[kepler-dev] Re: Bertram Ludäscher/SEEK/declarative modelling

Chad Berkley berkley at nceas.ucsb.edu
Fri Jan 30 08:37:39 PST 2004

Hi Robert,

I think Bertram has been a bit busy lately, as his wife just had a 
baby.  I'm forwarding this message to two of our relevant mailing 
lists.  I'm in meetings this week and next, but I'll try to read over 
your message in detail and get a response to you asap.

Thanks for your interest in the SEEK/Kepler projects.


On Jan 30, 2004, at 7:19 AM, r.muetzelfeldt at ed.ac.uk wrote:

> Dear Chad,
> I live in Edinburgh, and popped into the NESC Workflow meeting in
> December to see Eric Simon.  I noted that you were speaking, and hoped
> to meet you to discuss my interests in ecological modelling 
> (specifically the
> promotion of declarative modelling approaches), and its possible 
> relevance
> to SEEK.  However, I got talking to Bertram Ludäscher instead, who said
> that he was interested in my ideas, and that I should summarise my
> position in an email.  However, I've not had a reply from the two 
> emails I've
> sent him, and was wondering what you think I should do to try to re-
> establish contact.
> I've appended my email to Bertram below.  Perhaps you are interested in
> picking up the threads?
> Thanks,
> Robert Muetzelfeldt
> ================================================
> Dear Bertram,
> I'm glad we made contact at the NESC meeting today - seems like 
> there's a
> nice bit of complementarity between SEEK's interest in ontologies for
> ecological data and corresponding ontologies for ecosystem modelling.
> To recap on my own interests:
> I've been interested in the methodology of ecological modelling for 
> some
> 30 years.  About 20 years ago I started collaborating with people in 
> the
> AI department here in Edinburgh (Alan Bundy, Dave Robertson, Mike
> Uschold)
> on the Eco project, which sort to formalise the models and the way we 
> can
> reason with them: this resulted in a book "Eco-Logic : Logic-Based
> Approaches to Ecological Modeling" published by MIT Press.   About a 
> year
> ago I took early retirement in order to be able to concentrate 
> full-time
> on my metamodelling interests.
> I still have an interest in knowledge-based aspects of modelling, but 
> some
> 6 or so years ago decided to first promote a culture of 'declarative
> modelling within the ecosystem research community.   The vehicle for 
> this
> is Simile ( http://www.simulistics.com ), a visual modelling 
> environment
> which uses System Dynamics (stock-and-flow) notation (like Stella,
> Modelmaker, Powersim, Vensim...), but, unlike these other packages,
> supports object- based modelling: multiple instances of a class of 
> object,
> with the possibility of dynamic creation and destruction of instanves,
> associations (in the UML sense) between object classes, etc.   
> (However,
> it is not 'object-oriented' in the standard sense: I'm happy to 
> discuss if
> you want to explore this topic.)
> Simile is a nice and powerful package, supporting complex models, both 
> in
> terms of the number of equations and the number of object  instances.  
> It
> is written in Prolog and Tcl/Tk for the GUI, but generates C++ for
> efficient model execution.    We have now formed a spin-out company -
> Simulistics Ltd - (I'm a shareholder but not an employee) though we are
> keen to be involved as collaborators in interesting research projects, 
> and
> quite happy to discuss possible open-source models.
> As far as I am concerned, the main role of Simile is as a
> 'proof-of-concept demonstrator' for the virtues of a declarative 
> modelling
> approach in ecosystem research.   I get deeply depressed when I see
> models
> implemented in procedural programming languages, a mode of thinking
> that
> persists in the great majority of the integrated modelling environments
> currently being developed - the large number of them is sufficient
> evidence of their inadequacy for providing a common framework for
> modelling.   It seems quite clear to me that we must abstract out the
> specification of the model from one particular form of processing the
> model (running simulations) - as is commonplace in most other design
> contexts (e.g.architecture, electronic circuit design...), and even in
> other biological modelling domains: witness the importance of SBML
> (Systems Biology Markup Language, http://www.sbml.org ) in modelling 
> cell
> processes.   Please have a look at p.17 of
> http://gaim.sr.unh.edu/Products/News/Summer2003/rgsum03.pdf for an
> outline
> of my views on this subject: rather stating the obvious, I'm afraid, 
> but
> what else can I do?   I also have a EU position paper coming out on 
> this
> topic, which I can send if you're interested.
> The paper that I showed you, on Simile as a possible data flow language
> for web services integation, is available at
> http://www.decmod.org/documents/webservices/index.html .   This is a 
> very
> sketchy 'thinking-out-loud' note - not implemented, but I think it 
> would
> be useful to explore the degree of common ground with the dataflow
> concepts that Simile supports and those of purpose-built 
> dataflow/workflow
> systems, as you mentioned.   Interestingly, I had a good chat with Eric
> Simon after talking to you: some of his Powerpoint slides were 
> virtually
> identical to the ones in this note, so the possibility of some form of
> harmonisation with other tools must be good.
> I am currently working on an XML representation of Simile models, with
> XSLT transforms for displaying and processing the models in various 
> ways -
> including an an approach based on XSSS (XML StyleSheet Switching) to
> allow
> the same model to be viewed in a web browser through different XSLT
> 'filters' (analogous to CSS switching for HTML documents).
> I would really love to get back into knowledge-based modelling, one 
> aspect
> of which is the seamless integration of data, data analysis and 
> modelling
> through common ontologies.   It seems that this has a certain resonance
> with your interests and involvement in SEEK, and it would be great to
> explore this in more depth.
> Hope you enjoyed Edinburgh - it's a great city - and looking forward to
> meeting up again sometime.
> Best wishes,
> Robert

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