[Vp-reproduce-subgroup] White paper submitted
Jacob Barhak
jacob.barhak at gmail.com
Wed Apr 28 18:37:52 PDT 2021
Sure Reinhard,
Transparency is part of the procedure we took in assembling this paper.
This is why I asked James to write to the entire group. I asked the same
from many people in this subgroup.
Your request is especially import to go public so that everyone wil be
aware of it. I really an trying to be as transparent as possible.
Please check the current version. If its not sufficient, it can be
corrected further.
The reason the working group was put at the title was to avoid an issue of
authors arguing about ranking. I have seen those before, although not in
this group, and although those are part of human nature, such matters are
non productive, so I tried to eliminate them. Also, one idea was to put
the mailing list as the corresponding author. We do not know how long
people will be active in the group, yet if we put the mailing list rather
than the author emails, there is a better chance that someone active will
answer correspondence. So there are practical aspects here to consider.
The paper was after all assembled by a group that collaborated under that
hat of the working group. So the affiliation is important here. Please read
the paper, it actually describes how it was formed.
Reinhard, I understand your concerns about how things were viewed. Yet I
think you are covered from a legal perspective by the disclaimer I added
and by the fact that all contributions can be traced back to the authors
through the google docs.
However, Reinhard, in the subgroups we do form opinions and those are
structured in a hierarchical order. So the affiliation exists by the
structure you created. If you want to break the legal affiliation, you
should also break the structure you created.
More than that, this paper was tasked by the leads. So once it is formed,
you cannot really detach it from the working group. You asked for it.
Yet I think that the disclaimer will do the trick for what you asked.
Hopefully it puts this matter to rest.
Jacob
On Wed, Apr 28, 2021, 19:43 Laubenbacher,Reinhard <
Reinhard.Laubenbacher at medicine.ufl.edu> wrote:
> Jacob,
> let me make some comments in my role as co-lead of this working group.
> I am not an author of this manuscript, nor have I read it carefully, and I
> am not commenting on the content or the format.
>
>
> 1. I believe that it was absolutely appropriate for James to write to
> you, as the de facto corresponding author of the manuscript. This has
> nothing to do with transparency, as you implicate, inappropriately.
> 2. Anybody who sees this manuscript will assume that it originates
> from the working group as a whole. Nobody is going to wait until they get
> to the end to see author contributions. This is a problem for several
> reasons, potentially a really big one. First of all, it misrepresents
> authorship, since the vast majority of the approx. 200 members of the group
> have never seen this document. And, since the working group is
> semi-officially "sanctioned" by the NIH, this could be construed as
> presenting official positions of the NIH. So, I request that you a) list
> all authors of the manuscript, presumably with their permission, at the
> beginning of the manuscript. You can make a reference to the WG in a number
> of appropriate ways, for instance thanking the WG for discussions that
> helped develop ideas, etc. b) add a disclaimer that the opinions
> expressed in the manuscript are those of the authors alone and not the NIH.
> Otherwise, the leadership of the WG could face significant legal issues, as
> I am sure you can appreciate.
>
> James and I plan to have a discussion in the steering group meeting on
> Friday about proper procedures for such issues.
>
> Thank you.
> Reinhard
>
> ------------------------------
> *From:* Jacob Barhak <jacob.barhak at gmail.com>
> *Sent:* Wednesday, April 28, 2021 7:21 PM
> *To:* James A Glazier <jaglazier at gmail.com>
> *Cc:* Laubenbacher,Reinhard <Reinhard.Laubenbacher at medicine.ufl.edu>;
> Shapiro, Bruce <Bruce.Shapiro at medicine.ufl.edu>; James Sluka <
> JSluka at indiana.edu>; vp-integration-subgroup at lists.simtk.org <
> vp-integration-subgroup at lists.simtk.org>;
> vp-reproduce-subgroup at lists.simtk.org <
> vp-reproduce-subgroup at lists.simtk.org>; John Gennari <gennari at uw.edu>;
> Winston Garira <Winston.Garira at univen.ac.za>
> *Subject:* Re: White paper submitted
>
> *[External Email]*
> Greeting contributors,
>
> Below is an email James Glazier sent yesterday - he did not reply all, yet
> I think this should be made public.
>
> James, we were clear about the contributors at the end of the manuscript -
> we can certainly add a disclaimer. I changed the title draft and added a
> disclaimer sentence after the contributors list in the draft.
>
> When submitted to Cureus the names of the contributors were used as
> authors so it was a non-issue. If you choose to submit to iScience you can
> do the same. You still owe the group an answer if you choose to go in that
> direction or we reopen a venue. And BioArXiv was banned by Sheriff, so we
> cannot go there anyway unless he removes is objection.
>
> Also note that I got a response from Cureus editor to my query about the
> rejection. In short he is open to resubmission after revisions - his topic
> editor found the paper confusing. However, I asked that he provides a
> proper review - the amount of work invested in formatting alone deserves a
> proper review rather than a laconic answer. If we get proper review, I
> suggest considering this option. In the mean time I suggest we move forward
> considering other alternatives.
>
> I do ask we move forward fast - the value of the paper is significant
> already and discussions on style will delay it and reduce the impact.
>
> Hopefully we can move this forward quickly.
>
> Jacob
>
>
>
> On Tue, Apr 27, 2021 at 12:52 PM James A Glazier <jaglazier at gmail.com>
> wrote:
>
> Dear Jacob:
>
> Reinhard and I have reviewed the document you say that you circulated in
> your email below. If that is indeed the document that you submitted, there
> is a critical issue that will need to be addressed. The paper currently
> says it is written "by the WG." It was indeed written by several members of
> the WG, but since it was not approved by all members of the WG, you can't
> say that it is "by the WG," which implies endorsement by all members. My
> comment approving the draft was based on the substantive content of the
> draft. I did not realize that you would present it as "by the WG" instead
> of with a normal author list and affiliations. It should also not be posted
> in its current form on biorxiv or any other venue without a proper author
> list. If it is currently posted anywhere, the version will have to be
> updated to remove the implied endorsement by the WG.
>
> We can discuss with you appropriate ways to credit the working group.
>
> JAG
> On 4/26/2021 7:40 PM, Jacob Barhak wrote:
>
> Sorry James,
>
> This was a clear cut rejection upfront - declared as final decision. The
> editor is checking what happened - it is not what you think - there is
> history there - I quoted the editor his own words from last year and the
> response practically contradicts his words - there is a problem here and it
> is not with the paper.
>
> The paper has sufficient information to be worth publishing as a review -
> if academic journals do not see this, the problem is with them. This is
> not rushed work - and two days were invested into formatting to fit the
> venue - this is not raw material - it has been processed. I deserve peer
> review and this was denied.
>
> James - I proved once that the academic publication system is not working
> by submitting one paper to and just jumping from journal to journal until
> publication - almost in original form - the process took around 4 years and
> around 9 Journals - this is how I learned that the system is broken and
> also learned that that some venues are more problematic that others-
> Elsevier and PLOS were specifically problematic and hence I avoid them.
>
> To move things forward, please just decide if you want to submit it to
> iScience or let us elect another journal. It will be faster and better that
> way.
>
>
> Jacob
>
>
>
>
>
> On Mon, Apr 26, 2021 at 5:39 PM James A Glazier <jaglazier at gmail.com>
> wrote:
>
> Dear Jacob:
>
> The issue was not one of formatting in a technical sense, but rather that
> the material in the draft was not sufficiently integrated. The editor
> specifically mentioned that we call the document a white paper in the text,
> when it should be called an article and correctly noted that it looked like
> the report of a discussion panel rather than an article.
>
> Ultimately, this response means that turning the current draft into
> something publishable will be more work. It will have to be integrated more
> carefully and duplicate materials and inconsistencies eliminated. You need
> to decide if this effort is worthwhile for you.
>
> I expect that almost any journal will respond similarly.
>
> JAG
> On 4/26/2021 4:27 AM, Jacob Barhak wrote:
>
> Greetings white paper contributors,
>
> Cureus returned an answer regarding the white paper - they declined the
> submission - in short the rejection is based on style and journal scope.
>
> Since I used the tools provided by the Journal to do the formatting,
> especially of the references - I am confused - I will write the editor, yet
> I suggest we move on to the next voted selection of iScience.
>
> I will start the process quickly and hopefully we will have a better
> response this time.
>
> Jacob
>
>
> #### CureUS response ####
>
>
> Dear authors,
>
> Thank you for your submission. Unfortunately, we must decline this article
> because its practical utility to the medical community is unclear. The
> overall impression one gets from the article is that it has been written
> more in the style of a colloquial summary of a panel discussion than a
> review. This impression is further confirmed by the fact that the article
> refers to itself twice as a white paper. In addition, little attempt has
> been made to adhere to the Cureus author guide (
> https://www.cureus.com/author_guide
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cureus.com_author-5Fguide&d=DwMFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=IhVKTHWPVZrs3-x_k5EgLLBllwafYlq_orZAnMh_4h4&s=0XqFWZp8ZRRGzcyyZ_KZSX-AK8qa6bH6R0kSj5X3Pfw&e=>).
> Specifically, author affiliations contain acronyms, the subheadings are not
> in the sentence case, spaces and bulleted lists have been used haphazardly
> throughout the article, and reference formatting is almost nonexistent.
>
> We would encourage you to submit your next article to Cureus provided it
> falls within the scope of the journal. Thanks for your time.
>
> On Thu, Apr 22, 2021 at 4:50 AM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
>
> Greetings White paper contributors,
>
> Since no objection was raised the paper was just submitted to Cureus as
> previously elected.
>
> You will find an updated version after changes necessary for submission
> were implemented in this link:
>
> 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=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=IhVKTHWPVZrs3-x_k5EgLLBllwafYlq_orZAnMh_4h4&s=_598dcguG3wVco_CINP2EdTUlGyrC3sS-AKh6jw95Ks&e=>
>
>
> The changes were mostly minor typos and reference management - a few
> references needed correction and one was deleted since it no longer showed
> any relevant information.
>
> to give you all perspective - only formatting and handling of references
> towards publication in the necessary format took 2 work days dedicated for
> this alone.
>
> So all those who want to add anything to the paper to be considered post
> review, I urge you to:
> 1. submit any changes now - do not wait - once the review is returned no
> changes or additions will be considered and my experience is that Cureus
> provides review rapidly, so time is limited.
> 2. If you add references, please provide a DOI / link to help process
> those. And please avoid adding many references - processing those takes a
> long time.
> 3. Do not send changes to me alone using reply - please use REPLY ALL so
> everyone will see the discussion - we want to be as transparent as possible
>
>
> I hope for a quick review process.
>
> Jacob
>
>
> On Fri, Apr 16, 2021 at 6:08 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
>
> Greetings white paper contributors
>
> The voting period on the venue has ended and the selected venue we will
> send the white paper to is Cureus.
>
> John Rice and myself voted for that venue and will cover the publication
> fees.
>
> In case of any issue with this venue we will move to iScience that James
> Gazier voted for.
>
> The paper will need formatting to fit the venue - it handles references in
> a specific way. However, I intend to mostly cut and paste the text in this
> version - without change:
>
> 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=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=IhVKTHWPVZrs3-x_k5EgLLBllwafYlq_orZAnMh_4h4&s=_598dcguG3wVco_CINP2EdTUlGyrC3sS-AKh6jw95Ks&e=>
>
> The process we went through ensures we reach a level of consensus and that
> the manuscript can be legally submitted on behalf of you all. If anyone has
> any strong objections to stop the submission process, please stop now.
> Otherwise I will start the submission process next week.
>
> Please remember this is a large team with many people so there will be
> compromises. Moreover, the paper will undergo review and we will have to
> make changes.
>
> During the writing process I presented some deadlines and denied
> contributions that happened after the deadline was over. I know Tomas
> Halikar wanted to contribute and now Jim Saluka wants to contribute. I also
> know John Gennari schedule prevented him from properly reviewing the paper
> and I know that Sheriff asked for several modifications. All this can be
> corrected when the paper gets reviewed and we get the review - we will then
> open the paper for modifications and potentially other contributions.
> However, the time then will be limited, so to conserve time, I suggest that
> those interested in changes or additions, continue the discussion in
> parallel to the formal submission process.
>
> Cureus review process is typically quick compared to many venues I
> encountered in the past. Once the paper comes back from review we will have
> limited time to respond, so to conserve time I will consider only text that
> we submitted and contributions.modifications made until that time. So if
> you have any important additions, please create your own copy of the
> document and publicly share the link with these mailing lists. Similar to
> what Sheriff did.
>
> So please do not stop discussion on the paper - As Jonathan Karr
> suggested, we may have different versions suitable for different venues so
> your contributions are valuable - however, for the sake of getting our work
> published I ask that we do things in a timely manner.
>
> Again, if you have things to communicate about the paper - do not wait
> until review is back - it will be too late then - instead comment now so
> your contributions can be considered when post review modifications start.
>
> I hope we have a fast review and can make this work amplified by Cureus
> soon.
>
> Jacob
>
>
>
> On Thu, Apr 15, 2021 at 7:13 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
>
> Greetings Contributors,
>
> Since there are only a few hours before the voting period ends, I will
> vote to break a tie between CureuUs and iScience.
>
> I was about to abstain, yet it seems the tie needs to be broken
> distinctively.
>
> I will vote for Cureus. My reasons are:
> - I am familiar with this venue submission process
> - the venue has opened up to allow more references - thus dismissing my
> original remark on it
> - I will be the person handling submission and it will save me time to
> submit somewhere familiar.
> - The review process in this venue is relatively fast.
> - It has an option for rushed pubmed central publication
> - the open publication costs are reasonable compared to many other venues
>
> Unless 3 other people will vote for another venue in the next few hours,
> it seems this is the venue that the paper will be submitted to for review.
> However, things may change.
>
> John and I will split the publication costs since we both voted on this
> venue. If anyone else wants to split costs, feel free to publicly vote for
> this venue - otherwise it will be John and myself.
>
> Please note that there are a few more hours to vote - a bit less than 6
> hours from the time of this email - if you support another conclusion for a
> venue, you are welcome to vote.
>
> Jacob
>
>
>
>
> On Wed, Apr 14, 2021 at 11:03 AM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
>
> Greetings white paper contributors,
>
> Please vote on a venue for the paper. There are less than two days to vote
> to influence the submission venue.
>
> We had 2 votes by now
> Cureus by John Rice
> iScience by James Glazier
>
> John Rice was first, yet did not reply to all as requested and sent me
> the email - I forwarded his vote to the list first. James was the first
> that replied to all, so technically he is the first valid vote.
>
> So currently there is a tie that should be broken by first vote which is
> open to interpretation. Since time is running out, I suggest people choose
> to make the choice distinctive, otherwise I will vote to break the tie and
> was hoping to avoid voting since I had a lot of influence already and
> wanted to yield control.
>
> So please, if you have a preference on venue, please vote for one venue
> by 1am CDT April 16th.
>
>
> I hope we have a conclusive decision.
>
> Jacob
>
>
>
>
> On Mon, Apr 12, 2021, 17:17 James Glazier <jaglazier at gmail.com> wrote:
>
> iScience
> James A. Glazier
>
> On Mon, Apr 12, 2021 at 12:40 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
>
> Greetings White paper Contributors,
>
> This is your chance to decide on the venue. If you name is on this list,
> please take a few minutes anv vote for the venue:
> Jonathan Karr
> Rahuman Sheriff
> James Osborne
> Gilberto Gonzalez Parra
> Eric Forgoston
> Ruth Bowness
> Yaling Liu
> Robin Thompson
> Winston Garira
> Marcella Torres
> Hana M. Dobrovolny
> Tingting Tang
> William Waites
> James Glazier
> James R. Faeder
>
> Currently one vote was cast and unless there will be more votes, the venue
> voted for will be chosen. So if you have a strong preference, this is your
> chance to influence the publication venue.
>
> You will find eligible venues below as well as additional details.
>
> I look forward to your votes.
>
> Jacob
>
>
>
> On Thu, Apr 8, 2021 at 7:04 PM John Rice <john.rice at noboxes.org> wrote:
>
> No objection to any but will VOTE CUREUS.
>
> My understanding it was created to provide a peer reviewed open source
> indexed journal that could accommodate new forms of papers and new relevant
> topical areas. Good timing for them lifting the limit on references, so
> assume this paper could be submitted in current form subject only to
> reviewers’ response.
>
> Don’t know that it has a model credibility related topic section yet.
>
> John
>
>
>
> Typed with two thumbs on my iPhone. (757) 318-0671
>
> “Upon this gifted age, in its dark hour,
> Rains from the sky a meteoric shower
> Of facts . . . they lie unquestioned, uncombined.
> Wisdom enough to leech us of our ill
> Is daily spun; but there exists no loom
> To weave it into fabric.”
>
> –Edna St. Vincent Millay,
>
>
>
> On Apr 8, 2021, at 01:23, Jacob Barhak <jacob.barhak at gmail.com> wrote:
>
>
> Greeting White paper contributors,
>
> The old Thread that contained discussions towards creations and approval
> of the white paper have become too long, so I started a new maling thread.
>
> You can find the old discussion thread here:
>
> https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-April/000052.html
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.simtk.org_pipermail_vp-2Dreproduce-2Dsubgroup_2021-2DApril_000052.html&d=DwMFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=IhVKTHWPVZrs3-x_k5EgLLBllwafYlq_orZAnMh_4h4&s=8leyv5HlkO-_Bz-45yTUPP7KdOU8XYkSyMHpttk_yQg&e=>
>
> To summarize, we have reached a point where 17 authors approved the
> following version for submission, pending some minor changes like
> spelling and grammar correction.
>
> To avoid any confusion - here is the paper version we approved is here:
>
> 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=sJ6xIWYx-zLMB3EPkvcnVg&r=V2tasLrHIoHXI4x389UktfPi_k0_MebL7A4aArl8_-pi3_iSbG9bbq-XW0FJK4zM&m=IhVKTHWPVZrs3-x_k5EgLLBllwafYlq_orZAnMh_4h4&s=_598dcguG3wVco_CINP2EdTUlGyrC3sS-AKh6jw95Ks&e=>
>
> At this point we need to select a venue to submit the paper to. Here is a
> short list I collected after incorporating all the suggestions and removed
> all venues that had any objections. To your convenience I added additional
> notes form personal knowledge - I did not look at issues such as
> publication fees for open access - different venues may have different
> rules and may require some additional investment, so please look at the
> venue you are choosing and learn the limitations/benefits before you vote:
>
> Here is the short list:
>
> 1. Cureus - will require cutting out some references due to limitation
> 2. Nature - if you vote for this venue please specify flavour such as
> Nature Scientific Reports
> 3. Science
> 4. Briefings in Bioinformatics
> 5. Trends in Biotechnology - requires distilling the paper
> 6. Journal of The Royal Society Interface
> 7. Annual Review of Public Health
> 8. BMJ
> 9. Annual Review of Biomedical Engineering
> 10. F1000research - if you vote for this this venue please
> specify Gateway / Collection
> 11. iScience
> 12. bulletin of mathematical biology
> 13. Bioinformatics.
>
>
> I ask that each contributor who has a preference among those Journals
> reply to all to this message and pick one venue. Please pick only one
> considering all aspects of the venue. You are welcome to include your
> reasoning, yet vote towards only one venue. You are welcome to change your
> mind - yet only your last vote will count.
>
> In case of a tie in the number of votes, the venue that got the first
> counted vote will be chosen.
>
> After we select, I will put the work to format the submission towards that
> venue and include all necessary submission matters. In case of fees, those
> who voted for the venue will be responsible for covering publication fees.
>
> At this point I assume no one has any objections to any venues and we are
> all ok with submitting this version - so we are just prioritizing according
> to the majority of wishes while keeping the process transparent and giving
> some incentive to early bird vote.
>
> If any of my assumptions are not correct, please correct me now!
>
> This is the best way I think we can create consensus in such a large group
> - and consensus is legally necessary for publication.
>
> I ask that we limit the voting time to approximately one week. So votes
> should be cast by 1am April 16th CDT.
>
> I will send another reminder during this week, yet I assume one week is
> sufficient to make a simple choice of prefered venue and those not voting
> elect to abstain from choosing and prefer the majority choice.
>
> I look forward to your votes.
>
> Jacob
>
>
>
> _______________________________________________
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>
>
>
> --
> James A. Glazier
> Indiana University
>
> --
> James A. Glazier, PhD
> Professor of Intelligent Systems Engineering, Adjunct Professor of Physics
> Director, Biocomplexity Institute
> Indiana University, Bloomington
> (812) 391-2159 (cell)
>
> --
> James A. Glazier, PhD
> Professor of Intelligent Systems Engineering, Adjunct Professor of Physics
> Director, Biocomplexity Institute
> Indiana University, Bloomington
> (812) 391-2159 (cell)
>
>
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