[seek-dev] Re: Bertram Ludäscher/SEEK/declarative modelling
berkley at nceas.ucsb.edu
Fri Jan 30 08:37:39 PST 2004
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
> 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?
> 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
> 30 years. About 20 years ago I started collaborating with people in
> AI department here in Edinburgh (Alan Bundy, Dave Robertson, Mike
> on the Eco project, which sort to formalise the models and the way we
> reason with them: this resulted in a book "Eco-Logic : Logic-Based
> Approaches to Ecological Modeling" published by MIT Press. About a
> ago I took early retirement in order to be able to concentrate
> on my metamodelling interests.
> I still have an interest in knowledge-based aspects of modelling, but
> 6 or so years ago decided to first promote a culture of 'declarative
> modelling within the ecosystem research community. The vehicle for
> is Simile ( http://www.simulistics.com ), a visual modelling
> 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
> with the possibility of dynamic creation and destruction of instanves,
> associations (in the UML sense) between object classes, etc.
> 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
> terms of the number of equations and the number of object instances.
> 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,
> 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
> approach in ecosystem research. I get deeply depressed when I see
> implemented in procedural programming languages, a mode of thinking
> 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
> processes. Please have a look at p.17 of
> http://gaim.sr.unh.edu/Products/News/Summer2003/rgsum03.pdf for an
> of my views on this subject: rather stating the obvious, I'm afraid,
> what else can I do? I also have a EU position paper coming out on
> 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
> sketchy 'thinking-out-loud' note - not implemented, but I think it
> be useful to explore the degree of common ground with the dataflow
> concepts that Simile supports and those of purpose-built
> systems, as you mentioned. Interestingly, I had a good chat with Eric
> Simon after talking to you: some of his Powerpoint slides were
> 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
> 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
> of which is the seamless integration of data, data analysis and
> 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,
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