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

[SED-ML-discuss] VW summer school whole-cell modeling

[Dagmar W. <dag...@un...>]

      Whole-cell modeling summer school

March 9-13, 2015 | Rostock, Germany


We are pleased to announce the hackathon-style summer school to be held 
next year in Rostock, Germany, with the aim of developing an open 
version of the Karr et al. whole-cell model 
(http://www.ncbi.nlm.nih.gov/pubmed/22817898 
<https://email.uni-rostock.de/owa/redir.aspx?C=Lm93qXabIEqEPI9uaAj3PCpHkjtEqtEISO3IjqYL59azPEvcYdjOmFD-fYHaDBUYauQc3eia5Tw.&URL=http%3a%2f%2fwww.ncbi.nlm.nih.gov%2fpubmed%2f22817898>).


The primary aim for the participants of the summer school is to learn 
about standards for modelling and simulation in computational biology. 
  But a secondary aim is to enjoy modeling, coding and diagramming the 
whole-cell model using openly available software and COMBINE standards 
(http://co.mbine.org 
<https://email.uni-rostock.de/owa/redir.aspx?C=Lm93qXabIEqEPI9uaAj3PCpHkjtEqtEISO3IjqYL59azPEvcYdjOmFD-fYHaDBUYauQc3eia5Tw.&URL=http%3a%2f%2fco.mbine.org>).


An anticipated outcome of the event is a roadmap for future developments 
needed in the different standardisation efforts involved in the summer 
school.  Together, we want to answer the important question: "What is 
missing in today's standards?"  We believe this will help provide 
guidelines for COMBINE.


In total, we will accept up to 50 students (PhD to early postdoc level), 
who will be fully funded through the Volkswagen Foundation. The 
application form is open until the *31st of October*.


Details of the summer school are available from the following website:


http://bit.ly/wholecell 
<https://email.uni-rostock.de/owa/redir.aspx?C=Lm93qXabIEqEPI9uaAj3PCpHkjtEqtEISO3IjqYL59azPEvcYdjOmFD-fYHaDBUYauQc3eia5Tw.&URL=http%3a%2f%2fbit.ly%2fwholecell>


Please consider putting up our poster in your institution 
(https://sites.google.com/site/vwwholecellsummerschool/documents),

and please also feel free to forward this e-mail to potentially 
interested colleagues.

Thank you for promoting this event!

Dagmar Waltemath and Falk Schreiber

[SED-ML-discuss] First draft of SED-ML Level 1 Version 3

[Frank B. <fbe...@ca...>]

Under: 

http://co.mbine.org/specifications/sed-ml.level-1.version-3-draft-1

We present a first draft, of SED-ML enhanced by the proposal for accessing data that we discussed in the past and formalized at HARMONY 2014. You will find one notable change, while we discussed on the list to name the new concept ‘dataSet’ and it all sounded good to us, there already is a SED-ML class DataSet that is being used in the reports. Instead the new class is called DataDescription. 

The relevant sections in the spec are 2.4.1-2.4.3. The hope is that this draft can fuel our discussions at COMBINE. 

Frank Bergmann, 
on behalf of the SED-ML editors

[SED-ML-discuss] [Combine-announce] Tutorial: Modelling and Simulation of Biological Models - Melbourne, Sept 14

[Golebiewski, M. <mar...@h-...>]

_______________________________________________
Combine-announce mailing list
Com...@eb...
https://listserver.ebi.ac.uk/mailman/listinfo/combine-announce

[SED-ML-discuss] [Combine-announce] Systems Biology Data Management Foundry: A meeting for practitioners - October 6-7, Heidelberg

[Golebiewski, M. <mar...@h-...>]

_______________________________________________
Combine-announce mailing list
Com...@eb...
https://listserver.ebi.ac.uk/mailman/listinfo/combine-announce

[SED-ML-discuss] [Combine-announce] COMBINE 2014 - Abstract Deadline TODAY

[Golebiewski, M. <mar...@h-...>]

_______________________________________________
Combine-announce mailing list
Com...@eb...
https://listserver.ebi.ac.uk/mailman/listinfo/combine-announce

[SED-ML-discuss] [Combine-announce] COMBINE & ERASysAPP Tutorial: Modelling and Simulation of Biological Models - Melbourne Sept 14, 2014

[Golebiewski, M. <mar...@h-...>]

_______________________________________________
Combine-announce mailing list
Com...@eb...
https://listserver.ebi.ac.uk/mailman/listinfo/combine-announce

Re: [SED-ML-discuss] id & name on AlgorithmParameter

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

Hi guys,

The metaid is already there and can be used as an optional identifier,
if people want to use it that way. The actual id attribute is only
needed when you need to reference something internally in the SED-ML
document itself.

For this case, given a KiSAO ID is mandatory and that the correct
KiSAO term doesn't yet exist, it would probably be better to use an
annotation to store the additional algorithm parameters.


Cheers,
David.

On Tue, Jun 10, 2014 at 3:47 AM, Bertrand Moreau
<ber...@th...> wrote:
> Hi Frank,
>
> More context on this specific issue: I am currently working on the
> integration of flux balance analysis in the BioPreDyn software, which uses
> SED-ML. However, while 'flux balance analysis' exists in KiSAO, it is not
> the case for several of its parameters (the objective function and the
> optimization sense in my case). I consider suggesting additional terms in
> the KiSAO ontology, but as a temporary fix I use algorithmParameter name
> attributes to encode values for those optional parameters.
>
> Best regards,
> Bertrand
>
>
> On Mon, Jun 9, 2014 at 3:50 PM, Frank Bergmann <fbe...@ca...> wrote:
>>
>> Hello all,
>>
>> with SED-ML L1V2 we introduced the algorithm parameters to SED-ML. We only
>> included them with 2 attributes: ‘kisaoID’ and ‘value’. I know we also
>> talked about optional id’s / name’s. Would that be useful to others? Just
>> for context, the c++ libSEDML library currently will not accept an id for
>> algorithm parameters:
>>
>> https://github.com/fbergmann/libSEDML/issues/6
>>
>>
>> Thanks
>> Frank
>>
>>
>>
>> ------------------------------------------------------------------------------
>> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
>> Find What Matters Most in Your Big Data with HPCC Systems
>> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
>> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
>> http://www.hpccsystems.com
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> This message and any attachments are the property of The CoSMo Company; they
> are strictly confidential and intended solely for the addressees. If you are
> not the intended recipient of this message, please delete it and immediately
> notify the sender. Any use not in accordance with the purpose of this
> message and any dissemination or disclosure, either whole or partial, is
> prohibited except with formal approval.
>
> Ce message et toutes les pieces jointes sont la propriete de The CoSMo
> Company ; ils sont etablis a  l'intention exclusive de ses destinataires et
> sont confidentiels. Si vous recevez ce message par erreur, merci de le
> detruire et d'en avertir immediatement l'expediteur. Toute utilisation non
> conforme a  sa destination, toute diffusion ou toute publication, totale ou
> partielle est interdite, sans autorisation expresse.
>
> ------------------------------------------------------------------------------
> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
> Find What Matters Most in Your Big Data with HPCC Systems
> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
> http://www.hpccsystems.com
> _______________________________________________
> 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] id & name on AlgorithmParameter

[Bertrand M. <ber...@th...>]

Hi Frank,

More context on this specific issue: I am currently working on the
integration of flux balance analysis in the BioPreDyn software
<https://github.com/bmoreau/biopredyn>, which uses SED-ML. However, while
'flux balance analysis' exists in KiSAO, it is not the case for several of
its parameters (the objective function and the optimization sense in my
case). I consider suggesting additional terms in the KiSAO ontology, but as
a temporary fix I use algorithmParameter name attributes to encode values
for those optional parameters.

Best regards,
Bertrand


On Mon, Jun 9, 2014 at 3:50 PM, Frank Bergmann <fbe...@ca...> wrote:

> Hello all,
>
> with SED-ML L1V2 we introduced the algorithm parameters to SED-ML. We only
> included them with 2 attributes: ‘kisaoID’ and ‘value’. I know we also
> talked about optional id’s / name’s. Would that be useful to others? Just
> for context, the c++ libSEDML library currently will not accept an id for
> algorithm parameters:
>
> https://github.com/fbergmann/libSEDML/issues/6
>
>
> Thanks
> Frank
>
>
>
> ------------------------------------------------------------------------------
> HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
> Find What Matters Most in Your Big Data with HPCC Systems
> Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
> Leverages Graph Analysis for Fast Processing & Easy Data Exploration
> http://www.hpccsystems.com
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>

-- 
This message and any attachments are the property of The CoSMo Company; 
they are strictly confidential and intended solely for the addressees. If 
you are not the intended recipient of this message, please delete it and 
immediately notify the sender. Any use not in accordance with the purpose 
of this message and any dissemination or disclosure, either whole or 
partial, is prohibited except with formal approval.

Ce message et toutes les pieces jointes sont la propriete de The CoSMo 
Company ; ils sont etablis a  l'intention exclusive de ses destinataires et 
sont confidentiels. Si vous recevez ce message par erreur, merci de le 
detruire et d'en avertir immediatement l'expediteur. Toute utilisation non 
conforme a  sa destination, toute diffusion ou toute publication, totale ou 
partielle est interdite, sans autorisation expresse.

[SED-ML-discuss] id & name on AlgorithmParameter

[Frank B. <fbe...@ca...>]

Hello all, 

with SED-ML L1V2 we introduced the algorithm parameters to SED-ML. We only included them with 2 attributes: ‘kisaoID’ and ‘value’. I know we also talked about optional id’s / name’s. Would that be useful to others? Just for context, the c++ libSEDML library currently will not accept an id for algorithm parameters:

https://github.com/fbergmann/libSEDML/issues/6


Thanks
Frank

[SED-ML-discuss] [Combine-announce] COMBINE 2014 abstract submission

[Huaiyu Mi <hua...@us...>]

Hi all,

If you plan to attend COMBINE 2014
(http://co.mbine.org/events/COMBINE_2014), and would like to give a
presentation (either talk or poster), please go to the following link to
submit the abstract.

https://www.surveymonkey.com/s/combine2014abstract

The deadline for submission is July 18, 2014.

Thanks,

Huaiyu


_______________________________________________
Combine-announce mailing list
Com...@eb...
https://listserver.ebi.ac.uk/mailman/listinfo/combine-announce

[SED-ML-discuss] Fwd: [sbml-discuss] COMBINE 2014 @ USC -- abstract submission by July 18

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

---------- Forwarded message ----------
From: Michael Hucka <mh...@ca...>
Date: Sat, Jun 7, 2014 at 6:28 AM
Subject: [sbml-discuss] COMBINE 2014 @ USC -- abstract submission by July 18
To: sbm...@go...


Dear systems biologists,

If you plan on attending COMBINE 2014 at USC in August [1], and would
like to present a poster or oral presentation, please go to the
following link to provide a title, abstract and other information:

  https://www.surveymonkey.com/s/combine2014abstract

The deadline for submission is July 18, 2014.

Thanks,
The COMBINE 2014 organizers

[1] http://co.mbine.org/events/COMBINE_2014

--
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 to sbm...@go....
To post to this group, send email to sbm...@go....
To view this discussion on the web visit
https://groups.google.com/d/msgid/sbml-discuss/20140606142845801603.1c66ac38%40caltech.edu.
For more options, visit https://groups.google.com/d/optout.


-- 


David Nickerson
about.me/david.nickerson

[SED-ML-discuss] [Combine-announce] ICSB2014 Preliminary program now available

[Nicolas Le N. <n.l...@gm...>]

[Disclaimer: COMBINE is a media partner of ICSB 2014 http://www.icsb14.com/pages/sponsors.php]

       *Preliminary program now available*

The preliminary program for the 15th International Conference on Systems Biology is now available online. This interdisciplinary conference features, keynotes, plenary and concurrent sessions covering the most up-to-date information in the fields of biology, computer science, engineering and chemistry.

Plenary session topics include:

   - Health and wellbeing
   - Ecology, evolution and the environment
   - Industrial Systems BiologY
   - Model systems and new technologies
   - High dimensional and multi-scale systems
   - Systems biology directions and outreach plenary

_Click here_ <http://dynamail.entegy.com.au/ch/42631/181nd/1715547/744e62dw0.html>to view the preliminary program.

*Register before 4 July 2104 and save $100!*

Enjoy the special early-bird rates and save $100 when you register on or before *4 July 2014*. _Click _ <http://dynamail.entegy.com.au/ch/42631/181nd/1765808/744e610nw5.html>_here_ <http://dynamail.entegy.com.au/ch/42631/181nd/1765808/744e610nw5-1.html>to register.

Discounted rates are also available for a group registration of at least 10 delegates. Visit our _website_ <http://dynamail.entegy.com.au/ch/42631/181nd/1765808/744e610nw5-2.html>for more details.

Register now <http://dynamail.entegy.com.au/ch/42631/181nd/1765840/744e6c1v8.html><http://dynamail.entegy.com.au/ch/42631/181nd/1715547/744e62dw0-1.html><http://dynamail.entegy.com.au/ch/42631/181nd/1687757/744e612hsq.html> 		


     *More speakers confirmed...*

*_Brenda Andrews_* <http://dynamail.entegy.com.au/ch/42631/181nd/1779202/744e6fcq6.html>
The Banting and Best Department of Medical Research, Canada

*_Edmund Crampin_* <http://dynamail.entegy.com.au/ch/42631/181nd/1779203/744e6gfv9.html>
The University of Melbourne, Australia

*_Roland Eils_* <http://dynamail.entegy.com.au/ch/42631/181nd/1779204/744e6f2jr.html>
Heidelberg University, Germany

*_Nicolas Le Novère_* <http://dynamail.entegy.com.au/ch/42631/181nd/1779205/744e6pyxx.html>
Babraham Institute, United Kingdom

*_John Tyson_* <http://dynamail.entegy.com.au/ch/42631/181nd/1779206/744e6dqdz.html>
Virginia Tech, USA


   *Sponsorship and exhibition opportunities *

Come face-to-face with up to 700 researchers from specialties including mathematics, engineering, computer science, physics, chemistry, and even linguistics, chief scientists, managers, principal investigators, group leaders, and department heads from across a broad range of industries within Asia Pacific and beyond.

*_View opportunities available now_* <http://dynamail.entegy.com.au/ch/42631/181nd/1779890/744e6168pb.pdf>

ICSB 2014 offers you an excellent opportunity to develop new connections, strengthen existing relationships, and build future business prospects.

Contact the ICSB 2014 sponsorship team today by calling *+61 2 9213 4024 *or emailing _*sp...@ic...*_ <mailto:sp...@ic...>

Facebook Like Button <http://dynamail.entegy.com.au/ch/42631/181nd/1683682/744e6qxxb.html> Twitter Tweet Button <http://dynamail.entegy.com.au/ch/42631/181nd/1683683/744e68skq.html> LinkedIn Share Button <http://dynamail.entegy.com.au/ch/42631/181nd/1683684/744e612wyv.html>


This email was sent from ICSB 2014, MCI Australia, Level 2, 369 Royal Parade, Parkville, VIC 3052, Australia to com...@eb....


Unsubscribe <http://dynamail.entegy.com.au/forms/u/7d5419d/42631/1027603.html>

Re: [SED-ML-discuss] Proposal & Prototype: Accessing data files with SED-ML

[Nicolas Le N. <n.l...@gm...>]

On 24/04/14 22:12, Pedro Mendes wrote:
> On 04/24/2014 05:03 PM, Jonathan Cooper wrote:
>> On 24/04/2014 17:00, Frank Bergmann wrote:
>>>>> The dimensionDescription could also be redundant, as it just duplicates info
>>>>> from the NuML. It's mainly useful if the data file isn't NuML...
>>>> is there a case for it to be duplicated in the SED-ML document to
>>>> allow tools to maybe do something with the information without having
>>>> to revert to loading the NuML document? But if we do duplicate it in
>>>> the SED-ML, what do we do in the case where the descriptions do not
>>>> match?
>>>>
>>> the point is that there are different numl constructs that describe dimensions … it could just be a tuple description element, it could be an atomic dimension description and the like. Having the dimensionDescription element is a new construct in the SED-ML ns that contains  one of the elements. It is so, that we can describe what elements to include.
>>
>> Ah, so the NuML could potentially contain more datasets than the SED-ML
>> is interested in, and the dimensionDescription selects the relevant subset?
>>
>
> Of course we could also specify that the NuML included has to contain
> only the data used. This would perhpas simplify the schema, but would be
> more restrictive in what people can do with data files, etc.

Absolutely. We could easily imagine a SED-ML file that describe several tasks using different parts of the data, or even several SED-ML files using the same data file. I think forcing the duplication of the data files is a bit annoying, and might lead to problems when developing a project (e.g. creating a new simulation by cloning the SED-ML file requires also cloning the data file etc.)


-- 
Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
Tel: +441223496433   Mob:+447833147074   n.l...@gm...
orcid.org//0000-0002-6309-7327  http://lenoverelab.org/perso/lenov/
Skype:n.lenovere  twitter:@lenovere  http://nlenov.wordpress.com/

Re: [SED-ML-discuss] Proposal & Prototype: Accessing data files with SED-ML

[Pedro M. <ped...@ma...>]

On 04/24/2014 05:03 PM, Jonathan Cooper wrote:
> On 24/04/2014 17:00, Frank Bergmann wrote:
>>>> The dimensionDescription could also be redundant, as it just duplicates info
>>>> from the NuML. It's mainly useful if the data file isn't NuML...
>>> is there a case for it to be duplicated in the SED-ML document to
>>> allow tools to maybe do something with the information without having
>>> to revert to loading the NuML document? But if we do duplicate it in
>>> the SED-ML, what do we do in the case where the descriptions do not
>>> match?
>>>
>> the point is that there are different numl constructs that describe dimensions … it could just be a tuple description element, it could be an atomic dimension description and the like. Having the dimensionDescription element is a new construct in the SED-ML ns that contains  one of the elements. It is so, that we can describe what elements to include.
>
> Ah, so the NuML could potentially contain more datasets than the SED-ML
> is interested in, and the dimensionDescription selects the relevant subset?
>

Of course we could also specify that the NuML included has to contain 
only the data used. This would perhpas simplify the schema, but would be 
more restrictive in what people can do with data files, etc.

Pedro

-- 
Pedro Mendes
Professor of Computational Systems Biology
School of Computer Science
Manchester Centre for Integrative Systems Biology
University of Manchester

Manchester Institute of Biotechnology
131 Princess Street
Manchester, M1 7DN, U.K.

Re: [SED-ML-discuss] Proposal & Prototype: Accessing data files with SED-ML

[Frank B. <fbe...@ca...>]

On Apr 24, 2014, at 5:03 PM, Jonathan Cooper <jon...@cs...> wrote:

> On 24/04/2014 17:00, Frank Bergmann wrote:
>>>> The dimensionDescription could also be redundant, as it just duplicates info
>>>> from the NuML. It's mainly useful if the data file isn't NuML...
>>> is there a case for it to be duplicated in the SED-ML document to
>>> allow tools to maybe do something with the information without having
>>> to revert to loading the NuML document? But if we do duplicate it in
>>> the SED-ML, what do we do in the case where the descriptions do not
>>> match?
>>> 
>> the point is that there are different numl constructs that describe dimensions … it could just be a tuple description element, it could be an atomic dimension description and the like. Having the dimensionDescription element is a new construct in the SED-ML ns that contains  one of the elements. It is so, that we can describe what elements to include.
> 
> Ah, so the NuML could potentially contain more datasets than the SED-ML 
> is interested in, and the dimensionDescription selects the relevant subset?
> 

If I understand you correctly then yes :) It would be perfectly fine to have this example: 

https://code.google.com/p/numl/source/browse/trunk/numl-spec-l1v1.pdf

<dimensionDescription>
<tupleDescription id=“test"> 
 <atomicDescription id=“ov" name="Objective Value" valueType="float" /> 
 <atomicDescription id=“rms” name="Root Mean Square" valueType="float" /> 
 <atomicDescription if=“sd” name="Standard Deviation" valueType="float" /> 
 </tupleDescription> 
<dimensionDescription>

in this case we would just have three values in the file … or we could have a compositeDescription of those … 

Frank

> Best wishes,
> Jonathan
> 
> 
> ------------------------------------------------------------------------------
> Start Your Social Network Today - Download eXo Platform
> Build your Enterprise Intranet with eXo Platform Software
> Java Based Open Source Intranet - Social, Extensible, Cloud Ready
> Get Started Now And Turn Your Intranet Into A Collaboration Platform
> http://p.sf.net/sfu/ExoPlatform
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Proposal & Prototype: Accessing data files with SED-ML

[Jonathan C. <jon...@cs...>]

On 24/04/2014 17:00, Frank Bergmann wrote:
>>> The dimensionDescription could also be redundant, as it just duplicates info
>>> from the NuML. It's mainly useful if the data file isn't NuML...
>> is there a case for it to be duplicated in the SED-ML document to
>> allow tools to maybe do something with the information without having
>> to revert to loading the NuML document? But if we do duplicate it in
>> the SED-ML, what do we do in the case where the descriptions do not
>> match?
>>
> the point is that there are different numl constructs that describe dimensions … it could just be a tuple description element, it could be an atomic dimension description and the like. Having the dimensionDescription element is a new construct in the SED-ML ns that contains  one of the elements. It is so, that we can describe what elements to include.

Ah, so the NuML could potentially contain more datasets than the SED-ML 
is interested in, and the dimensionDescription selects the relevant subset?

Best wishes,
Jonathan

Re: [SED-ML-discuss] Proposal & Prototype: Accessing data files with SED-ML

[Frank B. <fbe...@ca...>]

On Apr 24, 2014, at 4:51 PM, David Nickerson <dav...@gm...> wrote:

>> If we’re restricting the file type to NuML, then definitely remove the type
>> attribute (we can add it if we support other formats in the future).
> 
> +1
> 

fine .. 

>> The dimensionDescription could also be redundant, as it just duplicates info
>> from the NuML. It's mainly useful if the data file isn't NuML...
> 
> is there a case for it to be duplicated in the SED-ML document to
> allow tools to maybe do something with the information without having
> to revert to loading the NuML document? But if we do duplicate it in
> the SED-ML, what do we do in the case where the descriptions do not
> match?
> 

the point is that there are different numl constructs that describe dimensions … it could just be a tuple description element, it could be an atomic dimension description and the like. Having the dimensionDescription element is a new construct in the SED-ML ns that contains  one of the elements. It is so, that we can describe what elements to include. 

Frank

> ------------------------------------------------------------------------------
> Start Your Social Network Today - Download eXo Platform
> Build your Enterprise Intranet with eXo Platform Software
> Java Based Open Source Intranet - Social, Extensible, Cloud Ready
> Get Started Now And Turn Your Intranet Into A Collaboration Platform
> http://p.sf.net/sfu/ExoPlatform
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] proposal for accessing data in sed-ml

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

just to note that the proposal (in github) has now been updated with
Dagmar's suggested change.


Cheers,
David.

On Thu, Apr 24, 2014 at 2:28 PM, Frank Bergmann <fbe...@ca...> wrote:
> That sounds good to me, in order for the process to be as fast as possible, I moved the proposal document onto github, and we  can all edit from there. So far I only have dagmars git account though. You could either privately mail me yours and I add you as collaborator, or we do the normal fork/ pull request thing to get it done.
>
> https://github.com/fbergmann/sedml-data-proposal
>
> Frank
>
>
> On Apr 24, 2014, at 12:27 PM, Jonathan Cooper <jon...@cs...> wrote:
>
>> +1 from me!
>>
>> Best wishes,
>> Jonathan
>>
>> On 24/04/2014 12:24, Dagmar Waltemath wrote:
>>> Hi all,
>>>
>>> at the HARMONY right now we have been looking at the proposal for linking data in SED-ML files (using NuML).
>>> The PDF that was generated by Frank is at: http://co.mbine.org/standards/sed-ml/proposal
>>>
>>> I would like to suggest a renaming of one (two actually) of the proposed new elements:
>>> Could we change the name of the new listOfExperimentalData to become "listOfDataSets"? The reason I think this is a good idea is because we do not only use the container for experimental data, but also, for example, to describe the values for parametrisation of a model [which not necessarily comes from experimental data].
>>> We may also consider renaming "dataDescription" to "dataSet" then?
>>>
>>> The example in Franks PDF ("An Example") would then read:
>>>
>>> <listOfDataSets>
>>>   <dataSet id="Data1" name="Oscli Time Course Data" source="http://svn.code.sf.net/p/libsedml/code/trunk/Samples/data/oscli.numl" type="urn:sedml:format:numl">
>>>     <dimensionDescription>
>>>       <compositeDescription indexType="double" id="time" name="time" xmlns="http://www.numl.org/numl/level1/version1">
>>>         <compositeDescription indexType="string" id="SpeciesIds" name="SpeciesIds">
>>>           <atomicDescription valueType="double" name="Concentrations" />
>>>         </compositeDescription>
>>>       </compositeDescription>
>>>     </dimensionDescription>
>>>     <listOfDataSources>
>>>        <dataSource id="dataS1">
>>>          <slice reference="SpeciesIds" value="S1" />
>>>        </dataSource>
>>>        <dataSource id="dataTime" indexSet="time" />
>>>     </listOfDataSources>
>>>   </dataSet>
>>> </listOfDataSets>
>>>
>>> Please note, this is only re-naming elements and does not change the structure.
>>> Dagmar
>>>
>>>
>>> Dagmar Waltemath, Dept. of Systems Biology & Bioinformatics,
>>> University of Rostock, D-18051 Rostock, Germany
>>> Web: http://www.sbi.uni-rostock.de/sems
>>> Skype: dagmar.waltemath
>>>
>>> ------------------------------------------------------------------------------
>>> Start Your Social Network Today - Download eXo Platform
>>> Build your Enterprise Intranet with eXo Platform Software
>>> Java Based Open Source Intranet - Social, Extensible, Cloud Ready
>>> Get Started Now And Turn Your Intranet Into A Collaboration Platform
>>> http://p.sf.net/sfu/ExoPlatform
>>> _______________________________________________
>>> SED-ML-discuss mailing list
>>> SED...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>>
>>
>> ------------------------------------------------------------------------------
>> Start Your Social Network Today - Download eXo Platform
>> Build your Enterprise Intranet with eXo Platform Software
>> Java Based Open Source Intranet - Social, Extensible, Cloud Ready
>> Get Started Now And Turn Your Intranet Into A Collaboration Platform
>> http://p.sf.net/sfu/ExoPlatform
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> ------------------------------------------------------------------------------
> Start Your Social Network Today - Download eXo Platform
> Build your Enterprise Intranet with eXo Platform Software
> Java Based Open Source Intranet - Social, Extensible, Cloud Ready
> Get Started Now And Turn Your Intranet Into A Collaboration Platform
> http://p.sf.net/sfu/ExoPlatform
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Proposal & Prototype: Accessing data files with SED-ML

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

> If we’re restricting the file type to NuML, then definitely remove the type
> attribute (we can add it if we support other formats in the future).

+1

> The dimensionDescription could also be redundant, as it just duplicates info
> from the NuML. It's mainly useful if the data file isn't NuML...

is there a case for it to be duplicated in the SED-ML document to
allow tools to maybe do something with the information without having
to revert to loading the NuML document? But if we do duplicate it in
the SED-ML, what do we do in the case where the descriptions do not
match?

Re: [SED-ML-discuss] proposal for accessing data in sed-ml

[Frank B. <fbe...@ca...>]

That sounds good to me, in order for the process to be as fast as possible, I moved the proposal document onto github, and we  can all edit from there. So far I only have dagmars git account though. You could either privately mail me yours and I add you as collaborator, or we do the normal fork/ pull request thing to get it done. 

https://github.com/fbergmann/sedml-data-proposal

Frank


On Apr 24, 2014, at 12:27 PM, Jonathan Cooper <jon...@cs...> wrote:

> +1 from me!
> 
> Best wishes,
> Jonathan
> 
> On 24/04/2014 12:24, Dagmar Waltemath wrote:
>> Hi all,
>> 
>> at the HARMONY right now we have been looking at the proposal for linking data in SED-ML files (using NuML).
>> The PDF that was generated by Frank is at: http://co.mbine.org/standards/sed-ml/proposal
>> 
>> I would like to suggest a renaming of one (two actually) of the proposed new elements:
>> Could we change the name of the new listOfExperimentalData to become "listOfDataSets"? The reason I think this is a good idea is because we do not only use the container for experimental data, but also, for example, to describe the values for parametrisation of a model [which not necessarily comes from experimental data].
>> We may also consider renaming "dataDescription" to "dataSet" then?
>> 
>> The example in Franks PDF ("An Example") would then read:
>> 
>> <listOfDataSets>
>>   <dataSet id="Data1" name="Oscli Time Course Data" source="http://svn.code.sf.net/p/libsedml/code/trunk/Samples/data/oscli.numl" type="urn:sedml:format:numl">
>>     <dimensionDescription>
>>       <compositeDescription indexType="double" id="time" name="time" xmlns="http://www.numl.org/numl/level1/version1">
>>         <compositeDescription indexType="string" id="SpeciesIds" name="SpeciesIds">
>>           <atomicDescription valueType="double" name="Concentrations" />
>>         </compositeDescription>
>>       </compositeDescription>
>>     </dimensionDescription>
>>     <listOfDataSources>
>>        <dataSource id="dataS1">
>>          <slice reference="SpeciesIds" value="S1" />
>>        </dataSource>
>>        <dataSource id="dataTime" indexSet="time" />
>>     </listOfDataSources>
>>   </dataSet>
>> </listOfDataSets>
>> 
>> Please note, this is only re-naming elements and does not change the structure.
>> Dagmar
>> 
>> 
>> Dagmar Waltemath, Dept. of Systems Biology & Bioinformatics,
>> University of Rostock, D-18051 Rostock, Germany
>> Web: http://www.sbi.uni-rostock.de/sems
>> Skype: dagmar.waltemath
>> 
>> ------------------------------------------------------------------------------
>> Start Your Social Network Today - Download eXo Platform
>> Build your Enterprise Intranet with eXo Platform Software
>> Java Based Open Source Intranet - Social, Extensible, Cloud Ready
>> Get Started Now And Turn Your Intranet Into A Collaboration Platform
>> http://p.sf.net/sfu/ExoPlatform
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
> 
> 
> ------------------------------------------------------------------------------
> Start Your Social Network Today - Download eXo Platform
> Build your Enterprise Intranet with eXo Platform Software
> Java Based Open Source Intranet - Social, Extensible, Cloud Ready
> Get Started Now And Turn Your Intranet Into A Collaboration Platform
> http://p.sf.net/sfu/ExoPlatform
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] proposal for accessing data in sed-ml

[Pedro M. <ped...@ma...>]

I think this is great.
Pedro

On 04/24/2014 12:24 PM, Dagmar Waltemath wrote:
> Hi all,
>
> at the HARMONY right now we have been looking at the proposal for linking data in SED-ML files (using NuML).
> The PDF that was generated by Frank is at: http://co.mbine.org/standards/sed-ml/proposal
>
> I would like to suggest a renaming of one (two actually) of the proposed new elements:
> Could we change the name of the new listOfExperimentalData to become "listOfDataSets"? The reason I think this is a good idea is because we do not only use the container for experimental data, but also, for example, to describe the values for parametrisation of a model [which not necessarily comes from experimental data].
> We may also consider renaming "dataDescription" to "dataSet" then?
>
> The example in Franks PDF ("An Example") would then read:
>
> <listOfDataSets>
>    <dataSet id="Data1" name="Oscli Time Course Data" source="http://svn.code.sf.net/p/libsedml/code/trunk/Samples/data/oscli.numl" type="urn:sedml:format:numl">
>      <dimensionDescription>
>        <compositeDescription indexType="double" id="time" name="time" xmlns="http://www.numl.org/numl/level1/version1">
>          <compositeDescription indexType="string" id="SpeciesIds" name="SpeciesIds">
>            <atomicDescription valueType="double" name="Concentrations" />
>          </compositeDescription>
>        </compositeDescription>
>      </dimensionDescription>
>      <listOfDataSources>
>         <dataSource id="dataS1">
>           <slice reference="SpeciesIds" value="S1" />
>         </dataSource>
>         <dataSource id="dataTime" indexSet="time" />
>      </listOfDataSources>
>    </dataSet>
> </listOfDataSets>
>
> Please note, this is only re-naming elements and does not change the structure.
> Dagmar
>
>
> Dagmar Waltemath, Dept. of Systems Biology & Bioinformatics,
> University of Rostock, D-18051 Rostock, Germany
> Web: http://www.sbi.uni-rostock.de/sems
> Skype: dagmar.waltemath
>
> ------------------------------------------------------------------------------
> Start Your Social Network Today - Download eXo Platform
> Build your Enterprise Intranet with eXo Platform Software
> Java Based Open Source Intranet - Social, Extensible, Cloud Ready
> Get Started Now And Turn Your Intranet Into A Collaboration Platform
> http://p.sf.net/sfu/ExoPlatform
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>

-- 
Pedro Mendes
Professor of Computational Systems Biology
School of Computer Science
Manchester Centre for Integrative Systems Biology
University of Manchester

Manchester Institute of Biotechnology
131 Princess Street
Manchester, M1 7DN, U.K.

Re: [SED-ML-discuss] proposal for accessing data in sed-ml

[Jonathan C. <jon...@cs...>]

+1 from me!

Best wishes,
Jonathan

On 24/04/2014 12:24, Dagmar Waltemath wrote:
> Hi all,
>
> at the HARMONY right now we have been looking at the proposal for linking data in SED-ML files (using NuML).
> The PDF that was generated by Frank is at: http://co.mbine.org/standards/sed-ml/proposal
>
> I would like to suggest a renaming of one (two actually) of the proposed new elements:
> Could we change the name of the new listOfExperimentalData to become "listOfDataSets"? The reason I think this is a good idea is because we do not only use the container for experimental data, but also, for example, to describe the values for parametrisation of a model [which not necessarily comes from experimental data].
> We may also consider renaming "dataDescription" to "dataSet" then?
>
> The example in Franks PDF ("An Example") would then read:
>
> <listOfDataSets>
>    <dataSet id="Data1" name="Oscli Time Course Data" source="http://svn.code.sf.net/p/libsedml/code/trunk/Samples/data/oscli.numl" type="urn:sedml:format:numl">
>      <dimensionDescription>
>        <compositeDescription indexType="double" id="time" name="time" xmlns="http://www.numl.org/numl/level1/version1">
>          <compositeDescription indexType="string" id="SpeciesIds" name="SpeciesIds">
>            <atomicDescription valueType="double" name="Concentrations" />
>          </compositeDescription>
>        </compositeDescription>
>      </dimensionDescription>
>      <listOfDataSources>
>         <dataSource id="dataS1">
>           <slice reference="SpeciesIds" value="S1" />
>         </dataSource>
>         <dataSource id="dataTime" indexSet="time" />
>      </listOfDataSources>
>    </dataSet>
> </listOfDataSets>
>
> Please note, this is only re-naming elements and does not change the structure.
> Dagmar
>
>
> Dagmar Waltemath, Dept. of Systems Biology & Bioinformatics,
> University of Rostock, D-18051 Rostock, Germany
> Web: http://www.sbi.uni-rostock.de/sems
> Skype: dagmar.waltemath
>
> ------------------------------------------------------------------------------
> Start Your Social Network Today - Download eXo Platform
> Build your Enterprise Intranet with eXo Platform Software
> Java Based Open Source Intranet - Social, Extensible, Cloud Ready
> Get Started Now And Turn Your Intranet Into A Collaboration Platform
> http://p.sf.net/sfu/ExoPlatform
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Proposal & Prototype: Accessing data files with SED-ML

[Jonathan C. <jon...@cs...>]

Hi all,

Some thoughts on Frank's proposal:

  * If we're restricting the file type to NuML, then definitely remove
    the type attribute (we can add it if we support other formats in the
    future).
      o The dimensionDescription could also be redundant, as it just
        duplicates info from the NuML.It's mainly useful if the data
        file /isn't/ NuML...
  * Would there be any benefit of extending the slicing to take subsets
    of a dimension? Or is this better left until we can do more
    operations on n-d arrays...?
  * Using #id in the target attribute is consistent with what we
    introduced for repeatedTask, so that's good. I'm less happy with
    having to introduce modelReference in order to resolve XPath within
    the NuML - it seems cleaner to me for this to be specified within
    NuML itself.
  * We do need to think further about referencing a data set in
    setValue, since this would want a different element from the data
    set for each iteration around the associated loop. This gets even
    more complex with multiple nesting levels. Having a dataRange might
    well be the neatest solution here.
  * I like the suggestion for a construct to parametrise a model from a
    data set!


Having looked into NuML a bit more, while considering how to add support 
for it in my tools, I have a few concerns on that front too.

  * The ontologyTerm definition is rather verbose. It might be nicer
    (and more consistent with other RDF technologies) to allow defining
    a prefix which maps to an ontology URI, and then use
    ontologyTerm="prefix:term" when referencing.
  * The verbosity of NuML is also an issue for some data sets I deal
    with. I have protocols where the bulk of the time is spent in i/o if
    you read or write CSV files, let alone XML! Are there any plans to
    allow separating the dimension descriptions from the raw data?

Best wishes,
Jonathan


On 17/04/2014 20:56, Frank T. Bergmann wrote:
> Hello,
>
> I would like to propose that at next week's HARMONY, we bring things back to
> the roots, and start prototyping what we have been talking about over the
> last two years. I went ahead and started to try out what we discussed in the
> Google Document: accessing data files in SED-ML. This is done by referencing
> a NuML description, and narrowing down the data contained within the files
> to what is applicable. I wrote down precisely, what I feel is necessary to
> do so.
>
> http://co.mbine.org/specifications/sed-ml.proposal.accessing-data.version-1.
> pdf
>
> If we continue that way at the end of next week we might have a prototype
> for parameter estimation as well. Or at the least we could potentially
> exchange a simulation experiment referencing data elements as well.
>
> All the best, hope to see you at HARMONY
>
> Frank
>
>
>
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/NeoTech
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] proposal for accessing data in sed-ml

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

> I would like to suggest a renaming of one (two actually) of the proposed new elements:
> Could we change the name of the new listOfExperimentalData to become "listOfDataSets"? The reason I think this is a good idea is because we do not only use the container for experimental data, but also, for example, to describe the values for parametrisation of a model [which not necessarily comes from experimental data].
> We may also consider renaming "dataDescription" to "dataSet" then?

+1

[SED-ML-discuss] proposal for accessing data in sed-ml

[Dagmar W. <dag...@un...>]

Hi all,

at the HARMONY right now we have been looking at the proposal for linking data in SED-ML files (using NuML). 
The PDF that was generated by Frank is at: http://co.mbine.org/standards/sed-ml/proposal 

I would like to suggest a renaming of one (two actually) of the proposed new elements: 
Could we change the name of the new listOfExperimentalData to become "listOfDataSets"? The reason I think this is a good idea is because we do not only use the container for experimental data, but also, for example, to describe the values for parametrisation of a model [which not necessarily comes from experimental data]. 
We may also consider renaming "dataDescription" to "dataSet" then? 

The example in Franks PDF ("An Example") would then read:

<listOfDataSets>
  <dataSet id="Data1" name="Oscli Time Course Data" source="http://svn.code.sf.net/p/libsedml/code/trunk/Samples/data/oscli.numl" type="urn:sedml:format:numl">
    <dimensionDescription>
      <compositeDescription indexType="double" id="time" name="time" xmlns="http://www.numl.org/numl/level1/version1">
        <compositeDescription indexType="string" id="SpeciesIds" name="SpeciesIds">
          <atomicDescription valueType="double" name="Concentrations" />
        </compositeDescription>
      </compositeDescription>
    </dimensionDescription>
    <listOfDataSources>
       <dataSource id="dataS1">
         <slice reference="SpeciesIds" value="S1" />
       </dataSource>
       <dataSource id="dataTime" indexSet="time" />
    </listOfDataSources>
  </dataSet>
</listOfDataSets>

Please note, this is only re-naming elements and does not change the structure.
Dagmar


Dagmar Waltemath, Dept. of Systems Biology & Bioinformatics,
University of Rostock, D-18051 Rostock, Germany
Web: http://www.sbi.uni-rostock.de/sems
Skype: dagmar.waltemath