Jacob, you should probably also read this paper:
Minimum information requested in the annotation of biochemical models
(MIRIAM)
https://www.nature.com/articles/nbt1156
On 8/23/20 1:09 PM, Jacob Barhak wrote:
> Smart Choice Sheriff,
>
> This type of license is compatible with reuse in many scenarios
> including academia and industry.
>
> Happy to learn you made a good choice. I will be sure to mention
> biomodels as an example of good reasoning about licences.
>
> Jacob
>
>
> On Sun, Aug 23, 2020, 10:57 Rahuman Sheriff <
she...@ebi.ac.uk
> <mailto:
she...@ebi.ac.uk>> wrote:
>
> Thanks Jacob,
>
> All work we do in BioModels are under CC0. The models we curated are
> free to access and use under CC0.
>
> Thanks for your suggestions
>
> Best regards
> Sheriff
>
>
>> On 21 Aug 2020, at 06:16, Jacob Barhak <
jacob....@gmail.com
>> <mailto:
jacob....@gmail.com>> wrote:
>>
>> Yes Sheriff,
>>
>> You should continue doing good work. We both agree there.
>>
>>
>> Yet the community needs to expand beyond the academic endeavour
>> and work on becoming a proper standard. The current state where
>> people refer to SBML as as standard while it is not formalized is
>> not a good idea and has negative consequences. I suggest the term
>> specification should be used in publication until a formal
>> standard is issued.
>>
>> Also in your scoring mechanism you should include a score for
>> licensing. Not all licences are the same and some are more
>> problematic than others for reuse.
>>
>> You should give public-domain-like licences such as CC zero higher
>> scores than other licences that may create issues. I have done
>> some indemnification work in the past and had to score open
>> software packages according to multiple criteria and I remember
>> the difficulties.
>>
>> When you start discussing adding license components to your
>> score, do feel free to start the discussion online. I think I can
>> contribute some ideas.
>>
>> Jacob
>>
>>
>> On Thu, Aug 20, 2020, 19:16 Rahuman Sheriff <
she...@ebi.ac.uk
>> <mailto:
she...@ebi.ac.uk>> wrote:
>>
>>
>>
>>> On 20 Aug 2020, at 07:48, Jacob Barhak
>>>> <
jacob....@gmail.com <mailto:
jacob....@gmail.com>>
>>> <
https://www.omicsdi.org/> platform for this purpose.
>>>>> <
mack...@iu.edu <mailto:
mack...@iu.edu>> wrote:
>>>>>
>>>>> Hmm, wasn’t actually arguing for a tax – just that
>>>>> in the current landscape, doing the extra work for
>>>>> reproducibility itself is a tax compared to those
>>>>> who publish without.____
>>>>> __ __
>>>>> Thanks for other points – Paul____
>>>>> __ __
>>>>>
>>>>>
>>>>> ____
>>>>> *Sorry for brevity of response – deeply immersed in
>>>>> covid19 work right now.____*
>>>>> ____
>>>>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>>>>> *Paul Macklin, Ph.D.
>>>>> *Associate Professor____
>>>>> Director of Undergraduate Studies
>>>>> *Intelligent Systems Engineering
>>>>> **Indiana University
>>>>> *
>>>>> Founder and Lead of PhysiCell
>>>>> <
http://physicell.mathcancer.org/> and MultiCellDS
>>>>> <
http://multicellds.org/>
>>>>> mobile:
626-372-1203 <tel:(626)%20372-1203>
>>>>> email:
mack...@iu.edu <mailto:
mack...@iu.edu>
>>>>> email: Paul.M...@MathCancer.org
>>>>> <mailto:
Paul.M...@MathCancer.org>
>>>>> web:
http://MathCancer.org <
http://mathcancer.org/>
>>>>> Twitter: @MathCancer
>>>>> <
http://www.twitter.com/MathCancer>
>>>>> ____
>>>>> __ __
>>>>> *From:*
sbml-d...@googlegroups.com
>>>>> <mailto:
sbml-d...@googlegroups.com>
>>>>> <
sbml-d...@googlegroups.com
>>>>> <mailto:
sbml-d...@googlegroups.com>>*On Behalf
>>>>> Of*Jacob Barhak
>>>>> *Sent:*Tuesday, August 11, 2020 7:12 PM
>>>>> *To:*sbml-discuss <
sbml-d...@googlegroups.com
>>>>> <mailto:
sbml-d...@googlegroups.com>>
>>>>> *Subject:*Re: [External] Re: [sbml-discuss] About
>>>>> half of the systems biology models could not be
>>>>> reproduced !!!____
>>>>> __ __
>>>>> Yes Paul,____
>>>>> __ __
>>>>> You raise some good points. ____
>>>>> __ __
>>>>> Technically SBML is perhaps the best technical
>>>>> specification I know for sharing models -
>>>>> despite not being a standard. and despite other
>>>>> shortcomings.____
>>>>> __ __
>>>>> Introducing a tax on publication to incentivizing
>>>>> reproducibility through reforming the
>>>>> publication system makes sense. I am not sure how
>>>>> to approach it since the publication system is
>>>>> decentralized and there is no common standard it
>>>>> adheres to other than some laws that change from
>>>>> location to location. If you have ideas, those can
>>>>> be discussed, yet it is a hard problem - I am not
>>>>> sure I have good suggestions - perhaps someone else
>>>>> has. .____
>>>>> __ __
>>>>> As for acceptance by a standard body - it is very
>>>>> important for dissemination. You see, the group
>>>>> dynamics that I witnessed when I suggested an SDO
>>>>> was such that reflects badly on the SBML community.
>>>>> Those bad examples represent control that is not
>>>>> property handled by a group of academics. However,
>>>>> this is not the discussion here. I rather see
>>>>> solutions and I believe that going through the
>>>>> legal process will fix things. ____
>>>>> __ __
>>>>> LGPL is better than other licenses, yet the copy
>>>>> left element is really problematic for the long
>>>>> term. In fact, GPL use has been declining. Also the
>>>>> legal Copyright mechanism that drives open source
>>>>> licenses has issues. You see, it gives control to
>>>>> the copyright holder than can be misused and
>>>>> disincentivize development and should not really
>>>>> appear in government funded work after funding goes
>>>>> away. There are better solutions these days that I
>>>>> mentioned in the discussion link I sent. If you
>>>>> want to discuss licenses, let us discuss those in
>>>>> the other link since I am not sure it will interest
>>>>> the SBML community in this thread and most of the
>>>>> discussion in there already. ____
>>>>> __ __
>>>>> And as for the COVID-19 model - feel free to
>>>>> contact me directly - it is not SBML related - SBML
>>>>> still cannot support all the mechanisms needed to
>>>>> implement it and funding to allow it has been
>>>>> denied. However, I will be happy to discuss it
>>>>> privately. ____
>>>>> __ __
>>>>> Hopefully separating discussions will help everyone
>>>>> focus.____
>>>>> __ __
>>>>> Jacob____
>>>>> __ __
>>>>> __ __
>>>>> __ __
>>>>> On Tue, Aug 11, 2020 at 5:16 PM Macklin, Paul
>>>>> <
mack...@iu.edu <mailto:
mack...@iu.edu>> wrote:____
>>>>>
>>>>> Thanks Jacob.____
>>>>> ____
>>>>> I’d definitely agree that this as much or more
>>>>> a cultural / social issue than a technical
>>>>> issue. Now that the technical bottlenecks of
>>>>> “can a model be shared” have been solved in
>>>>> some key domains thanks to very hard work by
>>>>> the members here, there can be work on making
>>>>> sure it happens. Publishing, granting agencies,
>>>>> and promotion/tenure groups at large do not
>>>>> incentivize reproducible / repeatable work over
>>>>> non-reproducible / non-repeatable work. They
>>>>> currently incentivize novelty and
>>>>> first-to-publish, making reproducibility a
>>>>> dis-incentivized performance tax. These and
>>>>> other incentives / dis-incentives have been
>>>>> active topics of discussion by the scientific
>>>>> community for a long time.____
>>>>> ____
>>>>> Acceptance by a standards body does not change
>>>>> any of that, and there’s still disagreement on
>>>>> who gets to the gatekeepers on what is / isn’t
>>>>> a standard, what is “proper”, etc. I’d trust
>>>>> scientific experts in the domain over an
>>>>> external organization outside of the domain of
>>>>> expertise. If there is an SDO that’s relevant
>>>>> to this community, I’d be very interested to
>>>>> hear it.____
>>>>> ____
>>>>> I was a little puzzled by your point on lack of
>>>>> proper licenses. LGPL—the license of libSBML—is
>>>>> a proper, standardized license that has allowed
>>>>> very good interoperability of open source
>>>>> software. Do you perhaps you mean data reuse
>>>>> licenses?____
>>>>> ____
>>>>> Thanks for pointing out your covid19 work –
>>>>> looking forward to reading it!____
>>>>> ____
>>>>> And thank you for your discussion. While I
>>>>> personally don’t agree with some of your
>>>>> points, I agree with the goals of open
>>>>> transparent and reproducible science, and I’m
>>>>> grateful for the discussion.____
>>>>> ____
>>>>> Very best – Paul ____
>>>>>
>>>>> ____
>>>>>
>>>>> *Sorry for brevity of response – deeply
>>>>> immersed in covid19 work right now.*____
>>>>> ____
>>>>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>>>>> *Paul Macklin, Ph.D.
>>>>> *Associate Professor____
>>>>> Director of Undergraduate Studies
>>>>> *Intelligent Systems Engineering
>>>>> **Indiana University
>>>>> *
>>>>> Founder and Lead of PhysiCell
>>>>> <
http://physicell.mathcancer.org/> and
>>>>> MultiCellDS <
http://multicellds.org/>
>>>>> mobile:
626-372-1203 <tel:(626)%20372-1203>
>>>>> email:
mack...@iu.edu <mailto:
mack...@iu.edu>
>>>>> email: Paul.M...@MathCancer.org
>>>>> <mailto:
Paul.M...@MathCancer.org>
>>>>> web:
http://MathCancer.org <
http://mathcancer.org/>
>>>>> Twitter: @MathCancer
>>>>> <
http://www.twitter.com/MathCancer>
>>>>> ____
>>>>> ____
>>>>> *From:*
sbml-d...@googlegroups.com
>>>>> <mailto:
sbml-d...@googlegroups.com><
sbml-d...@googlegroups.com
>>>>> <mailto:
sbml-d...@googlegroups.com>>*On
>>>>> Behalf Of*Jacob Barhak
>>>>> *Sent:*Tuesday, August 11, 2020 5:30 PM
>>>>> *To:*sbml-discuss
>>>>> <
sbml-d...@googlegroups.com
>>>>> <mailto:
sbml-d...@googlegroups.com>>
>>>>> *Subject:*Re: [External] Re: [sbml-discuss]
>>>>> About half of the systems biology models could
>>>>> not be reproduced !!!____
>>>>> ____
>>>>> Well Paul,____
>>>>> ____
>>>>> This is not about the star. It is about what
>>>>> this star means. ____
>>>>> ____
>>>>> We had this discussion before and an extended
>>>>> group of SBML editors declined joining an SDO
>>>>> and adopting proper procedures. ____
>>>>> ____
>>>>> I am not about to repeat the discussion - I
>>>>> also have little time and am also working on a
>>>>> newer version of my COVID-19 model as you can
>>>>> see from my link.____
>>>>> ____
>>>>> However, if someone is looking at this from the
>>>>> outside and has to decide if to adopt SBML, it
>>>>> doesn't give them an incentive - the group uses
>>>>> the terminology standard, yet does not invest
>>>>> the effort to handle the legal structure .
>>>>> However, to go back on track, even if SBML
>>>>> would become a formal standard, there should be
>>>>> more incentives for modelers to make
>>>>> things reproducible and some of those issues
>>>>> are discussed in the link I provided. It is a
>>>>> larger scope discussion that is less technical
>>>>> in nature. ____
>>>>> ____
>>>>> When you find time, feel free to join that
>>>>> discussion and look at what suggested solutions
>>>>> make sense. ____
>>>>> ____
>>>>> Jacob____
>>>>> ____
>>>>> ____
>>>>> ____
>>>>> ____
>>>>> ____
>>>>> On Tue, Aug 11, 2020 at 4:15 PM Macklin, Paul
>>>>> <
mack...@iu.edu <mailto:
mack...@iu.edu>>
>>>>> wrote:____
>>>>>
>>>>> An ISO or related gold star does nothing to
>>>>> incentivize using a standard.____
>>>>> ____
>>>>> If it’s useful (e.g., in giving access to a
>>>>> powerful ecosystem of compatible tools), it
>>>>> was already useful without the gold star.____
>>>>> ____
>>>>> ____
>>>>> ____
>>>>>
>>>>> ____
>>>>>
>>>>> *Sorry for brevity of response – deeply
>>>>> immersed in covid19 work right now.*____
>>>>> ____
>>>>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>>>>> *Paul Macklin, Ph.D.
>>>>> *Associate Professor____
>>>>> Director of Undergraduate Studies
>>>>> *Intelligent Systems Engineering
>>>>> **Indiana University
>>>>> *
>>>>> Founder and Lead of PhysiCell
>>>>> <
http://physicell.mathcancer.org/> and
>>>>> MultiCellDS <
http://multicellds.org/>
>>>>> mobile:
626-372-1203 <tel:(626)%20372-1203>
>>>>> email:
mack...@iu.edu <mailto:
mack...@iu.edu>
>>>>> email: Paul.M...@MathCancer.org
>>>>> <mailto:
Paul.M...@MathCancer.org>
>>>>> web:
http://MathCancer.org
>>>>> <
http://mathcancer.org/>
>>>>> Twitter: @MathCancer
>>>>> <
http://www.twitter.com/MathCancer>
>>>>> ____
>>>>> ____
>>>>> *From:*
sbml-d...@googlegroups.com
>>>>> <mailto:
sbml-d...@googlegroups.com><
sbml-d...@googlegroups.com
>>>>> <mailto:
sbml-d...@googlegroups.com>>*On
>>>>> Behalf Of*Jacob Barhak
>>>>> *Sent:*Tuesday, August 11, 2020 4:36 PM
>>>>> *To:*sbml-discuss
>>>>> <
sbml-d...@googlegroups.com
>>>>> <mailto:
sbml-d...@googlegroups.com>>
>>>>> *Subject:*[External] Re: [sbml-discuss]
>>>>> About half of the systems biology models
>>>>> could not be reproduced !!!____
>>>>> ____
>>>>> This message was sent from a non-IU
>>>>> address. Please exercise caution when
>>>>> clicking links or opening attachments from
>>>>> external sources.____
>>>>> ____
>>>>> Hi Sheriff,____
>>>>> ____
>>>>> Indeed you provide another example on why
>>>>> models should be reproducible. However,
>>>>> there are many obstacles on the way - some
>>>>> of those are not technical. Allow me to
>>>>> point to a recent open discussion that will
>>>>> reveal other issues:____
>>>>>
https://forum.comses.net/t/issues-with-regard-to-call-for-transparency-of-covid-19-models/8433/8
>>>>> ____
>>>>> ____
>>>>> You see, to allow transparency, one needs
>>>>> to create a proper environment. It is one
>>>>> thing pointing to the problem, another is
>>>>> trying to solve the problem. The solution
>>>>> should provide an incentive for others to
>>>>> use it. Currently there is no such good
>>>>> solution.____
>>>>> ____
>>>>> The SBML and COMBINE communities are trying
>>>>> to offer a solution, yet this solution is
>>>>> mostly technical , yet even the community
>>>>> solution they attempt to provide is far
>>>>> from sufficient since it does not provide
>>>>> an incentive. The inability to become a
>>>>> formal standard is one deterrent.____
>>>>> ____
>>>>> You referred to SBML as "standard SBML
>>>>> format" - this is a misconception. SBML is
>>>>> not a formal standard and is not issued by
>>>>> an SDO. SBML is a very nice specification
>>>>> driven by a community that is mostly
>>>>> government funded - I used it myself and
>>>>> think it has potential. However, why invest
>>>>> effort in a direction where its community
>>>>> includes objections to becoming a formal
>>>>> standard with all the legal elements?____
>>>>> ____
>>>>> This is one minor issue that needs mending
>>>>> to provide incentive to use SBML or other
>>>>> COMBINE standards. The link above describes
>>>>> other issues that need addressing,
>>>>> including proper licenses and use of
>>>>> government funding. ____
>>>>> ____
>>>>> Your paper did a first step of identifying
>>>>> the problem. I urge you to take the next
>>>>> step and join a larger discussion on how to
>>>>> create incentives and a proper environment.
>>>>> Your call to provide source code in a
>>>>> computer language is great, yet there is
>>>>> more to do. Hopefully you have ideas to
>>>>> contribute. ____
>>>>> ____
>>>>> Jacob____
>>>>> ____
>>>>>
>>>>> --
>>>>> Jacob Barhak Ph.D.
>>>>>
https://sites.google.com/view/jacob-barhak/home____
>>>>>
>>>>> ____
>>>>> ____
>>>>> <mailto:
jsl...@indiana.edu>> wrote:____
>>>>>
>>>>> Sheriff (and the SBML community in
>>>>> general)-____
>>>>> ____
>>>>> I quickly read the manuscript, nice
>>>>> work! Is there a published list of the
>>>>> models examined and their scores? I
>>>>> suspect that the reducibility of
>>>>> published models that don’t use a model
>>>>> standard like SBML is considerably
>>>>> lower than ~50%.____
>>>>> ____
>>>>> Jim____
>>>>> ____
>>>>> James P. Sluka, PhD
>>>>> Biocomplexity Institute____
>>>>> Intelligent Systems Engineering____
>>>>> School of Informatics, Computing and
>>>>> Engineering____
>>>>> Indiana University____
>>>>> Bloomington, IN USA____
>>>>> Office:
812-855-2441____
>>>>> Cell:
317-331-7465____
>>>>> JSl...@Indiana.edu
>>>>> <mailto:
JSl...@Indiana.edu>____
>>>>> ____
>>>>> ____
>>>>> ____
>>>>> *From:*
sbml-d...@googlegroups.com
>>>>> <mailto:
sbml-d...@googlegroups.com>[mailto:
sbml-d...@googlegroups.com
>>>>> <mailto:
sbml-d...@googlegroups.com>]*On
>>>>> Behalf Of*Rahuman Sheriff
>>>>> *Sent:*Tuesday, August 11, 2020 7:46 AM
>>>>> *To:*
sbml-discuss;combine...@googlegroups.com
>>>>> <mailto:
combine...@googlegroups.com>
>>>>> *Subject:*[sbml-discuss] About half of
>>>>> the systems biology models could not be
>>>>> reproduced !!!____
>>>>> ____
>>>>> Hi all____
>>>>> ____
>>>>> Sometimes ago there was a long thread /
>>>>> discussion on*reproducibility*in the
>>>>> SBML-dicuss mailing list. ____
>>>>> To continue on that topic, here is the
>>>>> contribution from BioModels.____
>>>>> ____
>>>>> Over the past 3 years we investigated
>>>>> >450 models published in 152 journals &
>>>>> identified the root cause for the lack
>>>>> of reproducibility. ____
>>>>> About half of models fail to directly
>>>>> reproduce simulation results! ____
>>>>> Read our #biorxiv_sysbio article
>>>>>
https://doi.org/10.1101/2020.08.07.239855____
>>>>> ____
>>>>> ____
>>>>> Our tweet here____
>>>>>
https://twitter.com/biomodels/status/1293148498565767168____
>>>>> ____
>>>>> ____
>>>>> Best regards____
>>>>> ____
>>>>> Sheriff____
>>>>> ____
>>>>> ____
>>>>>
>>>>> -----------------------------------------------------------------------
>>>>> Rahuman Sheriff PhD
>>>>> Project Leader - BioModels
>>>>> European Bioinformatics Institute
>>>>> European Molecular Biology
>>>>> Laboratory (EMBL-EBI)
>>>>> Welcome Trust Genome Campus
>>>>> Hinxton Cambridge CB10 1SD, UK
>>>>> Email:
she...@ebi.ac.uk
>>>>> <mailto:
she...@ebi.ac.uk>
>>>>> -----------------------------------------------------------------------
>>>>> We invite you to try the recent release
>>>>> of new BioModels platform at
>>>>>
http://www.ebi.ac.uk/biomodels/
>>>>> We would be grateful if you can
>>>>> send your suggestions through the
>>>>> dedicated feedback form on the new
>>>>> platform or at
>>>>>
biomodels-...@lists.sf.net
>>>>> <mailto:
biomodels-...@lists.sf.net>____
>>>>>
>>>>> ____
>>>>> --
>>>>> You received this message because you
>>>>> are subscribed to the Google Groups
>>>>> "sbml-discuss" group.
>>>>> To unsubscribe from this group and stop
>>>>> receiving emails from it, send an email
>>>>>
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>>>>> <mailto:
sbml-discuss...@googlegroups.com>.
>>>>> <
https://groups.google.com/d/msgid/sbml-discuss/20200811114604.5475A62AC85_F3284FCB%40hh-mx3.ebi.ac.uk?utm_medium=email&utm_source=footer>.____
>>>>> --
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>>>>> To unsubscribe from this group and stop
>>>>> receiving emails from it, send an email
>>>>>
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>>>>> <mailto:
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>>>>> To view this discussion on the web
>>>>> visithttps://
groups.google.com/d/msgid/sbml-discuss/3394c111991a477ea6e7a23d45bc5a09%40BL-CCI-D2S05.ads.iu.edu
>>>>> <
https://groups.google.com/d/msgid/sbml-discuss/3394c111991a477ea6e7a23d45bc5a09%40BL-CCI-D2S05.ads.iu.edu?utm_medium=email&utm_source=footer>.____
>>>>>
>>>>> --
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>>>>> To unsubscribe from this group and stop
>>>>> receiving emails from it, send an email
>>>>>
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>>>>> <mailto:
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>>>>> To view this discussion on the web
>>>>> visithttps://
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>>>>> <
https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3QBcAORygwSFeoVZKpvOEZtGjrQm%3DX5ZqL9itxmJwAnUA%40mail.gmail.com?utm_medium=email&utm_source=footer>.____
>>>>> --
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>>>>> To unsubscribe from this group and stop
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>>>>> To view this discussion on the web
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>>>>> <
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>>>>>
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>>>>> To view this discussion on the web
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>>>>> <
https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3Q9NzRjL-pocDeCkvfOjuWstTTK6pZKXafzYnEt1ETN3g%40mail.gmail.com?utm_medium=email&utm_source=footer>.____
>>>>> --
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>>>>> To unsubscribe from this group and stop
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>>>>> To view this discussion on the web
>>>>> visithttps://
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>>>>> <
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>>>>>
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>>>>> To view this discussion on the web
>>>>> visithttps://
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>>>>> <
https://groups.google.com/d/msgid/sbml-discuss/CAM_y%2B3QQsT4SaSW6jOcM9yahDc-gq1bH1oxt8mkRPnnu-udvww%40mail.gmail.com?utm_medium=email&utm_source=footer>.____
>>>>>
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>>>>
>>>>
>>>> --
>>>> You received this message because you are subscribed
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>>>> To unsubscribe from this group and stop receiving
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>>>>
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>>>> <mailto:
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>>>> To view this discussion on the web visit
>>>>
https://groups.google.com/d/msgid/sbml-discuss/A92158B8-82F3-4DAD-A659-8B78E8A5BD90%40ebi.ac.uk
>>>> <
https://groups.google.com/d/msgid/sbml-discuss/A92158B8-82F3-4DAD-A659-8B78E8A5BD90%40ebi.ac.uk?utm_medium=email&utm_source=footer>.
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