ecell-devel Mailing List for E-Cell System

Hi, Petteri!

I think that the samples in 'doc/sample' direcotry are for helping "modelers"
to use DM classes(ex, ODE solvers) in em. They handle practical cases, but are
not suited to testing. One of the reasons is that they are too complex to have
an analytical solution.
They may be appropriate for checking only whether DM classes work or not.
But we need to design new test models for testing the accuracy.

For example, about ODE solvers, a lot of test problems have been proposed.
One of the most classical sets is DETEST:

"Comparing Numerical Methods for Ordinary Differential Equations"
by Hull, T.E. for non-stiff ODE
"Comparing Numerical Methods for Stiff Systems of ODEs"
by Enright, W.H.

That was designed for testing the efficiency of ODE solvers, but also includes
simple problems like:

dy/dt = -y
y(0)=1.0

-> y = y(0)*exp(-t)

If you need more information about it, I'll send you sample scripts.
In the sample Python scritps, the results by ODE solvers are compared
with the analytical solution.

The case for stochasitc solvers like Gillespie method are more complicated
because it needs statistical analysis.


I don't know much about general form of test script. Could you tell me the
specifications of input and output? (Is it enough to return with some exception
when the accuracy is not guaranteed?) Then, I'll modify sample test scripts
to suite that.

Anyway, as you wrote, sample models in doc/sample directory should also
include some sample scripts in it.

Thanks.


Kaizu

2006/12/17, Koichi Takahashi <sh...@e-...>:
> Hei Petteri,
>
> Great work.  Testing is important.  I appreciate it.
>
> Two suggestions;
>
> - Kazunari Kaizu may have made a simple test suite for ODE solvers
>    somewhere.  He might be able to pass it for you incorporating
>    it as part of yours.
>
> - Satya, if some modules don't work on some platforms, these should
>    raise an exception when imported, not when called.   We've got
>    enough feedbacks from win users complaining they cannot run Session
>    Manager.
>
> sha
>
>
>
>
>
> > Hi Petteri,
> >
> > Thank you for your efforts. For Windows please use the newer version of
> > E-Cell, which can be found at:
> > http://prdownloads.sourceforge.net/ecell/ecell-3.1.105a-gtk%2Bpython.i386.exe?download
> > Currently, E-Cell does not support GA and SessionManager on Windows
> > because we are lacking some essential Python modules for the platform.
> >
> > satya
> >
> >
> >> Hei,
> >>
> >> In preparation to using `doc/samples' as test input data, I gave them
> >> a try on Wintel (ecell-3.1.103-gtk+python.i386.exe). Please see below
> >> for summary. Most of the samples don't have Python file to run them
> >> from command line. I could probably conjure simple ones on my own.
> >> However, the authors of `ga', `sessionmanager' and `simple' should
> >> have a look at those and fix them. Or admin should remove them
> >> altogether because such broken samples do no good and can be
> >> misleading in the worst case.
> >>
> >> Please propose how to proceed.
> >>
> >> --
> >> Petteri
> >>
> >> ====== branchG: NOK
> >>
> >> - no run.py file
> >>
> >> ===== CoupledOscillator: NOK
> >>
> >> - no run.py file
> >>
> >> ===== Drosophila: OK
> >>
> >> ===== Drosophila-cpp: OK
> >>
> >> ===== ga: NOK
> >>
> >> ecell3-session-manager ga.py
> >> Traceback (most recent call last):
> >>    File "ecell3-session-manager.merge", line 116, in ?
> >> ImportError: No module named SessionManager
> >>
> >> ===== Heatshock: NOK
> >>
> >> - no run.py file
> >>
> >> ===== LTD: OK
> >>
> >> ===== Pendulum: NOK
> >>
> >> - no run.py file
> >>
> >> ===== sessionmanager: NOK
> >>
> >> ecell3-session-manager ems.py
> >> Traceback (most recent call last):
> >>    File \&quot;ecell3-session-manager.merge\&quot;, line 116, in ?
> >> ImportError: No module named SessionManager
> >>
> >> ===== simple: NOK
> >>
> >> ecell3-session run.py
> >> t=      0.0
> >> S:Value=        1000000.0
> >> PyECS: SIGSEGV. Invalid memory reference.
> >>
> >> ===== SSystem: NOK
> >>
> >> - no run.py file
> >>
> >> ===== tauleap: NOK
> >>
> >> - no run.py file
> >>
> >> ==== Toy_Hybrid: NOK
> >>
> >> - no run.py file
> >>
> >>
> >>
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We are pleased to announce the 1st E-Cell Workshop, to be held at the 
SFC campus of Keio University on January 24th and 25th.  The official 
announcement page on e-cell.org is located at 
http://www.e-cell.org/ecell4workshop/1st-annual-e-cell-4-workshop-1/. 

This workshop will kick off development of the next version of E-Cell, 
version 4, wherein matters of features, organization, development plans, 
will be discussed.  All are welcome to attend.  If you are not currently 
on the list of participants, and wish to be included, please contact 
Yuri Matsuzaki (yu...@sf...) to RSVP. 

General questions or comments can be sent to me, Nathan Addy, at 
ad...@mo....

Best,
Nathan Addy