), in that certain modeling language
>>> might be appropriate only for some paradigms.
>>>
>>> People: James G, Eric F (?)
>>>
>>> *(4) "**Units standardization*" A common reason that models are not
>>> reproducible are errors in units, or misunderstanding about units, or
>>> simply a lack of information about units.
>>>
>>> People: Jacob B, Hana D
>>>
>>> *(5) "**A lack of annotations in models*". Once researchers publish
>>> models, they must annotate the model so that others can understand it.
>>> Quality annotation is essential for both search and reproducibility.
>>>
>>> People: John G.
>>>
>>> *(6) "**Models are hard to locate"* If your goal is to reproduce,
>>> understand and possibly reuse or integrate some other model, one must first
>>> find that model. This requires annotation (prior section) and repositories
>>> (Physiome Model Repository, BioModels) and search platforms
>>> (ModeleXchange).
>>>
>>> People: Jon K, John G.
>>>
>>> *(7) "**Common platforms to execute models" *A model is pretty
>>> worthless as a static object. For folk to understand and reproduce models
>>> they must be executable. Alas, there is no single or consistent way of
>>> executing a model -- and of course, this interacts direction with section
>>> #2 and #3, above: Execution platforms are usually only for one modeling
>>> paradigm, and often for one modeling language. The BioSimulators work goes
>>> here.
>>>
>>> People: Jon K.
>>>
>>> *(8) "**Credibility **and validity of models*" Once a model is
>>> published, how do folk know it is right? Model validation is a big topic
>>> and challenge. Credibility follows (in part) from validation, but also
>>> requires transparency and reproducibility, etc.
>>>
>>> People: John Rice, Jon K, Jacob B
>>>
>>> *(9) "**Environments to adapt and integrate models*" As I see it, one
>>> of the end-targets for this manuscript is to better enable model
>>> integration, to build better models. There are many challenges with the
>>> task of integrating two (or more) models. (One that has recently been
>>> discussed is that even if model A and model B are valid and correct, there
>>> is no guarantee that the combined model A+B is correct. I liked what
>>> William Waites and Katherine Morse posted on this subject.) This section is
>>> where SBML-comp and SemGen environments can be mentioned.
>>>
>>> People: John G.
>>>
>>> (*10) "Challenges for stochastic models" *Special challenges specific
>>> to stochaistic modeling. An obvious point to mention is repeatability --
>>> stochastic models don't necessarily give the same results with the same
>>> inputs.
>>>
>>> People: James G., Eric F
>>>
>>> *(11) "Licensing barriers" *Issues around "open source" and CC0
>>> licensing.
>>>
>>> People: Jacob B
>>>
>>> *(12) "Barriers to model implementations and applications"* (I might
>>> suggest this be re-phrased for better clarity). What this section should
>>> discuss are challenges is getting a community to actually use models for
>>> "real-world" applications or decision making. This is more of a
>>> cultural/societal challenge, and thus seems like a nice big-picture way to
>>> end.
>>>
>>> *People: ?? *I don't have any names here...
>>>
>>> *********************************************
>>>
>>> We didn't really talk much about it in the Zoom meeting, but there have
>>> been ideas tossed around about a "baker's dozen", i.e., adding a 13th
>>> challenge. We could also potentially merge some of the above.
>>>
>>> The "point persons" listed above is obviously a subset of co-authors.
>>> That's fine and appropriate. Just for transparency, I follow what I think
>>> is pretty standard policy for authorship issues, and nicely summarized by
>>> the International Committee of Medical Journal Editors (ICMJE); see
>>> 2019 updated document at http://www.icmje.org/icmje-recommendations.pdf
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.icmje.org_icmje-2Drecommendations.pdf&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=l29d3A9PItAUv4N0WkCuREqes9tSKSW7sk5GDEo6VBA&e=>
>>> (Or see, below my signature, a summary of the key points of this document).
>>>
>>> Finally, I've made the document editable by all at
>>> https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?ts=60a294c2
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1VvyP3YZQdQYjj8DFKOpQ4pn-5F0pdDGgiT_edit-3Fts-3D60a294c2&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=7h_7qlaNYzcnYViiFjrrVhBADdtnSQ8eh_Wg_vxmY4I&e=>
>>>
>>> -John G.
>>>
>>> ==========================================================================
>>> Associate Professor & Graduate Program Director <gennari at uw.edu>
>>> <gennari at uw.edu>
>>> Dep't of Biomedical Informatics and
>>> telephone:206-616-6641
>>> Medical Education, box 358047
>>> University of Washington
>>> Seattle, WA 98109-4714
>>> http://faculty.washington.edu/gennari/
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__faculty.washington.edu_gennari_&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=7h8T10a2oOTChEmXp5dGxDnAIghmjMroKsXSfcbIH9Y&e=>
>>>
>>> ==========================================================================
>>>
>>>
>>> The ICMJE recommends that authorship be based on the following 4
>>> criteria:
>>>
>>> 1. Substantial contributions to the conception or design of the
>>> work; or the acquisition, analysis, or interpretation of data for the work;
>>> AND
>>>
>>> 2. Drafting the work or revising it critically for important
>>> intellectual content; AND
>>>
>>> 3. Final approval of the version to be published; AND
>>>
>>> 4. Agreement to be accountable for all aspects of the work in
>>> ensuring that questions related to the accuracy or integrity of any part of
>>> the work are appropriately investigated and resolved.
>>>
>>>
>>>
>>>
>>> _______________________________________________
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