[Miase-discuss] Prototype & Examples & .miase

[Frank B. <fbergman@u.washington.edu>]

Hello all, 

I know I have been nagging about examples recently. So I thought it only
fair to contribute some as well: 

Examples:
=========

sedMLBIOM21: 
	- just like before, however now it also includes another data
generator, 
	  that takes the difference of v1-v2 and adds 20 ... just to have
some mathml

EllowitzRepressilator.miase: 
	- runs the repressilator and displays floating species


Brusselator.miase: 
	- runs the brusselator, displays time series and phase plot

Lorenz.miase:
	- runs a model of the Lorenz attractor, and generates 4 plots. 


In order not to tax your mail too much, I won't attach screenshots but show
you a screencast instead: 

http://screencast.com/t/XG9DDycH 


Prototype:
==========

In order to test these Examples you are welcome to test a first web
application, that will take a Sed-ML document with remote sources (i.e:
sedMLBIOM21.xml) and execute it, or a .miase file, (as I dubbed the zip file
including Sed-ML and all local sources). In order to help you create new
*valid* examples you can also upload an SBML file, specify uniform-time
course parameters, output species / parameters, and plot parameters. After
that you will be able to download either Sed-ML, or .miase file, which you
can then easily modify for more complicated examples. 

http://128.208.19.37/MIASETest/

The machine will not be always available, so please bear with me :) 

What is not in the prototype: 
=============================
- no ChangeXML / ChangeMath
- no Reports (I just did not know where to put them)
- no 3D plots
- limited support for post processing in data generators (I'm not quite sure
what 
  Subset of math-ml is allowed here). 
- the prototype does not write any attributes on the sedML node (not sure
whether the version attribute as it is now will survive). 

Known issues: 
=============
- Web Application does not give error messages, if you see an empty plot
that is and indication that things went wrong
- algorithm attribute on uniformTimeCourse will not be evaluated, the model
will always simulated with roadRunner ... I'll add an option to set
tolerances for the integrator soon
- TIME: ... the exported time variable will be referred to as: 

<dataGenerator id="time1" name="time">
      <listOfVariables>
        <variable id="time" taskReference="task1" target="time" />
      </listOfVariables><math xmlns="http://www.w3.org/1998/Math/MathML">
  <ci> time </ci>
</math></dataGenerator>
- XPATH: I will only support Xpath 1.0 for now, thus the queries should
prefix the
- .miase file: the .miase file generated could not be extracted by my mac
without 7zip, 
	Error message on OSX  unzip is "need PK compat. v4.5 (can do v2.1)"
p7zip works fine

.miase file
===========
As said before, for me it is of limited interest to always access remote
sources, and embedding was taken off the table. On the other hand I don't
want local sources get out of sync with the description. Thus my library
sticks all local sources (and optionally all remote ones too) into a zipfile
with name X.miase, inside that file it takes X.xml to be the Sed-ML
description. 

If we could decide on this as the standard way to do it that would be fine
with me, or we could decide on writing a manifest with the name of the
Sed-ML file as well ... I'd be interested in resolving this :) 


So far from me, please let me know your comments. 

Best
Frank

P.S: If anyone is interested in the C# library to read MIASE files, or the
sister-library to run them, let me know.