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

Re: [SED-ML-discuss] Sampling sensitivity analyses in SED-ML when uncertainty described in the model

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

Hi Andrew,

I don't see why nested simulations couldn't be used for this.  You don't need 
to set a variable within a nested simulation - it could just repeat the same 
inner simulation 'numberOfSamples' times, surely?  Assuming that the random 
seed wasn't reset each time, this should work.

Best wishes,
Jonathan

On 12/07/11 01:21, Andrew Miller wrote:
> Hi all,
>
> I've recently created and implemented proposal for representing
> parameter uncertainty in CellML models (so the posterior probability
> distribution for the parameter is part of the model); this immediately
> creates the possibility of performing sampling sensitivity analyses on
> the model to determine distributions of other parameters given the
> uncertainty in the model.
>
> Has anyone considered how to describe this type of simulation experiment
> in SED-ML? It is simpler than a parameter scan - essentially just an
> instruction to sample from the distributions already described in the
> model multiple times. Frank Bergemann's nested experiments proposal is
> also not directly useful in this case, because we don't want to
> explicitly set the values of variables, but instead, let them be sampled
> from the distribution in the model.
>
> I think one possible approach would be to inherit from UniformTimeCourse
> with a new simulation type, SamplingSensitivityAnalysis, with all the
> attributes and operations from UniformTimeCourse, along with
> 'numberOfSamples'.
>
> Best wishes,
> Andrew
>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss

[SED-ML-discuss] COMBINE 2011 - Early Bird Registration Deadline in 2 days

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

********************************************************************

 

                      C O M B I N E  2011

                      September 3-7, 2011

                      Heidelberg, Germany

 

             http://co.mbine.org/events/COMBINE_2011

 

      Early bird registration: until Friday, July 15th, 2011

 

********************************************************************

 

 

 

Dear Colleagues,

 

 

The deadline for early bird registration is approaching for the second COMBINE meeting taking place in Heidelberg (Germany), September 3-7, 2011. COMBINE 2011 will be hosted by the Heidelberg Institute for Theoretical Studies (HITS) and will follow immediately after the 12th International Conference on Systems Biology (ICSB2011).

 

We are please to announce that Michael White (University of Liverpool and University of Manchester) will treat us with a keynote lecture! Among other achievements, Mike and his group unravelled the role of oscillations in NF-kB signalling pathways, using a large panel of approaches including quantitative imaging and computational models.

 

If you are planning to join COMBINE 2011, please register and submit your abstracts as soon as possible using the following form:

 

http://www.surveymonkey.com/s/combine2011-registration <http://www.surveymonkey.com/s/combine2011-registration> 

 

 

The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of standards and formats in systems biology and related fields (http://co.mbine.org/) and creates a common platform for allied standardization efforts. The annual COMBINE meeting is a workshop-style event with oral presentations, posters and breakout sessions. Abstracts are welcome for posters and talks addressing topics such as the various standards encompassed by COMBINE (BioPax, SBGN, SBML, SED-ML), associated standardization efforts such as MIRIAM and the Systems Biology Ontology (SBO), and related standardization efforts like CellML or NeuroML, as well as for presentations of software systems using these standards.

 

 

We hope to see you in Heidelberg!

 

 

 

Martin Golebiewski

 

 

on behalf of the organizers:

 

 

* Gary Bader, University of Toronto, Canada

 

* Emek Demir, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, USA

 

* Martin Golebiewski, Heidelberg Institute for Theoretical Studies (HITS), Germany

 

* Michael Hucka, California Institute of Technology (Caltech), USA

 

* Nicolas Le Novère, European Bioinformatics Institute (EMBL-EBI), UK

 

* Sven Sahle, BioQuant at the University of Heidelberg, Germany

 

 

 

Martin Golebiewski


Phone: +49-6221-533-281
FAX: +49-6221-533-298
Email: mar...@h-... <blocked::mailto:mar...@h-.../omailto:mar...@h-.../t_blank> 

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_________________________________________________


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Managing Directors: Dr. h.c. Dr.-Ing. E.h. Klaus Tschira, Prof. Dr.-Ing. Andreas Reuter

 

[SED-ML-discuss] Sampling sensitivity analyses in SED-ML when uncertainty described in the model

[Andrew M. <ak....@au...>]

Hi all,

I've recently created and implemented proposal for representing 
parameter uncertainty in CellML models (so the posterior probability 
distribution for the parameter is part of the model); this immediately 
creates the possibility of performing sampling sensitivity analyses on 
the model to determine distributions of other parameters given the 
uncertainty in the model.

Has anyone considered how to describe this type of simulation experiment 
in SED-ML? It is simpler than a parameter scan - essentially just an 
instruction to sample from the distributions already described in the 
model multiple times. Frank Bergemann's nested experiments proposal is 
also not directly useful in this case, because we don't want to 
explicitly set the values of variables, but instead, let them be sampled 
from the distribution in the model.

I think one possible approach would be to inherit from UniformTimeCourse 
with a new simulation type, SamplingSensitivityAnalysis, with all the 
attributes and operations from UniformTimeCourse, along with 
'numberOfSamples'.

Best wishes,
Andrew

[SED-ML-discuss] IEEE e-Science 2011 Workshop on Interoperability in Scientific Computing

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

IEEE e-Science 2011 Workshop on Interoperability in Scientific Computing
========================================================================
5th December 2011, Stockholm, Sweden.
http://www.cs.ox.ac.uk/david.johnson/wisc11/
**FULL PAPERS DUE: MONDAY 18th JULY 2011**

The seventh IEEE e-Science conference, sponsored by the IEEE Computer
Society's Technical Committee for Scalable Computing (TCSC), will be
held in Stockholm, Sweden from 5th - 8th December 2011. The Workshop
on Interoperability in Scientific Computing will be held on the
morning of Monday 5th of December, and is co-located with the main
conference.

Approaches to modelling take many forms. The mathematical,
computational and encapsulated components of models can be diverse in
terms of complexity and scale, as well as in published implementation
(mathematics, source code, and executable files). Many of these
systems are attempting to solve real-world problems in isolation.
However the long-term scientific interest is in allowing greater
access to models and their data, and to enable simulations to be
combined in order to address ever more complex issues. Markup
languages, metadata specifications, and ontologies for different
scientific domains have emerged as pathways to greater
interoperability. Domain specific modelling languages allow for a
declarative development process to be achieved. Metadata
specifications enable coupling while ontologies allow cross platform
integration of data.

The goal of this workshop is to bring together researchers from across
scientific disciplines whose computational models require
interoperability. This may arise through interactions between
different domains, systems being modelled, connecting model
repositories, or coupling models themselves, for instance in
multi-scale or hybrid simulations. The outcomes of this workshop will
be to better understand the nature of multidisciplinary computational
modelling and data handling. Moreover we hope to identify common
abstractions and cross-cutting themes in future interoperability
research applied to the broader domain of scientific computing.

FINAL CALL FOR PAPERS

We invite submissions for high-quality papers (up to 8 pages in
length) within the context of scientific computing in any of the
traditional sciences (physics, chemistry, biology), engineering, or
scientific/mathematical modelling applied to the social sciences and
humanities. Papers should address progress, results or positions in
one or more of the following areas:

* Use of metadata standards for annotating scientific models and data
* Curating and publishing digital models and data to online repositories
* Meta-modelling and markup languages for model description
* Theoretical frameworks for combining disparate models, multi-scale models
* Using standardised data formats in computational models
* Domain-specific ontologies for the sciences

It is expected that the proceedings of the e-Science 2011 workshops
will be published by the IEEE Computer Society Press, USA, and will be
made available online through the IEEE Digital Library.

SUBMISSION PROCESS

Authors are invited to submit papers with unpublished, original work
of not more than 8 pages of double column text using single spaced 10
point size on 8.5 x 11 inch pages, as per IEEE 8.5 x 11 manuscript
guidelines.

Templates are available from here:
http://www.ieee.org/web/publications/pubservices/confpub/AuthorTools/conferenceTemplates.html.

Authors should submit a PDF or PostScript (level 2) file that will
print on a PostScript printer. Papers conforming to the above
guidelines should be submitted through the EasyChair submission system
here:
https://www.easychair.org/account/signin.cgi?conf=wisc11

Note, papers should NOT be submitted to the main e-Science 2011 paper
submission system, as they will not be directed to the workshop
organisers.

It is requested that at least one author of each accepted paper attend
the conference and workshop.

IMPORTANT DATES

**FULL PAPERS DUE: MONDAY 18th JULY 2011**
Notification of acceptance: 18th August 2011
Camera-ready: 16th September 2011
Workshop date: 5th December 2011

CHAIRS/ORGANISERS

David Johnson, Steve McKeever, (University of Oxford, UK)

PROGRAMME COMMITTEE

David Nickerson (University of Auckland, New Zealand)
Herbert Sauro (University of Washington, USA)
Steve Harris (University of Oxford, UK)
Jonathan Cooper (University of Oxford, UK)
Rutger Vos (University of Reading, UK)
Dagmar Waltemath (University of Rostock, Germany)
Daniele Gianni (European Space Agency)
Mike Stout (University of Nottingham, UK)

[SED-ML-discuss] SED-ML at COMBINE

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

Dear colleagues,

I would like to confirm that we will have a session covering SED-ML at 
the upcoming COMBINE http://co.mbine.org/events/COMBINE_2011.
According to the schedule, this session will be the one on Saturday the 
3rd of September (" Simulation and analysis").

Looking forward to see many of you's there with brilliant ideas and 
"wild" extension suggestions :-)
Dagmar


-- 

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

Re: [SED-ML-discuss] Ideas for future SED-ML directions, "functional curation"

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

On 06/25/2011 05:12 AM, David Nickerson wrote:
>> I'll be attending COMBINE (really must book that!) so would be glad to
>> discuss this further there. I assume this would fit best in the
>> "Simulation and analysis" session, which I note has moved to Saturday
>> morning? Clearly I'll have to travel slightly earlier than originally
>> anticipated...
> great! I'm hoping to get my COMBINE travel sorted early next week and
> then I'll be able to confirm my attendance, but I'm guessing most of
> the SED-ML editors and tool developers will be there so we should
> definitely arrange to get together and discuss this further (maybe
> independent of the scheduled presentations?).

I definitely  prefer to keep the discussions as part of COMBINE,
1) I'd assume there should be a broad interest in the question how to 
move on with SED-ML, so why not use COMBINE to find answers
2) Finding free time slots (for > 3 people) outside the regular COMBINE 
schedule will be very, very tough (as experience shows).

I'll contact the organisers to confirm there will be a SED-ML session, 
and find out when.
Dagmar

>
> Cheers,
> David.
>
> ------------------------------------------------------------------------------
> 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-d2d-c1
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>


-- 

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

[SED-ML-discuss] Software Showcase

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

Hello, 

We will start soon and begin to showcase applications supporting SED-ML on
the SED-ML website. If you want your software to be displayed there as well,
please fill out the following survey (it should only take a couple of
minutes to fill out). 

http://tinyurl.com/3mkoczr

We will announce here when the showcase is online.

best
Frank

Re: [SED-ML-discuss] Ideas for future SED-ML directions, "functional curation"

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

> I'll be attending COMBINE (really must book that!) so would be glad to
> discuss this further there. I assume this would fit best in the
> "Simulation and analysis" session, which I note has moved to Saturday
> morning? Clearly I'll have to travel slightly earlier than originally
> anticipated...

great! I'm hoping to get my COMBINE travel sorted early next week and
then I'll be able to confirm my attendance, but I'm guessing most of
the SED-ML editors and tool developers will be there so we should
definitely arrange to get together and discuss this further (maybe
independent of the scheduled presentations?).


Cheers,
David.

Re: [SED-ML-discuss] Ideas for future SED-ML directions, "functional curation"

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

Hi David,

On 20/06/2011 00:03, David Nickerson wrote:
> Hi Jonathan,
> Personally, I think the ideas you present in this article are all
> ideas that should be covered by SED-ML in combination with CellML and
> SBML. You can see my own take on very similar ideas in a paper I wrote
> back in 2008 describing the use of CellML 1.1 and the graphing and
> simulation metadata standards we were working on back then
> (http://www.ncbi.nlm.nih.gov/pubmed/18606438).
We did actually cite this in an earlier draft of our paper, but it was 
cut and only your 2009 paper cited due to length restrictions!
> Going forward, it would be good if we could come up with a list of
> specific features that SED-ML would need in order to meet the
> requirements that you propose in this article. Ideas like using
> ontological terms to identify targets in the source models, for
> instance, would greatly improve the reusability of SED-ML documents
> with multiple models.
It should also make it much easier to address CellML 1.1 models, or 
indeed non-XML formats.
> Your post-processing operators all look quite
> good, although the "apd" function is probably a bit too domain
> specific to be part of the core SED-ML language. This suggests that
> we'd want some way to build reusable functions like this from the base
> set defined in core SED-ML (as you in fact do in your proposed
> method). Have you given any thought to this type of idea? Or mocked up
> any examples of what a SED-ML document might look like if you had some
> of these features?
I'm actually working on exactly this at the moment. So far I have a 
reasonable draft of a MathML-based format for the post-processing that 
can do all that we used in our paper. Most of the functionality is 
indeed built up as a library of functions defined in the language 
itself, with "core" and "cardiac-specific" libraries. Once I have 
something a little more complete and tested I'll post more about it.

I'll be attending COMBINE (really must book that!) so would be glad to 
discuss this further there. I assume this would fit best in the 
"Simulation and analysis" session, which I note has moved to Saturday 
morning? Clearly I'll have to travel slightly earlier than originally 
anticipated...

> This is also relevant to the thread on the SED-ML roadmap, and I would
> guess that the features we are discussing here would fit best with
> Nicolas' proposed approach of going wild with SED-ML Level 2 :)
Indeed!

Best wishes,
Jonathan

Re: [SED-ML-discuss] Ideas for future SED-ML directions, "functional curation"

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

Hi Robert,

I've had a look at your website, and the ProcessDB software does indeed 
look interesting. It seems to be slightly more high level and domain 
specific in the protocol definition that what we have at present. The 
parameter fitting aspect is something we're hoping to extend this to in 
the future, so I was particularly interested in that aspect, and may 
well want to discuss it with you individually at a later date.

On the philosophical question, I don't think there is a strict dichotomy 
between the two viewpoints. While it is in my view desirable to decouple 
the system being modelled and the protocol being performed on that 
system, different protocols will often address a different aspect or 
portion of the whole system. For example in the cardiac field one 
typically considers a model of (the electrical activity of) a "whole 
cell", but many of the experiments will treat only a single ion channel 
within the cell, and thus a simulation of such a protocol involves using 
only a portion of the whole model. There is also the question of which 
experimental protocols a model has been developed to reproduce or 
predict, which could argue for a closer link. Functional curation can be 
used to examine these issues more closely.

Best wishes,
Jonathan


On 13/06/2011 22:26, Robert Phair wrote:
> Jonathan,
>
> I am not speaking for the SED-ML leadership, just as an interested 
> application developer. There have been discussions in the past within 
> the SBML community regarding the description of experimental 
> protocols, but as you say SED-ML describes a simulation experiment 
> rather than a biological experiment. The distinction is subtle, but real.
>
> For our ProcessDB software we took an approach that sounds more like 
> yours. We describe experimental protocols (in the way an 
> experimentalist would describe them) that then can be applied to any 
> relevant model. Indeed we frequently analyze multiple protocols 
> applied to the same model and fit them all simultaneously, which 
> sounds much like the problem you are addressing with functional curation.
>
> I'm also aware that Upi Bhalla's group in Bangalore had planned to 
> develop an experimental protocol markup language. I don't know where 
> they stand with that project nor how specific it was to neuroscience.
>
> I think your question goes to the heart of a philosophical issue very 
> much worth discussing. In many if not most published models, the 
> published equations include elements that correspond to the biological 
> system and other elements that describe the particular experimental 
> protocol used to reproduce the experimental data in the published paper.
>
> Often this means, as you point out, that it is not immediately 
> possible to test that model against new data from a different protocol.
>
> From our perspective, and I think yours too, the model equations 
> should be independent of any particular experimental protocol. Then it 
> would be possible to do exactly what you describe as functional 
> curation and what we describe as integrative biology - testing a model 
> (or models) against experimental data from multiple laboratories.
>
> The philosophical question is to what extent the mathematical 
> description of a biological model should be distinct from the 
> mathematical description of biological experiments that can be run on 
> the model. I know experienced modelers who assert the two are inseparable.
>
> In any case, I think I see exactly what you mean, and I'd be very 
> interested in further discussions either within SED-ML or separately 
> if SED-ML is found to have a different goal. We are a small 4-person 
> company, and are not operating open-source, but we are strong 
> supporters of SBML and biomodels.net <http://biomodels.net> because 
> model exchange is critical to integrative biology. The field needs 
> such standards.
>
> Regards,
> Robert
>
>
> On Mon, Jun 13, 2011 at 4:28 AM, Jonathan Cooper 
> <jon...@cs... <mailto:jon...@cs...>> wrote:
>
>     Dear all,
>
>     Some colleagues and I have been developing a framework for "functional
>     curation" of models - essentially enabling a set of models to be
>     tested
>     for reproduction of a particular behaviour under some protocol.
>     The idea
>     is to examine which of the models are capable of replicating
>     experimentally observed results, and evaluate their suitability for
>     reuse in particular modelling studies. This requires a description of
>     the protocol being performed on the models, and ideally a community
>     agreed standard for these. Clearly SED-ML is the obvious candidate
>     here,
>     and we'd love to use it. However, in its current form it has a few
>     limitations that preclude this application. Of particular note are the
>     fact that a SED-ML description is tied to a particular model, so
>     that it
>     can't describe a protocol which could be applied (potentially) to any
>     model, and also the limited post-processing currently available.
>     So we'd
>     like the opportunity to work with you to address these issues.
>
>     A paper describing our prototype system, and our ideas of what is
>     needed
>     from a protocol language, has now been accepted for publication, and a
>     preprint is available at
>     http://www.cs.ox.ac.uk/chaste/publications/2011-Cooper-Functional%20Curation.pdf
>     (with the supplement at
>     http://www.cs.ox.ac.uk/chaste/publications/2011-Cooper-Functional%20Curation%20Supplement.pdf).
>     We welcome your views on this, and in particular whether these ideas
>     would be suitable for future levels of SED-ML.
>
>     Some of you may also be interested in a related discussion thread
>     in the
>     context of the VPH-FET project, which is exploring proposal ideas for
>     FET funding from the EC. It is looking at "Automated testing / End
>     user:
>     Benchmark-based editorial model for computational modelling research"
>     (https://www.biomedtown.org/biomed_town/VPHFET/reception/VPHFETFORUMS/vphfet/0054)
>     and again SED-ML could be very relevant for such an application.
>
>     Best wishes,
>     Jonathan
>
>     ------------------------------------------------------------------------------
>     EditLive Enterprise is the world's most technically advanced content
>     authoring tool. Experience the power of Track Changes, Inline Image
>     Editing and ensure content is compliant with Accessibility Checking.
>     http://p.sf.net/sfu/ephox-dev2dev
>     _______________________________________________
>     SED-ML-discuss mailing list
>     SED...@li...
>     <mailto:SED...@li...>
>     https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
>
> -- 
> Robert D Phair PhD  |  Chief Scientific Officer  |  Integrative 
> Bioinformatics Inc
> Los Altos, CA
> www.integrativebioinformatics.com 
> <http://www.integrativebioinformatics.com>
>
> ProcessDB: Modeling for Biological Discovery

Re: [SED-ML-discuss] Ideas for future SED-ML directions, "functional curation"

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

Hi Jonathan,

> A paper describing our prototype system, and our ideas of what is needed
> from a protocol language, has now been accepted for publication, and a
> preprint is available at
> http://www.cs.ox.ac.uk/chaste/publications/2011-Cooper-Functional%20Curation.pdf
> (with the supplement at
> http://www.cs.ox.ac.uk/chaste/publications/2011-Cooper-Functional%20Curation%20Supplement.pdf).
> We welcome your views on this, and in particular whether these ideas
> would be suitable for future levels of SED-ML.

Personally, I think the ideas you present in this article are all
ideas that should be covered by SED-ML in combination with CellML and
SBML. You can see my own take on very similar ideas in a paper I wrote
back in 2008 describing the use of CellML 1.1 and the graphing and
simulation metadata standards we were working on back then
(http://www.ncbi.nlm.nih.gov/pubmed/18606438). In that paper, I used a
combination of the metadata with a perl script to generate APD
restitution plots (see Figure 7 and the associated description in the
online supplement). In that paper you can also see a primitive attempt
at linking simulation results to experimental data (figure 10). As we
migrate from the CellML graphing and simulation metadata approach to
using SED-ML, these are certainly ideas I am keen to see established
in SED-ML.

Going forward, it would be good if we could come up with a list of
specific features that SED-ML would need in order to meet the
requirements that you propose in this article. Ideas like using
ontological terms to identify targets in the source models, for
instance, would greatly improve the reusability of SED-ML documents
with multiple models. Your post-processing operators all look quite
good, although the "apd" function is probably a bit too domain
specific to be part of the core SED-ML language. This suggests that
we'd want some way to build reusable functions like this from the base
set defined in core SED-ML (as you in fact do in your proposed
method). Have you given any thought to this type of idea? Or mocked up
any examples of what a SED-ML document might look like if you had some
of these features?

This is also relevant to the thread on the SED-ML roadmap, and I would
guess that the features we are discussing here would fit best with
Nicolas' proposed approach of going wild with SED-ML Level 2 :)


Cheers,
David.

Re: [SED-ML-discuss] SED-ML roadmap (revived)

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

On 15/06/11 14:45, Richard Adams wrote:

> Possibly the 2 strand development might be good, but there also the
> practical considerations that most people (editors, developers) are
> developing SED-ML on a 'best-effort' semi-voluntary basis and we have
> limited resources. Speaking with my software-developer hat on, it will be a
> lot more effort to develop support for two strands in parallel.

This assumes that everyone has to support the whole SED-ML. As shown with 
SBML (and HTML before that) this is a pipe dream. Having different 
*co-exiting* levels allow people to choose the coverage. The alternative 
solution of a single development track has some advantages, but it also 
freeze the language, because we have to keep the changes to the existing 
coverage to a minimum while exploring new territories.

>  Also the '
> We allow ourselves to go a bit wild, and imagine more drastic changes' is
> not necessarily a linear progression either, and may need branches in the
> development tree, leading to fragmentation of an already small developer-base .

Yes ... if the implementation follows closely the development. Again, this 
brings obvious advantages, but also freezes the language. Now that L1V1 is 
out, the pressure to have implementations is a bit (just a bit) lower.

-- 
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] SED-ML roadmap (revived)

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

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

[SED-ML-discuss] SED-ML roadmap (revived)

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

Hello SED-ML'ers,

SED-ML L1V1 has been published. It supports time course simulations, 
which is great, but not sufficient. First changes have been suggested, 
e.g. the ID attribute for all SED-ML language elements. I am pretty sure 
you all agree that it is time to think about how to move on with SED-ML.

Nicolas had started a discussion on the future of SED-ML on this 
mailing-list a while ago, but we never reached a decision. Also others 
made a couple of suggestions, and I am sure everyone has some features 
in mind for SED-ML LxVx. So let's re-start again and help the editors to 
set up a roadmap that will serve as a guideline for the further development.

I am linking again to Nicolas' (still relevant) post on a roadmap from 
April this year:
http://sourceforge.net/mailarchive/forum.php?thread_name=AANLkTi%3Dt7PmeOyu7MLX0ikOx5Pgns4KNvwcT-ErpQU_h%40mail.gmail.com&forum_name=sed-ml-discuss
To sum up, Nicolas is proposing two parallel developments: further 
Versions of L1 and parallel development of L2:

[cite]
Level 1: In future versions we only add to the existing language, without
major restructuration. Examples are addition of simulation classes and
enriching output description.

Level 2: We allow ourselves to go a bit wild, and imagine more drastic
changes, so as to encore iterative simulation tasks etc.

This would allow development of solid implementations of Level 1, still
improving and evolving, without stalling the expansion of the language.
[/cite]


What do you others think:

1) How should the development process move on? Will we develop levels 
and/or versions in parallel? Or should we proceed on a single strand?
2) What are the short-term goals for the next 
version/level/version&level of SED-ML?

It would be nice to find consensus pretty timely, including a rough 
development guideline and also a list of rather specific questions to 
address...

Thanks,
Dagmar


-- 

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

[SED-ML-discuss] COMBINE 2011, Sept 3-7, Heidelberg (Germany) - Registration open

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

 

****************************************************************

 

                          Announcing

 

                      C O M B I N E  2011

 

                      September 3-7, 2011

                      Heidelberg, Germany

 

            http://co.mbine.org/events/COMBINE_2011

 

 

****************************************************************

 

 

 

Dear Colleagues,

 

Registration is open now for the second COMBINE meeting taking place in Heidelberg (Germany), September 3-7, 2011. COMBINE 2011 will be hosted by the Heidelberg Institute for Theoretical Studies (HITS) and will follow immediately after the 12th International Conference on Systems Biology (ICSB2011). 

 

If you are planning to join COMBINE 2011, please register and submit your abstracts as soon as possible using the following form:

 

  http://www.surveymonkey.com/s/combine2011-registration <http://www.surveymonkey.com/s/combine2011-registration> 

 

The deadline for early bird registration is July 15th, 2011. Attendees are responsible for arranging their own accommodations. We urge you to make your hotel bookings as soon as possible. Hotels fill early. Information on hotels can be found on the meeting website: 

 

  http://co.mbine.org/events/COMBINE_2011 <http://co.mbine.org/events/COMBINE_2011> 

 

 

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 (http://co.mbine.org/ <http://co.mbine.org/> ). In 2010, the systems biology standards community inaugurated a new, broader series of meetings to replace, among other events, individual SBML, SBGN, and BioPAX meetings, and create a common platform for allied standardization efforts. The annual COMBINE meeting is a workshop-style event with oral presentations, posters and breakout sessions. It provides an opportunity for the different communities to meet and discuss their standardization efforts, with the aim of working more closely together to ensure smooth interoperability between the standards.

 

COMBINE 2011 will include sessions about encoding biological pathway semantics, encoding mathematical model semantics, visual representation, interoperability, model simulation and analysis, tools and databases applying the standards, and similar topics. We will provide a more detailed agenda in the near future. Please refer to the meeting website for the session schedule and detailed information: http://co.mbine.org/events/COMBINE_2011 <http://co.mbine.org/events/COMBINE_2011> 

 

Oral presentations will be selected from the submitted abstracts. Abstracts are welcome for posters and talks addressing topics such as the various standards encompassed by COMBINE (BioPax, SBGN, SBML), associated standardization efforts such as MIRIAM, SED-ML and the Systems Biology Ontology (SBO), and related standardization efforts like CellML or NeuroML, as well as for presentations of software systems using these standards.

 

We hope to see you in Heidelberg!

 

 

Martin Golebiewski 

 

on behalf of the organizers:

 

* Gary Bader, University of Toronto, Canada

 

* Emek Demir, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, USA

 

* Martin Golebiewski, Heidelberg Institute for Theoretical Studies (HITS), Germany

 

* Michael Hucka, California Institute of Technology (Caltech), USA

 

* Nicolas Le Novère, European Bioinformatics Institute (EMBL-EBI), UK

 

* Sven Sahle, BioQuant at the University of Heidelberg, Germany

 

 

Re: [SED-ML-discuss] Ideas for future SED-ML directions, "functional curation"

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

Just a couple of comments, having not yet had time to read through
Jonathan's manuscript...

Using CellML 1.1 model composition, it is very easy to separate
boundary conditions from the mathematical model of the biological
system. I would hope that this is also something the SBML composition
package will give SBML models. In general, if you can mathematically
describe your boundary conditions (which includes the applied
protocol) then you can encode that in CellML and reuse the description
of your protocol with as many different models and parameterisations
of that model and protocol you want to. Using standard annotations
(which I think is the approach Jonathan is suggesting) then allows
tools to automate the composition of a mathematical model with a given
protocol (and other boundary conditions).

The tricky bit at present is what to do when your experimental
protocol/boundary conditions are not something that can be easily
encoded in CellML (or SBML). If you want to, for example, feed in
experimental data or previous simulation results. I think this is
where we want to be pushing the development of SED-ML. The difficult
issue is where you draw the line between what should be part of SED-ML
and what should be part of the underlying encoded model - or even if
we need to draw a line.

I regards to post-processing, adding functionality to this aspect of
SED-ML is definitely something to be worked on. Specific proposals can
be entered into the tracker on Sourceforge, and I'm guessing there
will be several to come out of Jonathan's article, so thanks for
stimulating the discussion Jonathan! Now I'll go read the article...


Cheers,
David.

On Tue, Jun 14, 2011 at 9:26 AM, Robert Phair
<rp...@in...> wrote:
> Jonathan,
>
> I am not speaking for the SED-ML leadership, just as an interested
> application developer. There have been discussions in the past within the
> SBML community regarding the description of experimental protocols, but as
> you say SED-ML describes a simulation experiment rather than a biological
> experiment. The distinction is subtle, but real.
>
> For our ProcessDB software we took an approach that sounds more like yours.
> We describe experimental protocols (in the way an experimentalist would
> describe them) that then can be applied to any relevant model. Indeed we
> frequently analyze multiple protocols applied to the same model and fit them
> all simultaneously, which sounds much like the problem you are addressing
> with functional curation.
>
> I'm also aware that Upi Bhalla's group in Bangalore had planned to develop
> an experimental protocol markup language. I don't know where they stand with
> that project nor how specific it was to neuroscience.
>
> I think your question goes to the heart of a philosophical issue very much
> worth discussing. In many if not most published models, the published
> equations include elements that correspond to the biological system and
> other elements that describe the particular experimental protocol used to
> reproduce the experimental data in the published paper.
>
> Often this means, as you point out, that it is not immediately possible to
> test that model against new data from a different protocol.
>
> From our perspective, and I think yours too, the model equations should be
> independent of any particular experimental protocol. Then it would be
> possible to do exactly what you describe as functional curation and what we
> describe as integrative biology - testing a model (or models) against
> experimental data from multiple laboratories.
>
> The philosophical question is to what extent the mathematical description of
> a biological model should be distinct from the mathematical description of
> biological experiments that can be run on the model. I know experienced
> modelers who assert the two are inseparable.
>
> In any case, I think I see exactly what you mean, and I'd be very interested
> in further discussions either within SED-ML or separately if SED-ML is found
> to have a different goal. We are a small 4-person company, and are not
> operating open-source, but we are strong supporters of SBML and
> biomodels.net because model exchange is critical to integrative biology. The
> field needs such standards.
>
> Regards,
> Robert
>
>
> On Mon, Jun 13, 2011 at 4:28 AM, Jonathan Cooper
> <jon...@cs...> wrote:
>>
>> Dear all,
>>
>> Some colleagues and I have been developing a framework for "functional
>> curation" of models - essentially enabling a set of models to be tested
>> for reproduction of a particular behaviour under some protocol. The idea
>> is to examine which of the models are capable of replicating
>> experimentally observed results, and evaluate their suitability for
>> reuse in particular modelling studies. This requires a description of
>> the protocol being performed on the models, and ideally a community
>> agreed standard for these. Clearly SED-ML is the obvious candidate here,
>> and we'd love to use it. However, in its current form it has a few
>> limitations that preclude this application. Of particular note are the
>> fact that a SED-ML description is tied to a particular model, so that it
>> can't describe a protocol which could be applied (potentially) to any
>> model, and also the limited post-processing currently available. So we'd
>> like the opportunity to work with you to address these issues.
>>
>> A paper describing our prototype system, and our ideas of what is needed
>> from a protocol language, has now been accepted for publication, and a
>> preprint is available at
>>
>> http://www.cs.ox.ac.uk/chaste/publications/2011-Cooper-Functional%20Curation.pdf
>> (with the supplement at
>>
>> http://www.cs.ox.ac.uk/chaste/publications/2011-Cooper-Functional%20Curation%20Supplement.pdf).
>> We welcome your views on this, and in particular whether these ideas
>> would be suitable for future levels of SED-ML.
>>
>> Some of you may also be interested in a related discussion thread in the
>> context of the VPH-FET project, which is exploring proposal ideas for
>> FET funding from the EC. It is looking at "Automated testing / End user:
>> Benchmark-based editorial model for computational modelling research"
>>
>> (https://www.biomedtown.org/biomed_town/VPHFET/reception/VPHFETFORUMS/vphfet/0054)
>> and again SED-ML could be very relevant for such an application.
>>
>> Best wishes,
>> Jonathan
>>
>>
>> ------------------------------------------------------------------------------
>> EditLive Enterprise is the world's most technically advanced content
>> authoring tool. Experience the power of Track Changes, Inline Image
>> Editing and ensure content is compliant with Accessibility Checking.
>> http://p.sf.net/sfu/ephox-dev2dev
>> _______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li...
>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
> --
> Robert D Phair PhD  |  Chief Scientific Officer  |  Integrative
> Bioinformatics Inc
> Los Altos, CA
> www.integrativebioinformatics.com
>
> ProcessDB: Modeling for Biological Discovery
>
> ------------------------------------------------------------------------------
> EditLive Enterprise is the world's most technically advanced content
> authoring tool. Experience the power of Track Changes, Inline Image
> Editing and ensure content is compliant with Accessibility Checking.
> http://p.sf.net/sfu/ephox-dev2dev
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>

Re: [SED-ML-discuss] Ideas for future SED-ML directions, "functional curation"

[Robert P. <rp...@in...>]

Jonathan,

I am not speaking for the SED-ML leadership, just as an interested
application developer. There have been discussions in the past within the
SBML community regarding the description of experimental protocols, but as
you say SED-ML describes a simulation experiment rather than a biological
experiment. The distinction is subtle, but real.

For our ProcessDB software we took an approach that sounds more like yours.
We describe experimental protocols (in the way an experimentalist would
describe them) that then can be applied to any relevant model. Indeed we
frequently analyze multiple protocols applied to the same model and fit them
all simultaneously, which sounds much like the problem you are addressing
with functional curation.

I'm also aware that Upi Bhalla's group in Bangalore had planned to develop
an experimental protocol markup language. I don't know where they stand with
that project nor how specific it was to neuroscience.

I think your question goes to the heart of a philosophical issue very much
worth discussing. In many if not most published models, the published
equations include elements that correspond to the biological system and
other elements that describe the particular experimental protocol used to
reproduce the experimental data in the published paper.

Often this means, as you point out, that it is not immediately possible to
test that model against new data from a different protocol.

>From our perspective, and I think yours too, the model equations should be
independent of any particular experimental protocol. Then it would be
possible to do exactly what you describe as functional curation and what we
describe as integrative biology - testing a model (or models) against
experimental data from multiple laboratories.

The philosophical question is to what extent the mathematical description of
a biological model should be distinct from the mathematical description of
biological experiments that can be run on the model. I know experienced
modelers who assert the two are inseparable.

In any case, I think I see exactly what you mean, and I'd be very interested
in further discussions either within SED-ML or separately if SED-ML is found
to have a different goal. We are a small 4-person company, and are not
operating open-source, but we are strong supporters of SBML and
biomodels.net because model exchange is critical to integrative biology. The
field needs such standards.

Regards,
Robert


On Mon, Jun 13, 2011 at 4:28 AM, Jonathan Cooper <
jon...@cs...> wrote:

> Dear all,
>
> Some colleagues and I have been developing a framework for "functional
> curation" of models - essentially enabling a set of models to be tested
> for reproduction of a particular behaviour under some protocol. The idea
> is to examine which of the models are capable of replicating
> experimentally observed results, and evaluate their suitability for
> reuse in particular modelling studies. This requires a description of
> the protocol being performed on the models, and ideally a community
> agreed standard for these. Clearly SED-ML is the obvious candidate here,
> and we'd love to use it. However, in its current form it has a few
> limitations that preclude this application. Of particular note are the
> fact that a SED-ML description is tied to a particular model, so that it
> can't describe a protocol which could be applied (potentially) to any
> model, and also the limited post-processing currently available. So we'd
> like the opportunity to work with you to address these issues.
>
> A paper describing our prototype system, and our ideas of what is needed
> from a protocol language, has now been accepted for publication, and a
> preprint is available at
>
> http://www.cs.ox.ac.uk/chaste/publications/2011-Cooper-Functional%20Curation.pdf
> (with the supplement at
>
> http://www.cs.ox.ac.uk/chaste/publications/2011-Cooper-Functional%20Curation%20Supplement.pdf
> ).
> We welcome your views on this, and in particular whether these ideas
> would be suitable for future levels of SED-ML.
>
> Some of you may also be interested in a related discussion thread in the
> context of the VPH-FET project, which is exploring proposal ideas for
> FET funding from the EC. It is looking at "Automated testing / End user:
> Benchmark-based editorial model for computational modelling research"
> (
> https://www.biomedtown.org/biomed_town/VPHFET/reception/VPHFETFORUMS/vphfet/0054
> )
> and again SED-ML could be very relevant for such an application.
>
> Best wishes,
> Jonathan
>
>
> ------------------------------------------------------------------------------
> EditLive Enterprise is the world's most technically advanced content
> authoring tool. Experience the power of Track Changes, Inline Image
> Editing and ensure content is compliant with Accessibility Checking.
> http://p.sf.net/sfu/ephox-dev2dev
> _______________________________________________
> SED-ML-discuss mailing list
> SED...@li...
> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>



-- 
Robert D Phair PhD  |  Chief Scientific Officer  |  Integrative
Bioinformatics Inc
Los Altos, CA
www.integrativebioinformatics.com

ProcessDB: Modeling for Biological Discovery

[SED-ML-discuss] Ideas for future SED-ML directions, "functional curation"

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

Dear all,

Some colleagues and I have been developing a framework for "functional 
curation" of models - essentially enabling a set of models to be tested 
for reproduction of a particular behaviour under some protocol. The idea 
is to examine which of the models are capable of replicating 
experimentally observed results, and evaluate their suitability for 
reuse in particular modelling studies. This requires a description of 
the protocol being performed on the models, and ideally a community 
agreed standard for these. Clearly SED-ML is the obvious candidate here, 
and we'd love to use it. However, in its current form it has a few 
limitations that preclude this application. Of particular note are the 
fact that a SED-ML description is tied to a particular model, so that it 
can't describe a protocol which could be applied (potentially) to any 
model, and also the limited post-processing currently available. So we'd 
like the opportunity to work with you to address these issues.

A paper describing our prototype system, and our ideas of what is needed 
from a protocol language, has now been accepted for publication, and a 
preprint is available at 
http://www.cs.ox.ac.uk/chaste/publications/2011-Cooper-Functional%20Curation.pdf 
(with the supplement at 
http://www.cs.ox.ac.uk/chaste/publications/2011-Cooper-Functional%20Curation%20Supplement.pdf). 
We welcome your views on this, and in particular whether these ideas 
would be suitable for future levels of SED-ML.

Some of you may also be interested in a related discussion thread in the 
context of the VPH-FET project, which is exploring proposal ideas for 
FET funding from the EC. It is looking at "Automated testing / End user: 
Benchmark-based editorial model for computational modelling research" 
(https://www.biomedtown.org/biomed_town/VPHFET/reception/VPHFETFORUMS/vphfet/0054) 
and again SED-ML could be very relevant for such an application.

Best wishes,
Jonathan

[SED-ML-discuss] Announcing the SED-ML Web Tools

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

Hello, 

I'm very pleased to announce the availability of the first version of the
SED-ML Web Tools:

http://sysbioapps.dyndns.org/SED-ML%20Web%20Tools

A collection of tools for working with SED-ML. The first version that went
online today will allow you to: 

- Validate SED-ML models
- Simulate Simulation Experiments involving SBML models
- Correct / upgrade SED-ML descriptions to a new format. 

For more information see also: 

http://frank-fbergmann.blogspot.com/2011/06/introducing-sed-ml-web-tools.htm
l

Best
Frank

Re: [SED-ML-discuss] global id attributes

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

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

Re: [SED-ML-discuss] global id attributes

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

> How about this, rather than sprinkling ID’s here and there (and extending it
> later). How about the following, let us have an Id attribute on SedBase.
> This will make it easy for tool implementers and add some sort of
> consistency.

agreed, that sounds like a good route to take!


Cheers,
David.

Re: [SED-ML-discuss] global id attributes

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

Hello All, 

 

How about this, rather than sprinkling ID's here and there (and extending it
later). How about the following, let us have an Id attribute on SedBase.
This will make it easy for tool implementers and add some sort of
consistency. 

 

Best

Frank

 

From: Dagmar Waltemath [mailto:dag...@un...] 
Sent: Sunday, June 05, 2011 10:50 PM
To: sed...@li...
Subject: Re: [SED-ML-discuss] global id attributes

 

Hello Richard,

I am at one with you. I can see no reason not to have an ID on Change
elements. 
Dagmar


On 06/02/2011 10:39 AM, Richard Adams wrote: 

Hello All, 

 In the L1V1 specification (section 2.3.1) we have a slightly inconsistent
treatment of global identifiers. All elements have an 'id' attribute except
'Change' elements.

 

 As far as I can see, there is little logical reason for not including
Change elements, given that other elements, that also  are not
cross-referenced, contain id attributes (e.g., Curve, Output). It's really
useful for application developers to be able to identify elements precisely,
so could I propose that for the next level/version of SED-ML, that all
elements (including any new ones) contain an id attribute of type SId? 

 

 Best wishes

 

Richard

 

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

 

 

 

 

 

 

-- 


Dagmar Waltemath, Systems Biology and Bioinformatics group, 
University of Rostock, D-18051 Rostock, Germany
Web: http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/ 
e-mail: dag...@un...
<mailto:dag...@un...> 

[SED-ML-discuss] Fwd: [sbml-interoperability] New version of SBML Test Suite available

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

Dear all,

I am forwarding Mike's announcement of the new SBML test suite as it 
supports SED-ML files for all test models now.
If you go to the online version 
http://sbml.org/Facilities/Online_SBML_Test_Suite you can directly 
create sample SBML models together with the result plots and a SED-ML 
description of the simulation for each test model.
This provides a plethora of models and associated SED-ML for your 
testing :-)

Best,
Dagmar



-------- Original Message --------
Subject: 	[sbml-interoperability] New version of SBML Test Suite available
Date: 	Tue, 7 Jun 2011 04:14:36 +0200
From: 	Mike Hucka <mh...@ca...>
Reply-To: 	SBML Software Interoperability Discussion List 
<sbm...@ca...>
To: 	sbm...@ca... <sbm...@ca...>



We now have a new version of both the test cases and the Online SBML Test Suite available for people to try:

   http://sbml.org/Software/SBML_Test_Suite

Among the features in the new version are:

* SBML Level 3 Version 1 Core versions of all test cases
* SED-ML files for all tests and all SBML Level/Version combinations
* Dozens of new cases, including tests for features introduced in SBML Level 3
* New test tags and component tags
* Improvements to the Online SBML Test Suite user interface
* Updated online documentation for the test files and tags used

The front page for the Online SBML Test Suite is at

   http://sbml.org/Facilities/Online_SBML_Test_Suite

The downloadable archive of all test cases is at

   https://sourceforge.net/projects/sbml/files/test-suite/2.0.0/

We're interested in people's experiences with the new system, so please feel free to tell us how you like it and, especially, if you encounter any problems or can't figure something out.  The online system has received a reasonable amount of testing, but it's possible that bugs are still lurking, so don't be shy telling us!

Thanks,
The SBML Team
____________________________________________________________
To manage your sbml-interoperability list subscription, visit
https://utils.its.caltech.edu/mailman/listinfo/sbml-interoperability

For a web interface to the sbml-interoperability mailing list, visit
http://sbml.org/Forums/

For questions or feedback about the sbml-interoperability list,
contact sbm...@ca...

Re: [SED-ML-discuss] global id attributes

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

Hello Richard,

I am at one with you. I can see no reason not to have an ID on Change 
elements.
Dagmar


On 06/02/2011 10:39 AM, Richard Adams wrote:
> Hello All,
>  In the L1V1 specification (section 2.3.1) we have a slightly 
> inconsistent treatment of global identifiers. All elements have an 
> 'id' attribute except 'Change' elements.
>
>  As far as I can see, there is little logical reason for not including 
> Change elements, given that other elements, that also  are not 
> cross-referenced, contain id attributes (e.g., Curve, Output). It's 
> really useful for application developers to be able to identify 
> elements precisely, so could I propose that for the next level/version 
> of SED-ML, that all elements (including any new ones) contain an id 
> attribute of type SId?
>
>  Best wishes
>
> Richard
>
> Dr Richard Adams
> Software Development Team Leader,
> Centre For Systems Biology Edinburgh
> University of Edinburgh
> Tel: 0131 651 9019
> email : ric...@ed... <mailto:ric...@ed...>
> Web: http://csbe.bio.ed.ac.uk/adams.php
>
>
>
>
>


-- 

*Dagmar Waltemath*, Systems Biology and Bioinformatics group,
University of Rostock, D-18051 Rostock, Germany
Web: http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/
e-mail: dag...@un... 
<mailto:dag...@un...>

Re: [SED-ML-discuss] A SED-ML visualizer/editor tool

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

Hello Richard,

if you have some idea how to fix this, could you reply to the list as I 
ran into the same problem :-)

Cheers,
Dagmar


On 05/25/2011 09:41 PM, Robert Phair wrote:
> Richard,
>
> Did a Windows install and tried to load a file from the examples 
> folder. Got this exception:
>
> java.lang.ClassCastException: org.eclipse.ui.ide.FileStoreEditorInput 
> cannot be cast to org.eclipse.ui.IFileEditorInput
>
> Probably I just did something wrong during install, but I would like 
> to look at your tool. Any ideas?
>
> Thanks.
>
> Robert
>
> On Tue, May 24, 2011 at 11:41 AM, Richard Adams 
> <ric...@ed... <mailto:ric...@ed...>> wrote:
>
>     Dear SED-MLers,
>       I'd like to bring to your attention a new tool for editing,
>     viewing and running SED-ML files - the SED-ED editor.   The main
>     aims of the app are to
>       make it easier to view and understand the contents of SED-ML
>     documents, to provide a UI for validation support, to help  with
>     the generation of  XPath expressions accurately, and to provide
>     tooling to support the proposed Sedx archive format.
>
>       Features include:
>
>        -  Create   new SED-ML files  from scratch.
>        -  Edit existing SED-ML files  using a graphical/form based
>     editor.
>        -  Auto-generation of XPath expressions to identify selected
>     elements and attributes in your model.
>        -  Previews of model changes.
>        -  Model agnostic, at least for editing (simulating  is SBML
>     only ).
>        -  Create, edit, view and expand sedx archive files.
>        -  Graphical layout of SED-ML components (  including
>     autolayout, align, zoom).
>        -  SED-ML validation and display of errors/warnings.
>
>     Example SED-ML files and sedx archives  are included in the
>     download to help you get started.
>
>
>     This is an early, alpha release of the editor, which we've tested
>     and believe to work on at least the example models, but we'd
>     really appreciate any feedback on missing features / bugs to make
>     the application more robust at an early stage.
>
>     The download instructions and a screenshot are below, for those
>     interested.
>
>      Thanks for your attention,
>
>      Best wishes
>
>          Richard
>
>     Availability:
>
>     The SED-ED editor is available in three forms:
>     1) As a standalone application for Windows/Mac/Linux, accessible
>     from https://sourceforge.net/projects/jlibsedml/files/
>          To get started:
>     1.  Download, unzip, double-click the launch icon in the unzipped
>     folder
>     2. When the application starts, click Window->Help to open the
>     Help pages which tell you  how  to use the application and work
>     with the included examples.
>
>     2) As a plugin for the SBSIVisual workbench. This has the same
>     editing functionality as the standalone app but also enables
>     simulation of  least ODE based SBML models, defined in SEDML. To
>     get started:
>     1. Download and extract SBSIVisual from
>     http://sourceforge.net/projects/sbsi/
>     2. Follow the instructions in the README file to launch the app
>     for your platform.
>     3.  To install the SED-ED plugin,  go to Help->Install New
>     Software, and in the ensuing dialog choose the 'Public SBSI' from
>     the 'Work with'  drop down list.
>     4. In the list of plugins, select  the 'SEDML tools' and follow
>     the prompts to install the plugin.
>     5. Once the plugin is installed you can create a new Project (
>     File->New->SBSI system) and drag the examples folder into the new
>     project.
>     6. The SED-ED help pages can be accessed from Window->Help. The
>     example files will be put in your application folder.
>
>     3) As an Eclipse plugin. This is essentially the same installation
>     as  2), step 3 onwards,  except you'll need to manually add the
>     update site URL http://www.sbsi.ed.ac.uk/update in step 3. The
>     example files will be put into the top-level folder of your
>     Eclipse install.
>
>
>
>
>
>
>
>
>
>
>     Dr Richard Adams
>     Software Development Team Leader,
>     Centre For Systems Biology Edinburgh
>     University of Edinburgh
>     Tel: 0131 651 9019
>     email : ric...@ed... <mailto: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.
>
>     ------------------------------------------------------------------------------
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>     Download your free trial now.
>     http://p.sf.net/sfu/quest-d2dcopy1
>     _______________________________________________
>     SED-ML-discuss mailing list
>     SED...@li...
>     <mailto:SED...@li...>
>     https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss
>
>
>
>
> -- 
> Robert D Phair PhD  |  Chief Scientific Officer  |  Integrative 
> Bioinformatics Inc
> Los Altos, CA
> www.integrativebioinformatics.com 
> <http://www.integrativebioinformatics.com>
>
> ProcessDB: Modeling for Biological Discovery


-- 

*Dagmar Waltemath*, Systems Biology and Bioinformatics group,
University of Rostock, D-18051 Rostock, Germany
Web: http://www.sbi.uni-rostock.de/team/single/dagmar-waltemath/
e-mail: dag...@un... 
<mailto:dag...@un...>