[cellml-discussion] SBML L3 dist package

2011-05-24 Thread Andrew Miller

Hi Darryl,

I'm working on approaches for representing parameter uncertainty in 
CellML, and was wondering if you had any more recent draft 
specifications for the SBML dist package than the 2005 version on the 
SBML site (which currently only seems to have the 2005 draft and your 
presentation from 2010) that you were willing to share?


I think the realisastions based approach discussed in your 2010 
presentation could be a good way to go in CellML for representing 
distributions, alongside either a fixed set of univariate and 
multivariate distributions or a general facility for describing a 
distribution (possibly as a series of univariate distributions, 
optionally conditional on other parameters, including other randomly 
sampled parameters) from p.d.fs (solver software would either pattern 
match for known p.d.fs, or try to analytically or numerically invert the 
function).


We obviously also need some kind of operator to say that a parameter has 
a fixed but uncertain value, and that a given distribution is the 
probability distribution for the parameter (I think using MathML to 
describe that, with a csymbol operator, would be the most consistent 
with the approach taken in CellML); for example, if we believe that 
parameter x has a fixed value:


e.g. x(0) ~ N(mu=0, sigma^2 = 1)

  apply
csymbol 
definitionURL=http://www.cellml.org/1.2#uncertainWithDistribution/

apply
  csymbol 
definitionURL=http://www.cellml.org/1.2#atBoundVariableValue/

  cix/ci
  cn cellml:units=second0/cn
/apply
apply
  csymbol 
definitionURL=http://www.cellml.org/1.2#distributionFrompdf/

  apply
csymbol definitionURL=http://www.cellml.org/1.2#normalpdf/
cn cellml:units=metre0/cn
cn cellml:units=square_metre1/cn
  /apply
/apply
  /apply

Or (x(0), y(0)) ~ a distribution from realisations...

  apply
csymbol 
definitionURL=http://www.cellml.org/1.2#uncertainWithDistribution/

vector
  apply
csymbol 
definitionURL=http://www.cellml.org/1.2#atBoundVariableValue/

cix/ci
cn cellml:units=second0/cn
  /apply
  apply
csymbol 
definitionURL=http://www.cellml.org/1.2#atBoundVariableValue/

ciy/ci
cn cellml:units=second0/cn
  /apply
/vector
apply
  csymbol 
definitionURL=http://www.cellml.org/1.2#distributionFromRealisations/
  !-- For consistency with the univariate case, this represented 
in MathML as a 'vector of vectors' rather than a matrix; we could 
perhaps treat a MathML matrix as syntactic sugar for a vector of vectors 
anyway. --

  vector
vectorcn units=metre1/cncn units=metre2/cn/vector
vectorcn units=metre3/cncn units=metre3/cn/vector
vectorcn units=metre1/cncn units=metre5/cn/vector
vectorcn units=metre2/cncn units=metre4/cn/vector
vectorcn units=metre1/cncn units=metre5/cn/vector
vectorcn units=metre1/cncn units=metre3/cn/vector
vectorcn units=metre3/cncn units=metre5/cn/vector
vectorcn units=metre2/cncn units=metre5/cn/vector
vectorcn units=metre1/cncn units=metre4/cn/vector
vectorcn units=metre3/cncn units=metre5/cn/vector
!-- And so on - obviously this could lead to big files... --
  /vector
/apply
  /apply

Any comments you may have on this approach would be greatly appreciated.

Best wishes,
Andrew
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[cellml-discussion] Workshop on Interoperability in Scientific Computing

2011-05-24 Thread David Nickerson
IEEE e-Science 2011 Workshop on Interoperability in Scientific Computing

5th December 2011, Stockholm, Sweden.
http://www.comlab.ox.ac.uk/david.johnson/wisc11/

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.

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)
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