sed-ml-discuss — Migrating to google groups: https://groups.google.com/d/forum/sed-ml-discuss

Re: [SED-ML-discuss] The 'numberOfPoints' attribute

[Chris M. <my...@ec...>]

I think as long as the libraries are updated and a backwards compatible API function call exists, then it should not break software.  So, I would say the libraries should hide this alias from the user.  I’m fine though to make the specification say “numberOfSteps” for the new version.

Chris

> On Jun 27, 2017, at 1:20 PM, Herbert Sauro <uw....@gm...> wrote:
> 
> Given that the sedml community is still very small, it would be better to get it right at this early stage, hence I prefer option
> 
> 2) change the name to set thing else, e.g. numberOfSteps
> 
> For those clinging to earlier versions they can check the version of the sedml and interpret numberofpoints in the old way. In that sense I don't think it affects backward compatibility.
> 
> Herbett
> 
> 
> On Tue, Jun 27, 2017 at 1:08 PM Kyle Medley <me...@co... <mailto:me...@co...>> wrote:
> It seems to me that breaking backwards compatibility defeats one of the major advantages of having a standard encoding, so I would prefer option 1. If people are not happy with that, I have a different suggestion:
> 
> 4) Allow 'numberOfPoints', and do not change its meaning, but also create a new attribute 'numberOfSteps' with the same semantics. 'numberOfPoints' would not be deprecated.
> 
> Cheers,
> 
> Kyle
> 
> J Kyle Medley, PhD Candidate
> Bioengineering/BPSD, Sauro Lab
> University of Washington, Seattle
> skype: jkylemedley
> On 6/27/17 12:46 PM, Lucian Smith wrote:
>> At HARMONY, the issue was brought up that the 'numberOfPoints' attribute is confusing, because the literal number of expected points in the output file is one more than that: the initial conditions, and the number of *computed* points.
>> 
>> It was proposed that we fix this for SED-ML Level 1 Version 3.  There are a few options:
>> 
>> 1) No change:  simply make it more clear in the spec that 'numberOfPoints' means 'number of computed points' aka 'number of steps'.
>> 
>> 2) Change the name of the attribute to 'numberOfSteps' or possibly 'numberOfComputedPoints'.
>> 
>> 3) Deprecate but allow 'numberOfPoints', and make a new 'numberOfSteps' attribute that people are encouraged to use instead.
>> 
>> Any opinions?  It seems like the advantage is preventing future confusion, and the cost is having a non-backwards-compatible spec, and the cost of implementation changes for the groups that currently support SED-ML.
>> 
>> -Lucian
>> 
>> 
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot <http://sdm.link/slashdot>
>> 
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li... <mailto:SED...@li...>
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss>
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot <http://sdm.link/slashdot>_______________________________________________
> SED-ML-discuss mailing list
> SED...@li... <mailto:SED...@li...>
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot_______________________________________________ <http://sdm.link/slashdot_______________________________________________>
> SED-ML-discuss mailing list
> SED...@li... <mailto:SED...@li...>
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss>

Re: [SED-ML-discuss] The 'numberOfPoints' attribute

[Herbert S. <uw....@gm...>]

Given that the sedml community is still very small, it would be better to
get it right at this early stage, hence I prefer option

2) change the name to set thing else, e.g. numberOfSteps

For those clinging to earlier versions they can check the version of the
sedml and interpret numberofpoints in the old way. In that sense I don't
think it affects backward compatibility.

Herbett



On Tue, Jun 27, 2017 at 1:08 PM Kyle Medley <me...@co...> wrote:

> It seems to me that breaking backwards compatibility defeats one of the
> major advantages of having a standard encoding, so I would prefer option 1.
> If people are not happy with that, I have a different suggestion:
>
> 4) Allow 'numberOfPoints', and do not change its meaning, but also create
> a new attribute 'numberOfSteps' with the same semantics. 'numberOfPoints'
> would not be deprecated.
>
> Cheers,
>
> Kyle
>
> J Kyle Medley, PhD Candidate
> Bioengineering/BPSD, Sauro Lab
> University of Washington, Seattle
> skype: jkylemedley
>
> On 6/27/17 12:46 PM, Lucian Smith wrote:
>
> At HARMONY, the issue was brought up that the 'numberOfPoints' attribute
> is confusing, because the literal number of expected points in the output
> file is one more than that: the initial conditions, and the number of
> *computed* points.
>
> It was proposed that we fix this for SED-ML Level 1 Version 3.  There are
> a few options:
>
> 1) No change:  simply make it more clear in the spec that 'numberOfPoints'
> means 'number of computed points' aka 'number of steps'.
>
> 2) Change the name of the attribute to 'numberOfSteps' or possibly
> 'numberOfComputedPoints'.
>
> 3) Deprecate but allow 'numberOfPoints', and make a new 'numberOfSteps'
> attribute that people are encouraged to use instead.
>
> Any opinions?  It seems like the advantage is preventing future confusion,
> and the cost is having a non-backwards-compatible spec, and the cost of
> implementation changes for the groups that currently support SED-ML.
>
> -Lucian
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
> _______________________________________________
> SED-ML-discuss mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>

Re: [SED-ML-discuss] The 'numberOfPoints' attribute

[Kyle M. <me...@co...>]

It seems to me that breaking backwards compatibility defeats one of the 
major advantages of having a standard encoding, so I would prefer option 
1. If people are not happy with that, I have a different suggestion:

4) Allow 'numberOfPoints', and do not change its meaning, but also 
create a new attribute 'numberOfSteps' with the same semantics. 
'numberOfPoints' would not be deprecated.

Cheers,

Kyle

J Kyle Medley, PhD Candidate
Bioengineering/BPSD, Sauro Lab
University of Washington, Seattle
skype: jkylemedley

On 6/27/17 12:46 PM, Lucian Smith wrote:
> At HARMONY, the issue was brought up that the 'numberOfPoints' 
> attribute is confusing, because the literal number of expected points 
> in the output file is one more than that: the initial conditions, and 
> the number of *computed* points.
>
> It was proposed that we fix this for SED-ML Level 1 Version 3.  There 
> are a few options:
>
> 1) No change:  simply make it more clear in the spec that 
> 'numberOfPoints' means 'number of computed points' aka 'number of steps'.
>
> 2) Change the name of the attribute to 'numberOfSteps' or possibly 
> 'numberOfComputedPoints'.
>
> 3) Deprecate but allow 'numberOfPoints', and make a new 
> 'numberOfSteps' attribute that people are encouraged to use instead.
>
> Any opinions?  It seems like the advantage is preventing future 
> confusion, and the cost is having a non-backwards-compatible spec, and 
> the cost of implementation changes for the groups that currently 
> support SED-ML.
>
> -Lucian
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

[SED-ML-discuss] The 'numberOfPoints' attribute

[Lucian S. <luc...@gm...>]

At HARMONY, the issue was brought up that the 'numberOfPoints' attribute is
confusing, because the literal number of expected points in the output file
is one more than that: the initial conditions, and the number of *computed*
points.

It was proposed that we fix this for SED-ML Level 1 Version 3.  There are a
few options:

1) No change:  simply make it more clear in the spec that 'numberOfPoints'
means 'number of computed points' aka 'number of steps'.

2) Change the name of the attribute to 'numberOfSteps' or possibly
'numberOfComputedPoints'.

3) Deprecate but allow 'numberOfPoints', and make a new 'numberOfSteps'
attribute that people are encouraged to use instead.

Any opinions?  It seems like the advantage is preventing future confusion,
and the cost is having a non-backwards-compatible spec, and the cost of
implementation changes for the groups that currently support SED-ML.

-Lucian

[SED-ML-discuss] SED-ML notes from HARMONY 2017

[David N. <dav...@gm...>]

Hi all,

As with previous meetings, we will try to keep track of SED-ML related
discussions using a google doc:
https://docs.google.com/document/d/1l2jx5K6msZhB-kfZKjeN2WgRVgfkVuCYnM8yYhIsUsw/edit?usp=sharing.
Please feel free to add, comment, correct as we go!

We are currently not planning on broadcasting the sessions, but if you
would like to join in please let us know and I'm sure we can work
something out. The first SED-ML session starts here in Seattle in
about 40 minutes. Full schedule available here:
https://docs.google.com/spreadsheets/d/1cXuTGNOpd9--fAaHXND9BoFY7H47YvaV2-xCktCDYKQ/edit?usp=sharing


Cheers,
David.

Re: [SED-ML-discuss] Election of two SED-ML editors 2017

[David N. <dav...@gm...>]

Hi all,

Final reminder, voting closes *today* for the election of two new
SED-ML editors.

Vote here: https://goo.gl/forms/VzDYBvkfWUkh0Cjr1


Cheers,
David.


On 20 June 2017 at 10:42, David Nickerson <dav...@gm...> wrote:
> Hi all,
>
> Just a reminder that voting closes this Friday for the election of two
> new SED-ML editors.
>
> Vote here: https://goo.gl/forms/VzDYBvkfWUkh0Cjr1
>
> Cheers,
> David.
>
>
> On 9 June 2017 at 18:45, David Nickerson <dav...@gm...> wrote:
>> Hi all,
>>
>> This is a call for votes for electing two new SED-ML Editors to
>> replace Ion Moraru and Sven Sahle, whose current terms have ended.
>> Every member of the SED-ML forum (as determined by membership of the
>> sed...@li... mailing list) is entitled to vote.
>>
>> Please vote for up to two candidates using the voting form at:
>> https://goo.gl/forms/VzDYBvkfWUkh0Cjr1
>>
>> Voting will end on June 23, 2017.
>>
>> Thank you in advance for your participation in this important process!
>>
>>
>> Cheers,
>> David.



-- 


David Nickerson
about.me/david.nickerson

Re: [SED-ML-discuss] Election of two SED-ML editors 2017

[David N. <dav...@gm...>]

Hi all,

Just a reminder that voting closes this Friday for the election of two
new SED-ML editors.

Vote here: https://goo.gl/forms/VzDYBvkfWUkh0Cjr1

Cheers,
David.


On 9 June 2017 at 18:45, David Nickerson <dav...@gm...> wrote:
> Hi all,
>
> This is a call for votes for electing two new SED-ML Editors to
> replace Ion Moraru and Sven Sahle, whose current terms have ended.
> Every member of the SED-ML forum (as determined by membership of the
> sed...@li... mailing list) is entitled to vote.
>
> Please vote for up to two candidates using the voting form at:
> https://goo.gl/forms/VzDYBvkfWUkh0Cjr1
>
> Voting will end on June 23, 2017.
>
> Thank you in advance for your participation in this important process!
>
>
> Cheers,
> David.

[SED-ML-discuss] COMBINE 2017 registration is open

[David N. <dav...@gm...>]

COMBINE 2017: 8th Computational Modeling in Biology Network Workshop
==========================================================

Oct. 9th - 13th, 2017, Università degli Studi di Milano Bicocca, Milan, ITALY
http://co.mbine.org/events/COMBINE_2017
------------------------------------------------------------------------------

The "Computational Modeling in Biology" Network (COMBINE) is an
initiative to coordinate the development of the various community
standards and formats in systems biology and related fields. COMBINE
2017 will be a workshop-style event with oral presentations, posters,
and breakout sessions. The five meeting days will include talks about
the COMBINE standards and associated or related standardization
efforts, as well as presentations of tools using these standards. Oral
presentations will be selected from the submitted abstracts. In
addition, poster sessions will allow people to inform each other about
their software and other projects in a setting that fosters
interaction and in-depth discussion.


CONFIRMED SPEAKERS
------------------

Shailesh Appukuttan, UNIC, CNRS, France
James Faeder, University of Pittsburgh, USA
Martin Golebiewsk, Heidelberg Institute for Theoretical Studies (HITS), Germany.
Nicolas La Novere, Babraham Institute, Cambridge, UK.
Carlos F. Lopez, Department of Cancer Biology Vanderbilt University
School of Medicine, USA
Marco Nobile, DISCo, Università degli Studi di Milano Bicocca, Italy


CALL FOR ABSTRACTS
------------------

We solicit high-quality abstracts, to be refereed by the COMBINE
Coordinators below, for either oral or poster presentation at the
Workshop. Abstracts will appear on the COMBINE website only, there
will be no formal publication.

Please see the COMBINE website for submission instructions.  The
submission process is hosted by Easychair.



TOPICS OF INTEREST
------------------

Topics include, but are not limited to:
- Data exchange, pipelines and model standards for systems biology
- Graphical notation standards for systems biology
- Standards for sharing and analysing biological pathway data
- Standards for computational biological models
More on the COMBINE standards at http://co.mbine.org/standards


IMPORTANT DATES
---------------

Abstract submission: July 1, 2017
Notification:        July 23, 2017
COMBINE Workshop:    October 9-13 2017


REGISTRATION
------------

Registrations are now open. The registration fee is set to 270 EUR and
it includes breaks and the social event.

We apologize for the cumbersome procedure; please read carefully the
instructions for payment on the registration form. You can register at
https://goo.gl/forms/omoiLmBda4rElye33


LOCAL CHAIRS
------------

Marco Antoniotti, Alex Graudenzi, Giancarlo Mauri, DISCo),
(Università degli Studi di Milano Bicocca)

If you have any questions, please contact <marco.antoniotti [.at.] unimib.it>


COMBINE COORDINATORS
--------------------

Gary Bader (Toronto)
Padraig Gleeson (UCL)
Martin Golebiewski (Heidelberg)
Michael Hucka (Caltech)
Nicolas Le Novère (Babraham)
Chris J. Myers (Utah)
David Nickerson (Auckland)
Falk Schreiber (Monash)
Dagmar Waltemath (Rostock)


ACKNOWLEDGEMENTS
----------------

COMBINE 2017 is generously supported by:
- Department of Informatics, Systems and Communication (DISCo),
  Università degli Studi di Milano Bicocca (ITALY)
- Centre of Systems Biology,
  Università degli Studi di Milano Bicocca (ITALY)

[SED-ML-discuss] Election of two SED-ML editors 2017

[David N. <dav...@gm...>]

Hi all,

This is a call for votes for electing two new SED-ML Editors to
replace Ion Moraru and Sven Sahle, whose current terms have ended.
Every member of the SED-ML forum (as determined by membership of the
sed...@li... mailing list) is entitled to vote.

Please vote for up to two candidates using the voting form at:
https://goo.gl/forms/VzDYBvkfWUkh0Cjr1

Voting will end on June 23, 2017.

Thank you in advance for your participation in this important process!


Cheers,
David.

Re: [SED-ML-discuss] Compute Mean/Stddev of Stochastic Traces?

[Kyle M. <me...@co...>]

Thanks David!

J Kyle Medley, PhD Student
Bioengineering/BPSD, Sauro Lab
University of Washington, Seattle
skype: jkylemedley

On 6/6/17 7:24 PM, David Nickerson wrote:
> Hi Kyle,
>
> I use the C++ libSEDML and you can see a couple of maybe useful
> examples of using custom annotations here
> https://github.com/nickerso/get-simulator/blob/OutputTypes/src/sedml.cpp#L606
> and https://github.com/nickerso/get-simulator/blob/OutputTypes/src/sedml.cpp#L1131.
>
> Cheers,
> David.
>
>
> On 7 June 2017 at 13:23, Chris Myers <my...@ec...> wrote:
>> I’m using jlibSEDML.  Some of the code is here:
>>
>> https://github.com/MyersResearchGroup/iBioSim/blob/master/analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/util/SEDMLutilities.java
>>
>> and more here:
>>
>> https://github.com/MyersResearchGroup/iBioSim/blob/master/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/analysisView/AnalysisView.java
>>
>> Chris
>>
>> On Jun 6, 2017, at 6:24 PM, Kyle Medley <me...@co...> wrote:
>>
>> Thanks for your help Chris! Out of curiosity, are you using libSEDML (C++ or
>> C#?) or are you writing the XML yourself? I was just curious because it
>> would be helpful to have an example of how to work with custom annotations
>> in libSEDML.
>>
>> J Kyle Medley, PhD Student
>> Bioengineering/BPSD, Sauro Lab
>> University of Washington, Seattle
>> skype: jkylemedley
>>
>> On 06/06/2017 04:14 PM, Chris Myers wrote:
>>
>> I believe that we agreed at COMBINE that using repeated task for this was
>> overkill.  Instead, you should be able to specify the number of runs, then
>> be able to select in your graph which run or statistic to plot.  We use this
>> KISAO term:
>>
>> http://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000326
>>
>> to specify number of runs for a stochastic simulation.  We have currently
>> added a custom annotation to the dataGenerator to indicate which data set to
>> generate data from.  For example, this can be a run number or a statistic
>> like mean, using custom annotation for now.  See attached example.
>>
>> Chris
>>
>>
>>
>>
>> On Jun 6, 2017, at 2:06 PM, Kyle Medley <me...@co...> wrote:
>>
>> Hi All,
>>
>> I was just wondering if it is possible to compute the mean and standard
>> deviations of stochastic simulations in SED-ML. Frank has a great demo of
>> running multiple stochastic traces, but I'm not sure how to extend it to
>> allow computing the first two moments. My understanding is that a repeated
>> task generates data with one more dimension than the input, so Frank's
>> example is essentially flattening the data before plotting it. I'm not sure
>> if it's possible to manipulate these higher dimensions in a dataGenerator or
>> use some clever MathML to sum along one axis. Any ideas?
>>
>> Thanks,
>> Kyle
>>
>> --
>> J Kyle Medley, PhD Student
>> Bioengineering/BPSD, Sauro Lab
>> University of Washington, Seattle
>> skype: jkylemedley
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org!
>> http://sdm.link/slashdot_______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>
>>
>>
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org!
>> http://sdm.link/slashdot_______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>
>

Re: [SED-ML-discuss] Compute Mean/Stddev of Stochastic Traces?

[Kyle M. <me...@co...>]

Thanks so much!

J Kyle Medley, PhD Student
Bioengineering/BPSD, Sauro Lab
University of Washington, Seattle
skype: jkylemedley

On 06/06/2017 06:23 PM, Chris Myers wrote:
> I’m using jlibSEDML.  Some of the code is here:
>
> https://github.com/MyersResearchGroup/iBioSim/blob/master/analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/util/SEDMLutilities.java
>
> and more here:
>
> https://github.com/MyersResearchGroup/iBioSim/blob/master/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/analysisView/AnalysisView.java
>
> Chris
>
>> On Jun 6, 2017, at 6:24 PM, Kyle Medley <me...@co... 
>> <mailto:me...@co...>> wrote:
>>
>> Thanks for your help Chris! Out of curiosity, are you using libSEDML 
>> (C++ or C#?) or are you writing the XML yourself? I was just curious 
>> because it would be helpful to have an example of how to work with 
>> custom annotations in libSEDML.
>> J Kyle Medley, PhD Student
>> Bioengineering/BPSD, Sauro Lab
>> University of Washington, Seattle
>> skype: jkylemedley
>> On 06/06/2017 04:14 PM, Chris Myers wrote:
>>> I believe that we agreed at COMBINE that using repeated task for 
>>> this was overkill.  Instead, you should be able to specify the 
>>> number of runs, then be able to select in your graph which run or 
>>> statistic to plot.  We use this KISAO term:
>>>
>>> http://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000326 
>>> <http://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=http://www.biomodels.net/kisao/KISAO#KISAO_0000326>
>>>
>>> to specify number of runs for a stochastic simulation.  We have 
>>> currently added a custom annotation to the dataGenerator to indicate 
>>> which data set to generate data from.  For example, this can be a 
>>> run number or a statistic like mean, using custom annotation for 
>>> now.  See attached example.
>>>
>>> Chris
>>>
>>>
>>>
>>>
>>>> On Jun 6, 2017, at 2:06 PM, Kyle Medley <me...@co...> wrote:
>>>>
>>>> Hi All,
>>>>
>>>> I was just wondering if it is possible to compute the mean and 
>>>> standard deviations of stochastic simulations in SED-ML. Frank has 
>>>> a great demo 
>>>> <http://sysbioapps.dyndns.org/SED-ML_Web_Tools/Home/SimulateUrl?url=http%3A%2F%2Fsvn.code.sf.net%2Fp%2Flibsedml%2Fcode%2Ftrunk%2FSamples%2Fsedx-archives%2Fnestedv3%2Fv3-example3-repeated-stochastic-runs.sedx> 
>>>> of running multiple stochastic traces, but I'm not sure how to 
>>>> extend it to allow computing the first two moments. My 
>>>> understanding is that a repeated task generates data with one more 
>>>> dimension than the input, so Frank's example is essentially 
>>>> flattening the data before plotting it. I'm not sure if it's 
>>>> possible to manipulate these higher dimensions in a dataGenerator 
>>>> or use some clever MathML to sum along one axis. Any ideas?
>>>>
>>>> Thanks,
>>>> Kyle
>>>> -- 
>>>> J Kyle Medley, PhD Student
>>>> Bioengineering/BPSD, Sauro Lab
>>>> University of Washington, Seattle
>>>> skype: jkylemedley
>>>> ------------------------------------------------------------------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org <http://slashdot.org/>! 
>>>> http://sdm.link/slashdot_______________________________________________
>>>> SED-ML-discuss mailing list
>>>> SED...@li... 
>>>> <mailto:SED...@li...>
>>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites,Slashdot.org <http://slashdot.org>!http://sdm.link/slashdot
>>>
>>>
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org <http://slashdot.org>! 
>> http://sdm.link/slashdot_______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li... 
>> <mailto:SED...@li...>
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Compute Mean/Stddev of Stochastic Traces?

[David N. <dav...@gm...>]

Hi Kyle,

I use the C++ libSEDML and you can see a couple of maybe useful
examples of using custom annotations here
https://github.com/nickerso/get-simulator/blob/OutputTypes/src/sedml.cpp#L606
and https://github.com/nickerso/get-simulator/blob/OutputTypes/src/sedml.cpp#L1131.

Cheers,
David.


On 7 June 2017 at 13:23, Chris Myers <my...@ec...> wrote:
> I’m using jlibSEDML.  Some of the code is here:
>
> https://github.com/MyersResearchGroup/iBioSim/blob/master/analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/util/SEDMLutilities.java
>
> and more here:
>
> https://github.com/MyersResearchGroup/iBioSim/blob/master/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/analysisView/AnalysisView.java
>
> Chris
>
> On Jun 6, 2017, at 6:24 PM, Kyle Medley <me...@co...> wrote:
>
> Thanks for your help Chris! Out of curiosity, are you using libSEDML (C++ or
> C#?) or are you writing the XML yourself? I was just curious because it
> would be helpful to have an example of how to work with custom annotations
> in libSEDML.
>
> J Kyle Medley, PhD Student
> Bioengineering/BPSD, Sauro Lab
> University of Washington, Seattle
> skype: jkylemedley
>
> On 06/06/2017 04:14 PM, Chris Myers wrote:
>
> I believe that we agreed at COMBINE that using repeated task for this was
> overkill.  Instead, you should be able to specify the number of runs, then
> be able to select in your graph which run or statistic to plot.  We use this
> KISAO term:
>
> http://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000326
>
> to specify number of runs for a stochastic simulation.  We have currently
> added a custom annotation to the dataGenerator to indicate which data set to
> generate data from.  For example, this can be a run number or a statistic
> like mean, using custom annotation for now.  See attached example.
>
> Chris
>
>
>
>
> On Jun 6, 2017, at 2:06 PM, Kyle Medley <me...@co...> wrote:
>
> Hi All,
>
> I was just wondering if it is possible to compute the mean and standard
> deviations of stochastic simulations in SED-ML. Frank has a great demo of
> running multiple stochastic traces, but I'm not sure how to extend it to
> allow computing the first two moments. My understanding is that a repeated
> task generates data with one more dimension than the input, so Frank's
> example is essentially flattening the data before plotting it. I'm not sure
> if it's possible to manipulate these higher dimensions in a dataGenerator or
> use some clever MathML to sum along one axis. Any ideas?
>
> Thanks,
> Kyle
>
> --
> J Kyle Medley, PhD Student
> Bioengineering/BPSD, Sauro Lab
> University of Washington, Seattle
> skype: jkylemedley
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org!
> http://sdm.link/slashdot_______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org!
> http://sdm.link/slashdot_______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>



-- 


David Nickerson
about.me/david.nickerson

Re: [SED-ML-discuss] Compute Mean/Stddev of Stochastic Traces?

[Chris M. <my...@ec...>]

I’m using jlibSEDML.  Some of the code is here:

https://github.com/MyersResearchGroup/iBioSim/blob/master/analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/util/SEDMLutilities.java <https://github.com/MyersResearchGroup/iBioSim/blob/master/analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/util/SEDMLutilities.java>

and more here:

https://github.com/MyersResearchGroup/iBioSim/blob/master/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/analysisView/AnalysisView.java <https://github.com/MyersResearchGroup/iBioSim/blob/master/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/analysisView/AnalysisView.java>

Chris

> On Jun 6, 2017, at 6:24 PM, Kyle Medley <me...@co...> wrote:
> 
> Thanks for your help Chris! Out of curiosity, are you using libSEDML (C++ or C#?) or are you writing the XML yourself? I was just curious because it would be helpful to have an example of how to work with custom annotations in libSEDML.
> J Kyle Medley, PhD Student
> Bioengineering/BPSD, Sauro Lab
> University of Washington, Seattle
> skype: jkylemedley
> On 06/06/2017 04:14 PM, Chris Myers wrote:
>> I believe that we agreed at COMBINE that using repeated task for this was overkill.  Instead, you should be able to specify the number of runs, then be able to select in your graph which run or statistic to plot.  We use this KISAO term:
>> 
>> http://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000326 <http://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=http://www.biomodels.net/kisao/KISAO#KISAO_0000326>
>> 
>> to specify number of runs for a stochastic simulation.  We have currently added a custom annotation to the dataGenerator to indicate which data set to generate data from.  For example, this can be a run number or a statistic like mean, using custom annotation for now.  See attached example.
>> 
>> Chris
>> 
>> 
>> 
>> 
>>> On Jun 6, 2017, at 2:06 PM, Kyle Medley < <mailto:me...@co...>me...@co... <mailto:me...@co...>> wrote:
>>> 
>>> Hi All,
>>> 
>>> I was just wondering if it is possible to compute the mean and standard deviations of stochastic simulations in SED-ML. Frank has a great demo <http://sysbioapps.dyndns.org/SED-ML_Web_Tools/Home/SimulateUrl?url=http%3A%2F%2Fsvn.code.sf.net%2Fp%2Flibsedml%2Fcode%2Ftrunk%2FSamples%2Fsedx-archives%2Fnestedv3%2Fv3-example3-repeated-stochastic-runs.sedx> of running multiple stochastic traces, but I'm not sure how to extend it to allow computing the first two moments. My understanding is that a repeated task generates data with one more dimension than the input, so Frank's example is essentially flattening the data before plotting it. I'm not sure if it's possible to manipulate these higher dimensions in a dataGenerator or use some clever MathML to sum along one axis. Any ideas?
>>> 
>>> Thanks,
>>> Kyle
>>> -- 
>>> J Kyle Medley, PhD Student
>>> Bioengineering/BPSD, Sauro Lab
>>> University of Washington, Seattle
>>> skype: jkylemedley
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org <http://slashdot.org/>!  <http://sdm.link/slashdot_______________________________________________>http://sdm.link/slashdot_______________________________________________ <http://sdm.link/slashdot_______________________________________________>
>>> SED-ML-discuss mailing list
>>> SED...@li... <mailto:SED...@li...>
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss>
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot <http://sdm.link/slashdot>
>> 
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li... <mailto:SED...@li...>
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss <https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss>
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Compute Mean/Stddev of Stochastic Traces?

[Kyle M. <me...@co...>]

Thanks for your help Chris! Out of curiosity, are you using libSEDML 
(C++ or C#?) or are you writing the XML yourself? I was just curious 
because it would be helpful to have an example of how to work with 
custom annotations in libSEDML.

J Kyle Medley, PhD Student
Bioengineering/BPSD, Sauro Lab
University of Washington, Seattle
skype: jkylemedley

On 06/06/2017 04:14 PM, Chris Myers wrote:
> I believe that we agreed at COMBINE that using repeated task for this 
> was overkill.  Instead, you should be able to specify the number of 
> runs, then be able to select in your graph which run or statistic to 
> plot.  We use this KISAO term:
>
> http://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000326 
> <http://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=http://www.biomodels.net/kisao/KISAO#KISAO_0000326>
>
> to specify number of runs for a stochastic simulation.  We have 
> currently added a custom annotation to the dataGenerator to indicate 
> which data set to generate data from.  For example, this can be a run 
> number or a statistic like mean, using custom annotation for now.  See 
> attached example.
>
> Chris
>
>
>
>
>> On Jun 6, 2017, at 2:06 PM, Kyle Medley <me...@co... 
>> <mailto:me...@co...>> wrote:
>>
>> Hi All,
>>
>> I was just wondering if it is possible to compute the mean and 
>> standard deviations of stochastic simulations in SED-ML. Frank has a 
>> great demo 
>> <http://sysbioapps.dyndns.org/SED-ML_Web_Tools/Home/SimulateUrl?url=http%3A%2F%2Fsvn.code.sf.net%2Fp%2Flibsedml%2Fcode%2Ftrunk%2FSamples%2Fsedx-archives%2Fnestedv3%2Fv3-example3-repeated-stochastic-runs.sedx> 
>> of running multiple stochastic traces, but I'm not sure how to extend 
>> it to allow computing the first two moments. My understanding is that 
>> a repeated task generates data with one more dimension than the 
>> input, so Frank's example is essentially flattening the data before 
>> plotting it. I'm not sure if it's possible to manipulate these higher 
>> dimensions in a dataGenerator or use some clever MathML to sum along 
>> one axis. Any ideas?
>>
>> Thanks,
>> Kyle
>> -- 
>> J Kyle Medley, PhD Student
>> Bioengineering/BPSD, Sauro Lab
>> University of Washington, Seattle
>> skype: jkylemedley
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org <http://slashdot.org>! 
>> http://sdm.link/slashdot_______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li... 
>> <mailto:SED...@li...>
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Compute Mean/Stddev of Stochastic Traces?

[Chris M. <my...@ec...>]

I believe that we agreed at COMBINE that using repeated task for this was overkill.  Instead, you should be able to specify the number of runs, then be able to select in your graph which run or statistic to plot.  We use this KISAO term:

http://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000326 <http://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=http://www.biomodels.net/kisao/KISAO#KISAO_0000326>

to specify number of runs for a stochastic simulation.  We have currently added a custom annotation to the dataGenerator to indicate which data set to generate data from.  For example, this can be a run number or a statistic like mean, using custom annotation for now.  See attached example.

Chris


> On Jun 6, 2017, at 2:06 PM, Kyle Medley <me...@co...> wrote:
> 
> Hi All,
> 
> I was just wondering if it is possible to compute the mean and standard deviations of stochastic simulations in SED-ML. Frank has a great demo <http://sysbioapps.dyndns.org/SED-ML_Web_Tools/Home/SimulateUrl?url=http%3A%2F%2Fsvn.code.sf.net%2Fp%2Flibsedml%2Fcode%2Ftrunk%2FSamples%2Fsedx-archives%2Fnestedv3%2Fv3-example3-repeated-stochastic-runs.sedx> of running multiple stochastic traces, but I'm not sure how to extend it to allow computing the first two moments. My understanding is that a repeated task generates data with one more dimension than the input, so Frank's example is essentially flattening the data before plotting it. I'm not sure if it's possible to manipulate these higher dimensions in a dataGenerator or use some clever MathML to sum along one axis. Any ideas?
> 
> Thanks,
> Kyle
> -- 
> J Kyle Medley, PhD Student
> Bioengineering/BPSD, Sauro Lab
> University of Washington, Seattle
> skype: jkylemedley
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

[SED-ML-discuss] Compute Mean/Stddev of Stochastic Traces?

[Kyle M. <me...@co...>]

Hi All,

I was just wondering if it is possible to compute the mean and standard 
deviations of stochastic simulations in SED-ML. Frank has a great demo 
<http://sysbioapps.dyndns.org/SED-ML_Web_Tools/Home/SimulateUrl?url=http%3A%2F%2Fsvn.code.sf.net%2Fp%2Flibsedml%2Fcode%2Ftrunk%2FSamples%2Fsedx-archives%2Fnestedv3%2Fv3-example3-repeated-stochastic-runs.sedx> 
of running multiple stochastic traces, but I'm not sure how to extend it 
to allow computing the first two moments. My understanding is that a 
repeated task generates data with one more dimension than the input, so 
Frank's example is essentially flattening the data before plotting it. 
I'm not sure if it's possible to manipulate these higher dimensions in a 
dataGenerator or use some clever MathML to sum along one axis. Any ideas?

Thanks,
Kyle

-- 
J Kyle Medley, PhD Student
Bioengineering/BPSD, Sauro Lab
University of Washington, Seattle
skype: jkylemedley

Re: [SED-ML-discuss] Axis Labels on plot2D?

[Lucian S. <luc...@gm...>]

Nobody has worked on l1v3 at all, so whenever anyone works on it, whoever
that might be will put in whatever they want ;-)

(Presumably, they'll start with the discussion at COMBINE last year and go
from there.)

-Lucian

On Wed, May 31, 2017 at 1:48 PM, Kyle Medley <me...@co...> wrote:

> Thanks for your response David! Unfortunately I can't reply directly. I
> don't seem to be subscribed to the list. I think I already sent a
> subscription request but I sent another one just in case. Could someone
> please add me to the list? Thanks!
>
> Also, just for clarification - are you saying this is slated for post-L1V3
> at this point? Or is there still a chance it could make it in?
>
>
>
> --
> J Kyle Medley, PhD Student
> Bioengineering/BPSD, Sauro Lab
> University of Washington, Seattle
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>

Re: [SED-ML-discuss] Axis Labels on plot2D?

[David N. <dav...@gm...>]

Hi Kyle,

The hope is that those minor tweaks discussed at HARMONY will make it
into L1V3, but will require the spec changes to be proposed and
discussed with the community. The L1V3 draft hasn't changed for a few
years now waiting for a second implementation, so if tool developers
implement "draft" versions of these features it would greatly help
form the proposed updates to the current draft L1V3.

Cheers,
David.



On 1 June 2017 at 08:48, Kyle Medley <me...@co...> wrote:
> Thanks for your response David! Unfortunately I can't reply directly. I
> don't seem to be subscribed to the list. I think I already sent a
> subscription request but I sent another one just in case. Could someone
> please add me to the list? Thanks!
>
> Also, just for clarification - are you saying this is slated for post-L1V3
> at this point? Or is there still a chance it could make it in?
>
>
>
> --
> J Kyle Medley, PhD Student
> Bioengineering/BPSD, Sauro Lab
> University of Washington, Seattle
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss



-- 


David Nickerson
about.me/david.nickerson

Re: [SED-ML-discuss] Axis Labels on plot2D?

[Kyle M. <me...@co...>]

Sorry, spoke too soon. I think I'm in.

J Kyle Medley, PhD Student
Bioengineering/BPSD, Sauro Lab
University of Washington, Seattle

On 5/31/17 1:48 PM, Kyle Medley wrote:
> Thanks for your response David! Unfortunately I can't reply directly. 
> I don't seem to be subscribed to the list. I think I already sent a 
> subscription request but I sent another one just in case. Could 
> someone please add me to the list? Thanks!
>
> Also, just for clarification - are you saying this is slated for 
> post-L1V3 at this point? Or is there still a chance it could make it in?
>
>

Re: [SED-ML-discuss] Axis Labels on plot2D?

[Herbert S. <uw....@gm...>]

Ideally it should go in this year since it was decided last year.

Herbert

On Wed, May 31, 2017 at 1:48 PM, Kyle Medley <me...@co...> wrote:
> Thanks for your response David! Unfortunately I can't reply directly. I
> don't seem to be subscribed to the list. I think I already sent a
> subscription request but I sent another one just in case. Could someone
> please add me to the list? Thanks!
>
> Also, just for clarification - are you saying this is slated for post-L1V3
> at this point? Or is there still a chance it could make it in?
>
>
>
> --
> J Kyle Medley, PhD Student
> Bioengineering/BPSD, Sauro Lab
> University of Washington, Seattle
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Axis Labels on plot2D?

[Kyle M. <me...@co...>]

Thanks for your response David! Unfortunately I can't reply directly. I 
don't seem to be subscribed to the list. I think I already sent a 
subscription request but I sent another one just in case. Could someone 
please add me to the list? Thanks!

Also, just for clarification - are you saying this is slated for 
post-L1V3 at this point? Or is there still a chance it could make it in?


-- 
J Kyle Medley, PhD Student
Bioengineering/BPSD, Sauro Lab
University of Washington, Seattle

Re: [SED-ML-discuss] Axis Labels on plot2D?

[David N. <dav...@gm...>]

Hi Kyle,

This was something discussed at the COMBINE meeting last year. As you
can see from the discussion document
(https://docs.google.com/document/d/1uNNkjATFUQ78FspKkBTwJ2UmevmCGfovaKI22sr3VF8/edit?usp=sharing),
it was hoped that a proposal to make this change to the L1V3 draft
specification would quickly follow - but unfortunately this hasn't
happened yet.

Features like this are on the agenda to try and tidy up at HARMONY.


Cheers,
David.


On 31 May 2017 at 17:18, Kyle Medley <me...@co...> wrote:
> Hi All,
>
> I was just wondering if SED-ML supports axis labels for plot2D? I can't seem
> to find any examples that use them.
>
> Thanks,
> Kyle
>
> --
> J Kyle Medley, PhD Student
> Bioengineering/BPSD, Sauro Lab
> University of Washington, Seattle
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss



-- 


David Nickerson
about.me/david.nickerson

[SED-ML-discuss] Axis Labels on plot2D?

[Kyle M. <me...@co...>]

Hi All,

I was just wondering if SED-ML supports axis labels for plot2D? I can't 
seem to find any examples that use them.

Thanks,
Kyle

-- 
J Kyle Medley, PhD Student
Bioengineering/BPSD, Sauro Lab
University of Washington, Seattle

Re: [SED-ML-discuss] Call for nominations for two SED-ML editors

[David N. <dav...@gm...>]

Hi all,

Just a reminder that you have until the 4th of June (this Sunday) to
nominate candidates for the SED-ML editor election.

Cheers,
David.


On 21 May 2017 at 09:08, David Nickerson <dav...@gm...> wrote:
> Hi all,
>
> This is a call for nominations for two SED-ML editors to replace Sven
> Sahle and Ion Moraru, whose terms ended on the 31st of December 2016.
>
> The length of a SED-ML Editor's term is 3 years, belatedly starting
> from the 1st of January 2017.
>
> The current editors are Ion Moraru (to be replaced), Sven Sahle (to be
> replaced), Brett Olivier (until 2017), David Nickerson (until 2017),
> and Lucian Smith (until 2018).
>
> We would like to ask you to nominate suitable candidates. You may
> nominate anyone (including yourself) who you think is qualified to act
> as an editor. You can fill out this survey multiple times in order to
> nominate multiple candidates. The current members of the editorial
> board can not be nominated.
>
> The nomination page is at: https://goo.gl/forms/jh6GGU5grUG0Bnv42
>
> The call for nomination is open from now until the 4th of June 2017.
> After the nomination phase, we will issue a call for voting.
>
> Thanks,
> David.



-- 


David Nickerson
about.me/david.nickerson

[SED-ML-discuss] HARMONY 2017: Hotel Update

[Kiri C. <kir...@uw...>]

Dear all,

We were able to extend the deadline for booking at the University Inn
<http://www.universityinnseattle.com/> with special group code to *June 2nd*.
If you haven't booked hotels yet, please do so. More details are available
at the Harmony website
<http://co.mbine.org/events/HARMONY_2017#Accommodation>.

*Also, if you have booked at a nearby Watertown Hotel instead of the
University Inn, **please let me know. *Both places are operated by the same
company, so we might be able to get some deals out for you.

Thank you.

On behalf of the HARMONY 2017 local organizers,

Herbert Sauro

Kyle Medley

Kiri Choi