[Vp-reproduce-subgroup] [Vp-integration-subgroup] [EXT] Re: White paper revision

Tomas Helikar thelikar2 at unl.edu
Tue May 18 07:30:28 PDT 2021


Since John is taking the lead on the new version, my suggestion is to 
let him do it the way that will be most efficient for him. I think 
everyone, including John, have noted your concerns.

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 9:27 AM, Jacob Barhak wrote:
> Non-NU Email
> ------------------------------------------------------------------------
> 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 
> <mailto: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
>     <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.postbox-2Dinc.com&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=8pX0Br54uLoNQ-PxHY_Nt9ks6sIqSjFiajTJf6yTLYE&s=hJenfL7Oc5LHMtfzjwCDD7iz11gFb7qHTa9Hbu2i1Lk&e=>
>     | cellcollective.org
>     <https://urldefense.proofpoint.com/v2/url?u=http-3A__helikarlab.org&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=8pX0Br54uLoNQ-PxHY_Nt9ks6sIqSjFiajTJf6yTLYE&s=sM2xjtRiGe7zBH5cWvHqEuH6DqVSiUxQjrE9DZ6JJVI&e=>
>     twitter: @helikarlab
>     <https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_helikarlab&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=8pX0Br54uLoNQ-PxHY_Nt9ks6sIqSjFiajTJf6yTLYE&s=bdp23tv-IbXxRa2YpzF18AkQutpCxDtfC7-siSRd5io&e=>,
>     @biocollective
>     <https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_biocollective&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=8pX0Br54uLoNQ-PxHY_Nt9ks6sIqSjFiajTJf6yTLYE&s=WcTsfij98jsXskRk-5qag6ax8_-PZrtIZ5o5R_QV-VQ&e=>
>
>     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 <mailto: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 <mailto: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
>>>         <mailto: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
>>>             theInternational 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> <mailto: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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>>
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