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

[Bertram Ludaescher]

Hi Robert:

My apologies for not having replied earlier. Indeed I've been swamped
quite a bit lately (and it seems I now need at least 3 messages to
react -- Chad's was no. 3 ;-)

I will forward your information also to the GEON folks.

thanks

Bertram

>>>>> "CB" == Chad Berkley <berkley at nceas.ucsb.edu> writes:
CB> 
CB> Hi Robert,
CB> I think Bertram has been a bit busy lately, as his wife just had a 
CB> baby.  I'm forwarding this message to two of our relevant mailing 
CB> lists.  I'm in meetings this week and next, but I'll try to read over 
CB> your message in detail and get a response to you asap.
CB> 
CB> Thanks for your interest in the SEEK/Kepler projects.
CB> 
CB> chad
CB> 
CB> On Jan 30, 2004, at 7:19 AM, r.muetzelfeldt at ed.ac.uk wrote:
CB> 
>> 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
CB> 
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