[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
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>
> 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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