[sbml-svn] SF.net SVN: sbml:[12501] trunk/specifications/sbml-level-3/version-1/ distrib

[<dar...@us...>]

Revision: 12501
          http://sbml.svn.sourceforge.net/sbml/?rev=12501&view=rev
Author:   darrenjw
Date:     2010-12-31 13:08:41 +0000 (Fri, 31 Dec 2010)

Log Message:
-----------
some notes relating to the new distrib proposal

Modified Paths:
--------------
    trunk/specifications/sbml-level-3/version-1/distrib/distrib-draft.tex

Added Paths:
-----------
    trunk/specifications/sbml-level-3/version-1/distrib/distrib-notes.txt

Modified: trunk/specifications/sbml-level-3/version-1/distrib/distrib-draft.tex
===================================================================
--- trunk/specifications/sbml-level-3/version-1/distrib/distrib-draft.tex	2010-12-31 12:22:00 UTC (rev 12500)
+++ trunk/specifications/sbml-level-3/version-1/distrib/distrib-draft.tex	2010-12-31 13:08:41 UTC (rev 12501)
@@ -4,7 +4,7 @@
 
  \packageVersion{Version 1.0}
  \packageVersionDate{\today}
- \packageGeneralURL{http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/distrib}
+ \packageGeneralURL{http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Distributions_and_Ranges}
  \packageThisVersionURL{http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/distrib_proposal_2011}
 
  % -----------------------------------------------------------------------------

Added: trunk/specifications/sbml-level-3/version-1/distrib/distrib-notes.txt
===================================================================
--- trunk/specifications/sbml-level-3/version-1/distrib/distrib-notes.txt	                        (rev 0)
+++ trunk/specifications/sbml-level-3/version-1/distrib/distrib-notes.txt	2010-12-31 13:08:41 UTC (rev 12501)
@@ -0,0 +1,98 @@
+
+distrib - Uncertainty, distributions, and random numbers package for SBML L3
+
+This proposed package was discussed at the Seattle Hackathon:
+
+http://sbml.org/Events/Hackathons/The_2010_SBML-BioModels.net_Hackathon
+
+I presented an overview of the problem:
+
+Slides: http://sbml.org/images/3/3b/Djw-sbml-hackathon-2010-05-04.pdf
+Audio: http://sbml.org/images/6/67/Wilkinson-distributions-2010-05-04.mov
+
+building on the old proposal from the Newcastle group:
+
+http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Distributions_and_Ranges
+
+There was broad support at the meeting for development of such a
+package, and for the proposed feature set. Discussion following the
+presentation led to a consensus on the following points:
+
+* There is an urgent need for such a package
+
+* It is important to make a distinction between a description of
+* uncertainty regarding a model parameter and the mechanistic process
+* of selecting a random number from a probability distribution, for
+* applications such as parameter scans and experimental design
+
+* It is probably worth including the definition of PMFs, PDFs and CDFs
+* in the package
+
+* It is worth including the definition of random distributions using
+* particle representations within such a package, though some work
+* still needs to be done on the precise representation
+
+* It could be worth exploring the use of xinclude to point at particle
+* representations held in a separate file
+
+* Random numbers must not be used in rate laws or anywhere else that
+* is continuously evaluated, as then simulation behaviour is not
+* defined
+
+* Although there is a need for a package for describing extrinsic
+* noise via stochastic differential equations in SBML, such mechanisms
+* should not be included in this package due to the considerable
+* implications for simulator developers
+
+* We probably don't want to layer on top of UncertML
+* (www.uncertml.org), as this spec is fairly heavy-weight, and
+* somewhat tangential to our requirements
+
+* A random number seed is not part of a model and should not be
+* included in the package
+
+* The definition of truncated distributions and the specification of
+* hard upper and lower bounds on random quantities should be
+* considered.
+
+It was suggested that new constructs should be introduced into SBML by
+the package embedded as user-defined functions using the following
+syntax:
+
+<listOfFunctionDefinitions>
+  <functionDefinition id="myNormRand">
+    <distrib:####>
+      #### distrib binding information here ####
+    </distrib:####>
+    <math>
+      <lambda>
+        <bvar>
+          <ci>mu</ci>
+          <ci>sigma</ci>
+        </bvar>
+        <ci>mu</ci>
+      </lambda>
+    </math>
+  </functionDefinition>
+</listOfFunctionDefinitions>
+
+which allows the use of a "default value" by simulators which do not
+understand the package (but simulators which do will ignore the <math>
+element). The package would nevertheless be "required", as it will not
+be simulated correctly by software which does not understand the
+package.
+
+Informal discussions following the break-out covered topics such as
+how to work with vector random quantities in the absence of the vector
+element in the MathML subset used by SBML, and the care that must be
+taken with the semantics of random variables and the need to both a)
+reference multiple independent random quantities at a given time and
+b) make multiple references to the same random quantity at a given
+time.
+
+
+Constructive comments on any of this are welcome. 
+
+Regards,
+
+Darren


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