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

Re: [SED-ML-discuss] Question about the sedml zip file

[Nicolas Le N. <le...@eb...>]

On 06/10/11 22:25, Lucian Smith wrote:
> * Nicolas Le Novre<le...@eb...>  [2011-10-06 22:12] writes:
>> On 06/10/11 22:01, Lucian Smith wrote:
>>> A single SED-ML file can have as many simulations in it as you want.
>>
>> Yes, but this does not cover all the need. For instance if we have to pipe
>> the result of a simulation in another simulation. At least until we have a
>> system of nested simulations like Frank's. Similarly if we have to run
>> separate simulations of different models using different simulators, using
>> some kind of synchronisation mechanism.
>
> With Frank's nested simulations would it be possible to perform the second
> task as well?

No, I do not think so.

 > If not, that sounds like something that needs to be
> proposed.

Oh, yes. That has been proposed several times, although not formally. But I 
know a few groups working on that. Simple synchronisation would be quite 
easy, for instance by using the model changing facilities but at run-time 
instead of before starting the simulation task. But when it comes to 
synchronise simulation based on different approaches, or very different 
time scale or iteration, it is a bit more problematic. Plus you need to 
encode the synchronisation algorithms.

But we'll get there.

-- 
Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,
Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

Re: [SED-ML-discuss] Question about the sedml zip file

[Nicolas Le N. <le...@eb...>]

Indeed, I think SED-ML is not the right vehicle ... per se. But with NuML, 
I think we will be able to deal with multiple datasets.

When it comes to multiple alternative parameterisations, I believe the SBML 
distrib package would be a better solution.

On 06/10/11 22:24, Herbert Sauro wrote:
> I am thinking of the situation where some one has one model but multiple
> virtual patients. At the moment I deal with this by having an annotation
> that describes multiple datasets in the sbml file itself which can get
> quite big and all the patients are together in one file rather than
> being represented separately. Perhaps sedml is not the right vehicle for
> this use case?
>
> Herbert
> ------------------------------------------------------------------------------
>
>
All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________ SED-ML-discuss mailing
> list SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss


-- 
Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,
Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

Re: [SED-ML-discuss] Question about model IDs

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

The idea of an archive file works well when you have a single
transferable set of data that gets shipped from user to user with no
need to track or merge changes from different users (i.e., one
developer many users). DOCX archives work because Word provides very
sophisticated edit tracking and merging functionality - is this
functionality something that SED-ML tools want to develop and support?

An alternative, that we have been using successfully in the Physiome
Model Repository, is the idea of using mercurial repositories as a
"workspace" in which you contain all data related to a piece of work.
This piece of work could be anything from a complete model with
simulation descriptions and outputs, experimental data used to fit the
model, etc. to a single sub-component of a generic model constituent
designed as part of a component library. While we use mercurial, any
versioning system could be used instead. The advantage of this
approach is that the user is able to embed repositories within
repositories (subrepos in mercurial, submodules in git, externals in
svn) and manage the versioning of embedded repositories such that the
user can choose whether to track latest changes or fix on a specific
version that is know to be "correct".

We find that this allows modellers to easily[1] ship their work
between each other while maintaining a decent provenance record of the
developments. While it is not always going to be optimal to include
all types of data in a single type of repository, mercurial at least
(and probably the other systems), allows embedding different types of
repository within a repository. We're starting now to think about how
this would work when you start wanting to include datasets that are
huge (e.g., large image collections used to fit patient specific
cardiac models, or the simulation results of several million cell
models in a stomach). But at least in terms of the work currently
being done with CellML models, mercurial  repositories are proving
sufficient.

When a user simply wants to grab a particular piece of work from the
repository for their own use, the website (and soon webservices)
provide a way to download a static archive containing the contents of
the workspace. Again, we're still trying to work out what to do in the
case where an workspace links to datasets that can easily be multiple
gigabytes in size. And we are certainly open to any help on this
issue.

Cheers,
David.

[1] There is currently a lack of tool support for this, so users
pretty much have to manage their mercurial workspaces using mercurial
directly. This is not always ideal and is also something we are
thinking about and working on to some degree for certain applications.

On Fri, Oct 7, 2011 at 9:41 AM, Richard Adams <ric...@ed...> wrote:
>
> For those unfamiliar with the concept of the SEDX archive format: It's a
> zipped archive of a SED-ML file and >=1 model file. Would an equally simple
> solution be acceptable to incorporate other data files as well?
> For example, a zip with subfolders
> models/
> simulations/
> data/
> diagrams/
> results/
> Each resource could refer to other resources via relative URIs. E.g., in the
> scenario above, a SedML file would refer to ../models/model.xml. Of course,
> within an archive, external public resources can still be referred to if
> need be - for example, if a dataset is very large.
> In this approach all the folders are 'source' folders (i.e., inputs to
> computational tasks) except for results/, which could be used to contain the
> results of an experiment if need be.
> In SBSI we have the concept of a 'project' for modelling resources, with a
> defined folder structure largely similar to that proposed above, to enable
> tooling to reliably link and detect  resource files, and allow export of
> zipped archives for exchange between collaborators.  I'm not especially
> advocating its exact usage but just to say it's worked well for us.
> Best wishes
> Richard
> On 6 Oct 2011, at 17:05, Nicolas Le Novère wrote:
>
> It seems to me that the need of an archive is pervasive in all the M&S
> efforts. We want the models and the simulation descriptions together, but
> also the simulation results or the data-sets used to complement or fit the
> models, and of course the SBGN-ML files.
>
> And we are going in the same direction in DDMoRe, where the need is clearer
> since the mathematics only represent part of the "model".
>
> After all the  it is just like ODF or DOCX.
>
> I therefore propose to move that discussion to combine-discuss.
>
> On 06/10/11 16:43, Herbert Sauro wrote:
>
> Thank you Richard, that is exactly what I wanted to know, will read appendix
> D.  The zip file idea has been floated around for a while (since 2004 I
> think by Cliff Shaffer in particular) but in the past there was never
> anything to zip with the sbml model until the advent of sedml.
>
> Herbert
>
> Sent from my iPad, hence excuse my typos.
>
> ------------------------------------------------------------------------------
>
> All the data continuously generated in your IT infrastructure contains a
>
> definitive record of customers, application performance, security
>
> threats, fraudulent activity and more. Splunk takes this data and makes
>
> sense of it. Business sense. IT sense. Common sense.
>
> http://p.sf.net/sfu/splunk-d2dcopy1
>
> _______________________________________________
>
> SED-ML-discuss mailing list
>
> SED...@li...
>
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> --
> Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,
> Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
> Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere
> http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
> Dr Richard Adams
> Software Development Team Leader,
> Centre For Systems Biology Edinburgh
> University of Edinburgh
> Tel: 0131 651 9019
> email : ric...@ed...
> Web: http://csbe.bio.ed.ac.uk/adams.php
>
>
>
>
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>

Re: [SED-ML-discuss] Question about the sedml zip file

[Lucian S. <lp...@sp...>]

* Nicolas Le Novre <le...@eb...> [2011-10-06 22:12] writes:
> On 06/10/11 22:01, Lucian Smith wrote:
> > A single SED-ML file can have as many simulations in it as you want.
> 
> Yes, but this does not cover all the need. For instance if we have to pipe 
> the result of a simulation in another simulation. At least until we have a 
> system of nested simulations like Frank's. Similarly if we have to run 
> separate simulations of different models using different simulators, using 
> some kind of synchronisation mechanism.

With Frank's nested simulations would it be possible to perform the second 
task as well?  If not, that sounds like something that needs to be 
proposed.

-Lucian

[SED-ML-discuss] Question about the sedml zip file

[Herbert S. <hsauro@u.washington.edu>]

I am thinking of the situation where some one has one model but multiple virtual patients. At the moment I deal with this by having an annotation that describes multiple datasets in the sbml file itself which can get quite big and all the patients are together in one file rather than being represented separately. Perhaps sedml is not the right vehicle for this use case?

Herbert

Re: [SED-ML-discuss] Question about the sedml zip file

[Nicolas Le N. <le...@eb...>]

On 06/10/11 22:01, Lucian Smith wrote:
> A single SED-ML file can have as many simulations in it as you want.

Yes, but this does not cover all the need. For instance if we have to pipe 
the result of a simulation in another simulation. At least until we have a 
system of nested simulations like Frank's. Similarly if we have to run 
separate simulations of different models using different simulators, using 
some kind of synchronisation mechanism.

For these situations, some part of the description still live in external 
non-standard descriptions. And it is much easier to write those if the 
"elementary" simulation and model descriptions are separated.

-- 
Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,
Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

Re: [SED-ML-discuss] Question about the sedml zip file

[Moraru,Ion <Mo...@NE...>]

A single SED-ML file can store the info about all the different simulations.

Sent from my phone


On Oct 6, 2011, at 16:40, "Herbert Sauro" <hsauro@u.washington.edu<mailto:hsauro@u.washington.edu>> wrote:


Frank, does this mean that if I were to do multiple independent simulations,
either all the simulations go in to one sedml in one zip archive with the appropriate model
or do I have a separate zip file for each simulation I do. You indicate that

A "desire to be able to take the archive and run with it."

therefore does this suggest one simulation and one model per zip archive?

Is there a list of use cases anywhere that the current sedml is meant to support?

Herbert

Sent from my iPad, hence excuse my typos.
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
SED-ML-discuss mailing list
SED...@li...<mailto:SED...@li...>
https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Question about the sedml zip file

[Lucian S. <lp...@sp...>]

A single SED-ML file can have as many simulations in it as you want.  If 
you really wanted to break things up into multiple files, you could use 
xinclude or something.  But yes, if you want one set of simulations that 
are clearly distinct from a different set of simulations, you would need 
multiple .zip archives (in the current scheme).  If you want to separate 
your .sedml files but they all act on the same .xml files, it would 
probably be best to just create a directory with everything there.

-Lucian

* Sauro lab <hsauro@u.washington.edu> [2011-10-06 21:47] writes:
> 
> Frank, does this mean that if I were to do multiple independent simulations,
> either all the simulations go in to one sedml in one zip archive with the appropriate model
> or do I have a separate zip file for each simulation I do. You indicate that
> 
> A "desire to be able to take the archive and run with it."
> 
> therefore does this suggest one simulation and one model per zip archive?
> 
> Is there a list of use cases anywhere that the current sedml is meant to support?
> 
> Herbert 
> 
> Sent from my iPad, hence excuse my typos.
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Question about the sedml zip file

[Richard A. <ric...@ed...>]

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

Re: [SED-ML-discuss] Question about model IDs

[Richard A. <ric...@ed...>]

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[SED-ML-discuss] Question about the sedml zip file

[Herbert S. <hsauro@u.washington.edu>]

Frank, does this mean that if I were to do multiple independent simulations,
either all the simulations go in to one sedml in one zip archive with the appropriate model
or do I have a separate zip file for each simulation I do. You indicate that

A "desire to be able to take the archive and run with it."

therefore does this suggest one simulation and one model per zip archive?

Is there a list of use cases anywhere that the current sedml is meant to support?

Herbert 

Sent from my iPad, hence excuse my typos.

Re: [SED-ML-discuss] Question about the sedml zip file

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

> I read appendix D regarding the sedml archive and noted the following sentence: 
> 
> "A SED-ML archive is [a] zipped folder containing one SED-ML file and any number of model files."
> 
> I am sure you've discussed this to great length but why is there a restriction of one sedml file and many model files? I could imagine a situation where one has one model but multiple virtual patients where each patient may be simulated differently. At the moment all simulations would be stored in one file. 
> 

This stems from the desire to be able to take the archive and run with it. In other words we always want one SED-ML document there that can be executed. If you want the analogy consider a word / open office document. It also is just an archive but when you open it, you do get one document displayed. 

Frank

> Herbert
> 
> 
> Sent from my iPad, hence excuse my typos.
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

Re: [SED-ML-discuss] Question about model IDs

[Nicolas Le N. <le...@eb...>]

It seems to me that the need of an archive is pervasive in all the M&S 
efforts. We want the models and the simulation descriptions together, but 
also the simulation results or the data-sets used to complement or fit the 
models, and of course the SBGN-ML files.

And we are going in the same direction in DDMoRe, where the need is clearer 
since the mathematics only represent part of the "model".

After all the  it is just like ODF or DOCX.

I therefore propose to move that discussion to combine-discuss.

On 06/10/11 16:43, Herbert Sauro wrote:
>
> Thank you Richard, that is exactly what I wanted to know, will read appendix D.  The zip file idea has been floated around for a while (since 2004 I think by Cliff Shaffer in particular) but in the past there was never anything to zip with the sbml model until the advent of sedml.
>
> Herbert
>
> Sent from my iPad, hence excuse my typos.
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss


-- 
Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,
Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

[SED-ML-discuss] Question about the sedml zip file

[Herbert S. <hsauro@u.washington.edu>]

I read appendix D regarding the sedml archive and noted the following sentence: 

"A SED-ML archive is [a] zipped folder containing one SED-ML file and any number of model files."

I am sure you've discussed this to great length but why is there a restriction of one sedml file and many model files? I could imagine a situation where one has one model but multiple virtual patients where each patient may be simulated differently. At the moment all simulations would be stored in one file. 

Herbert


Sent from my iPad, hence excuse my typos.

[SED-ML-discuss] Question about model IDs

[Herbert S. <hsauro@u.washington.edu>]

Thank you Richard, that is exactly what I wanted to know, will read appendix D.  The zip file idea has been floated around for a while (since 2004 I think by Cliff Shaffer in particular) but in the past there was never anything to zip with the sbml model until the advent of sedml.

Herbert

Sent from my iPad, hence excuse my typos.

Re: [SED-ML-discuss] Question about model IDs

[Richard A. <ric...@ed...>]

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[SED-ML-discuss] Question about model IDs

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

I have a question about SED-ML which may have been answered already
but in section 1.2.2 (Models) of the SED-ML Version 1.1 document there
is the following sentence:

"The models to be used in the experiment (zero or many) are
referenced, using a link to a model description in some open, curated
model database (e. g. Biomodels Database [Li et al., 2010] or CellML
Repository [Beard et al., 2009])."

What happens in the case where the model is on a persons hard drive
and not stored at a repository ? Can they reference that model or how
would it work?

Herbert Sauro

[SED-ML-discuss] Fwd: [COMBINE 2011] Release of CellDesigner 4.2

[Nicolas Le N. <le...@eb...>]

Dear Colleagues,

See the release announcement for CellDesigner below. Note SED-ML in the new 
features.

-------- Original Message --------
Subject: [COMBINE 2011] Release of CellDesigner 4.2
Date: Wed, 5 Oct 2011 16:53:34 +0900
From: Akira Funahashi <fu...@bi...>
Reply-To: com...@go...
To: sbm...@ca..., com...@go...

We are pleased to announce the release of CellDesigner4.2.
CellDesigner4.2 is available from

  http://celldesigner.org/
  http://systems-biology.org/software/celldesigner/celldesigner-42.html
(quick link to download)

Overview:
=========
  CellDesigner is a modeling tool of biochemical networks with
  graphical user interface. It is designed to be SBML compatible, and
  SBW (Systems Biology Workbench) enabled. For details, please see our
  web site (http://celldesigner.org).

  CellDesigner runs on Windows, Mac OS X and Linux, and it can
  import/export SBML Level-1 and Level-2 documents (w/ and w/o
  CellDesigner specific <annotation> tags).

New Features:
=============
New Feature:
   * Reduced Notation support
     - Reduced representation of the process diagram.
   * Enable to add anchor points to Add Reactant/Add Prodcut Reaction arcs
   * Simulation - Parameter Polymorphism support
     - "Experiment" support
     - Store simulation condition in SED-ML.
   * New Simulator Support
     - SBMLsimulator (http://sourceforge.org/projects/sbml-simulator)
   * Database Connection
     - Connect to UniProt
     - Connect to MIRIAM annotation (PubMed / UniProt) via [Database] menu.
     - Connect to JWS Online Cellular Systems Modeling
     - Connect to Panther web
   * Plug-in Development enhancement
     - Develop your plugin on Eclipse, and you can call the plugin from
Plugin menu.
       =>See also Plugin Development Tutorial
   * SBGN View enhancement
     - Convert to SBGN Viewer on the View menu has been renamed Convert
to SBGN PD view.
     - The Show SBGN Compliants option has been added to the View menu.
   * [Change Toolbar Visible] menu has been added to the View menu.
   * Anchor Point enhancement
     - Anchor point function is available for the reaction which is
drawn using Add Reactant and Add Product.
   * import model function enhancement
     - Search by name function has been implemented in Import model
from BioModels.net or Pantherdb.org on the Database menu.

Updates:
   * COPASI libraries
   * SABIO-RK libraries
   * Sample files

Bug Fixes:
   * Fixed SBML validation error when saving the file
   * Fixed duplicate entry in KineticLaw annotation
   * Fixed Database connections (BioModels.net)
   * And lots of minor bug fixes :-)

Acknowledgment:
===============
  We appreciate Rainer Machne and Christoph Flamm at Univ. of Vienna
  for providing us a library version of SBML ODE Solver (SOSlib).
  We appreciate Ralph Gauges, Sven Sahle and Ursula Kummer at Univ. of
  Heidelberg for the development of a library version of COPASI.
  We appreciate Martin Golebiewski, Saqib Mir, Wolfgang Mueller and
  Isabel Rojas at EML Research gGmbH for the development of SABIO-RK Web 
Service.
  We appreciate Frank Bergmann and Herbert Sauro at Univ. of
  Washington for helping us support SBW-2.x on CellDesigner.
  We appreciate Andreas Drager Alexander Dorr, and Roland Keller at
  University of Tubingen for the development of SBMLsimulator.
  We also appreciate Huaiyu Mi, Anushya Muruganujan and Paul Thomas at
  University of Southern California for helping us supporting Panther
  pathways database connection.
  With the support of these libraries and frameworks, CellDesigner can
  now integrate with many simulation/analysis tools.
  And many thanks to the users who kindly provided us bug reports and
  feature requests.

Please feel free to contact us (in...@ce...) with any
questions or bug reports you may have.

Thanks,
--
CellDesigner Development Team
in...@ce...

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[SED-ML-discuss] Nested simulations and chains of procedures in PKPD

[Nicolas Le N. <le...@eb...>]

I am attending a session of the DDMoRe project. 2 hours of discussions 
about encoding workflows, nested simulations and chains of procedures in 
pharmacometrics activity. The markup encoding will use SED-ML and 
complement it for the pieces of the workflow that are not covered.

Same discussions that we have on declarative versus procedural approaches.

-- 
Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,
Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

Re: [SED-ML-discuss] Configuring algorithm-specific parameters

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

On 18/09/2011 23:43, David Nickerson wrote:
> I'm just wondering (thinking out loud) if we need to worry about 
> default values? The same algorithm with different parameter values can 
> give very different results - so with some parameters set but others 
> left to the implementation's default values you can get different 
> results for the same simulation experiment description. But I guess 
> this is really no different to different implementations of the same 
> algorithm can also give different results...so maybe something we 
> don't need to worry about? SED authors that want to do their best to 
> ensure a reproducible experiment would simply specify all algorithm 
> specific parameter values, and that is probably an acceptable burden 
> on authors - which I think answers my own question...

I agree that we don't want to provide default values.  While tolerances 
are very important, since one should only trust a numerical simulation 
if the tolerances are set such that the solution is sufficiently 
converged, the appropriate level will depend on the model.

Best wishes,
Jonathan

[SED-ML-discuss] combineVRL

[Sarah K. <ske...@ca...>]

Invitation to participate

During the 2011 COMBINE meeting
(http://co.mbine.org/events/COMBINE_2011) a number of delegates met to
discuss standardising the format for the output of validation of various
standards. This proved to be an extremely useful and productive meeting
and it was decided to form a project with the aim of developing a common
format for reporting validation results that is independent of the
method of validation; combineVRL (Validation Report Language).

We have started a sourceforge project
http://sourceforge.net/projects/combinevrl/

Notes from the meeting at COMBINE can be viewed here
http://sourceforge.net/p/combinevrl/code/4/tree/trunk/meetings/COMBINE-2011/NOTES%20FROM%20VALIDATION%20MEETING.pdf.

There is also a mailing list

https://lists.sourceforge.net/lists/listinfo/combinevrl-discuss

We invite any interested people to join and participate.

Thanks

Sarah Keating
on behalf of the validation breakout at COMBINE 2011

Re: [SED-ML-discuss] Overlap between SED-ML and SBML

[Nicolas Le N. <le...@eb...>]

Hi Richard ,

On 16/09/11 23:45, Richard Adams wrote:

> It seems that if it's possible to describe changes to a model during a
> simulation both in SED-ML and SBML, this will be confusing for both tool
> developers and end users, so perhaps we should try to establish some
> boundaries about the scope of a model, and a SED-ML description? At the
> moment it seems rather a grey area.

I agree that we should clarify the boundaries, but we should avoid to make 
them tight. IMHO, events such as:

If V > Vthreshold then V=Vreset

or

If Mass > Mlim then Mass=Mass/2

definitively belong to the model. The problem comes with things like "at 
t>T do this". I think those belong to SED-ML. But:

1) We cannot preclude them. Those events are just dependent on the value of 
a variable. Time is a variable. The fact that in SBML we have an implicit 
time, represented by a csymbol, does not make it special.

2) Until support of SED-ML everywhere, it is hard to tell people not to 
"abuse" SBML events (I do it see BIOMD0000000153).

However, the first thing is to provide structures in SED-ML to do it. Then 
we can encourage people to use SED-ML rather than SBML for that.

-- 
Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,
Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

Re: [SED-ML-discuss] Configuring algorithm-specific parameters

[Nicolas Le N. <le...@eb...>]

On 18/09/11 23:43, David Nickerson wrote:

> I'm just wondering (thinking out loud) if we need to worry about
> default values? The same algorithm with different parameter values can
> give very different results - so with some parameters set but others
> left to the implementation's default values you can get different
> results for the same simulation experiment description.

I would be very worried if the results were qualitatively different 
according to the tuning of the simulator. I know that happens quite a lot 
for instance in neuroscience and ecological modeling. But one could 
question the accuracy and usefulness of such models ...

> But I guess
> this is really no different to different implementations of the same
> algorithm can also give different results...

Exactly. My worry is that next, we will need to specify the hardware on 
which the simulation is ran ...

so maybe something we
> don't need to worry about? SED authors that want to do their best to
> ensure a reproducible experiment would simply specify all algorithm
> specific parameter values, and that is probably an acceptable burden
> on authors - which I think answers my own question...
>
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-- 
Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,
Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

Re: [SED-ML-discuss] Configuring algorithm-specific parameters

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

On Tue, Sep 13, 2011 at 8:59 PM, Nicolas Le Novère <le...@eb...> wrote:
> On 13/09/11 04:36, David Nickerson wrote:
>
>> That seems like a sensible approach, and if I remember the discussions
>> correctly its also why algorithm was moved to be an element instead of
>> an attribute. I should probably look myself, but does anyone know off
>> the top of their head whether KiSAO defines default values for all the
>> parameters for all the algorithms?
>
> Default values are not provided at the moment (and this is not on the
> agenda). We provide types, such as "double" or "integer".
>

I'm just wondering (thinking out loud) if we need to worry about
default values? The same algorithm with different parameter values can
give very different results - so with some parameters set but others
left to the implementation's default values you can get different
results for the same simulation experiment description. But I guess
this is really no different to different implementations of the same
algorithm can also give different results...so maybe something we
don't need to worry about? SED authors that want to do their best to
ensure a reproducible experiment would simply specify all algorithm
specific parameter values, and that is probably an acceptable burden
on authors - which I think answers my own question...

[SED-ML-discuss] FW: [Biomodels-net-discuss] [Combine-announce] COMBINE mailing lists

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

fyi

Dagmar


________________________________________
From: Nicolas Le Novère [le...@eb...]
Sent: 17 September 2011 19:36
To: com...@mb...
Subject: [Biomodels-net-discuss] [Combine-announce] COMBINE mailing lists

Dear Colleagues,

Some of you may not have attended the last day of COMBINE2011, and may not
be aware of new means of communication for this community. We set-up three
mailing lists:

To receive announcements from COMBINE, subscribe to:
com...@mb...
This list if very low flux, and members should not normally post on it.
(Note that the main list of each of the core COMBINE standards is already
subscriber, which is why you receive this message).

To discuss the goals, organization and operation of COMBINE, subscribe to:
com...@mb....
This list is open to all.

To report issues about the co.mbine.org website, send a mail to
com...@mb....
You cannot subscribe to this list, but only post message.

Best regards,

--
Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC,
Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468,
Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/

_______________________________________________
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