ecell-users — For users.

Re: [Ecell-users] set up ODE for species directly.

[Lu L. <lu...@eb...>]

Hi Moriyoshi and Yuri

Thank you very much, yes I think ExpressionFluxProcess will be helpful.
But I have several questions:

1. ExpressionFluxProcess represents a customized reaction rate or it
directly presents flux?
e.g.
Process ExpressionFluxProcess(a2b)
{
k 33;
Expression "K^2";
VariableReferenceList [S0 Variable:/cell:a -1][P0 Variable:/cell:b 1]
}

Then, if we only consider this one reaction, which of the following
expression is correct?
da/dt = -K^2[a]   and    db/dt = K^2[a]
or
da/dt = -K^2   and  db/dt = K^2

2. Since the unit for Expression must be "number/second" instead of
"concentration/second", if, in the expression, the MolarConc of some
variables are used, I must multiply self.getSuperSystem().sizeN_A once, in
order to inform the system that I changed the unit?
I just wonder how e-cell do this consistency check ?
If under some circumstances, I need to multiply the size twice.....can
e-cell detect it?

3 In the case of multi-compartment model, in which way I can indicate that
I multiplied correct compartment/compartments?
e.g.
Process ExpressionFluxProcess(Ca_ER2Cytosol)
{
Kch 3;
K1 2;
Expression "(Kch*C1.MolarConc^2/(K1^2+C1.MolarConc^2)) *
(C2.MolarConc-C1.MolarConc)";   #this expression is wrong since I haven't
multiply any compartment size!#
VariableReferenceList [C1 Variable:/cytosol:Ca 1][C2 Variable:/ER:Ca -1];
}

* in this example I want to represent ER release Ca to cytosol.
the first part of this expression,
Kch*C1.MolarConc^2/(K1^2+C1.MolarConc^2) should have no unit problem,
since the unit for Kch is per-second, and the unit for K1 is
concentration.
However, for the second part C2.MolarConc-C1.MolarConc, I should convert
its unit into Number instead of concentration. Which compartment size, and
what kind of expression I should use here.

4 which stepper I should use for ExpressioFluxProcess?
should it must be a continuous stepper?
Can I use ODEstepper?


I am looking forward to your reply.
Thank you very much !

yours Lu


> Hi,
>
> In which sence did you say "directly" ? Sounds like
> it's ExpressionFluxProcess that fits to your case; did
> you try it yet?
>
> Moriyoshi
>
>
> 2008/3/18, Lu Li <lu...@eb...>:
>> Hello
>>
>>  I wonder in e-cell, can I directly set up ODE for some species?
>>  And these species, even can play a role in some reactions, their flux
>>  will not be influenced by these reactions?
>>
>>  I am looking forward to your reply.
>>
>>  Best Wishes
>>  yours Lu Li
>>  --
>>  Lu Li
>>  PhD student in Computational Neurobiology
>>  EMBL-European Bioinformatics Institute, Cambridge, UK
>>
>>  -------------------------------------------------------------------------
>>  This SF.net email is sponsored by: Microsoft
>>  Defy all challenges. Microsoft(R) Visual Studio 2008.
>>  http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>>  _______________________________________________
>>  Ecell-users mailing list
>>  Ece...@li...
>>  https://lists.sourceforge.net/lists/listinfo/ecell-users
>>
>
>
> --
> Moriyoshi Koizumi <mor...@gm...>
> (also reachable on <mo...@sf...>)
>


-- 
Lu Li
PhD student in Computational Neurobiology
EMBL-European Bioinformatics Institute
Cambridge, UK
                .        .' '.             _
                 .        .   .           (_\
                  .         .         . -{{((|8<
                    ' .  . ' ' .  . '     (_/

Re: [Ecell-users] set up ODE for species directly.

[Moriyoshi K. <mo...@sf...>]

Besides this, you can specify 0 toh the coefficient of the variable
reference in question so that you can use it in an expression without
altering it by the value of the calculated process activity.

The values of the coefficients are disregarded within the evaluation of
the expression.

Moriyoshi

2008/3/19, Moriyoshi Koizumi <mo...@sf...>:
> Hi,
>
>  In which sence did you say "directly" ? Sounds like
>  it's ExpressionFluxProcess that fits to your case; did
>  you try it yet?
>
>  Moriyoshi
>
>
>  2008/3/18, Lu Li <lu...@eb...>:
>
> > Hello
>  >
>  >  I wonder in e-cell, can I directly set up ODE for some species?
>  >  And these species, even can play a role in some reactions, their flux
>  >  will not be influenced by these reactions?

-- 
Moriyoshi Koizumi <mor...@gm...>
(also reachable on <mo...@sf...>)

Re: [Ecell-users] set up ODE for species directly.

[Moriyoshi K. <mo...@sf...>]

Hi,

In which sence did you say "directly" ? Sounds like
it's ExpressionFluxProcess that fits to your case; did
you try it yet?

Moriyoshi


2008/3/18, Lu Li <lu...@eb...>:
> Hello
>
>  I wonder in e-cell, can I directly set up ODE for some species?
>  And these species, even can play a role in some reactions, their flux
>  will not be influenced by these reactions?
>
>  I am looking forward to your reply.
>
>  Best Wishes
>  yours Lu Li
>  --
>  Lu Li
>  PhD student in Computational Neurobiology
>  EMBL-European Bioinformatics Institute, Cambridge, UK
>
>  -------------------------------------------------------------------------
>  This SF.net email is sponsored by: Microsoft
>  Defy all challenges. Microsoft(R) Visual Studio 2008.
>  http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>  _______________________________________________
>  Ecell-users mailing list
>  Ece...@li...
>  https://lists.sourceforge.net/lists/listinfo/ecell-users
>


-- 
Moriyoshi Koizumi <mor...@gm...>
(also reachable on <mo...@sf...>)

[Ecell-users] set up ODE for species directly.

[Lu Li <lu...@eb...>]

Hello

I wonder in e-cell, can I directly set up ODE for some species?
And these species, even can play a role in some reactions, their flux 
will not be influenced by these reactions?

I am looking forward to your reply.

Best Wishes
yours Lu Li
-- 
Lu Li
PhD student in Computational Neurobiology
EMBL-European Bioinformatics Institute, Cambridge, UK

Re: [Ecell-users] Ecell installation problem

[Lu L. <lu...@eb...>]

Hi

It works!
Thank you very much for help.

Best Wishes
Lu

> Hi there,
>
> That is because the python module could not locate the binary libraries
> of E-Cell. You probably have to add /usr/local/lib to /etc/ld.so.conf
> and run /sbin/ldconfig with the root privilege then.
>
> Regards,
> Moriyoshi

-- 
Lu Li
PhD student in Computational Neurobiology
EMBL-European Bioinformatics Institute
Cambridge, UK
                .        .' '.             _
                 .        .   .           (_\
                  .         .         . -{{((|8<
                    ' .  . ' ' .  . '     (_/

Re: [Ecell-users] Ecell installation problem

[Moriyoshi K. <mo...@sf...>]

Hi there,

That is because the python module could not locate the binary libraries
of E-Cell. You probably have to add /usr/local/lib to /etc/ld.so.conf
and run /sbin/ldconfig with the root privilege then.

Regards,
Moriyoshi

2008/3/4, Lu Li <lu...@eb...>:
> Hello,
>
>  I'm trying to install e-cell (release 3.1.106) on a Debian Lenny (testing).
>  All the three steps (configure, make, make install) of the installation
>  ran smoothly without any error.
>  Unfortunately, after that when I try to run e-cell, that doesn't work and
>  I get the following error (I only give you this example, but other
>  commands return the same error, even one without any graphical interface):
>
>  $ ecell3-session-monitor
>  Traceback (most recent call last):
>   File "/usr/local/bin/ecell3-session-monitor", line 7, in ?
>     import ecell.ecs
>   File "/usr/local/lib/python2.4/site-packages/ecell/__init__.py", line
>  46, in ?
>     from Session import *
>   File "/usr/local/lib/python2.4/site-packages/ecell/Session.py", line 37,
>  in ?
>     import ecell.ecs
>   File "/usr/local/lib/python2.4/site-packages/ecell/ecs.py", line 30, in ?
>     from _ecs import *
>  ImportError: libecs.so.2: cannot open shared object file: No such file or
>  directory
>
>
>  Do you have any explanation for this behaviour and idea to solve the
>  situation?
>  Thank you for your help.
>
>  --
>  Lu Li
>  PhD student in Computational Neurobiology
>  EMBL-European Bioinformatics Institute
>  Cambridge, UK
>                 .        .' '.             _
>                  .        .   .           (_\
>                   .         .         . -{{((|8<
>                     ' .  . ' ' .  . '     (_/
>
>
>  -------------------------------------------------------------------------
>  This SF.net email is sponsored by: Microsoft
>  Defy all challenges. Microsoft(R) Visual Studio 2008.
>  http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>  _______________________________________________
>  Ecell-users mailing list
>  Ece...@li...
>  https://lists.sourceforge.net/lists/listinfo/ecell-users
>


-- 
Moriyoshi Koizumi <mor...@gm...>
(also reachable on <mo...@sf...>)

[Ecell-users] Ecell installation problem

[Lu L. <lu...@eb...>]

Hello,

I'm trying to install e-cell (release 3.1.106) on a Debian Lenny (testing).
All the three steps (configure, make, make install) of the installation
ran smoothly without any error.
Unfortunately, after that when I try to run e-cell, that doesn't work and
I get the following error (I only give you this example, but other
commands return the same error, even one without any graphical interface):

$ ecell3-session-monitor
Traceback (most recent call last):
  File "/usr/local/bin/ecell3-session-monitor", line 7, in ?
    import ecell.ecs
  File "/usr/local/lib/python2.4/site-packages/ecell/__init__.py", line
46, in ?
    from Session import *
  File "/usr/local/lib/python2.4/site-packages/ecell/Session.py", line 37,
in ?
    import ecell.ecs
  File "/usr/local/lib/python2.4/site-packages/ecell/ecs.py", line 30, in ?
    from _ecs import *
ImportError: libecs.so.2: cannot open shared object file: No such file or
directory


Do you have any explanation for this behaviour and idea to solve the
situation?
Thank you for your help.

-- 
Lu Li
PhD student in Computational Neurobiology
EMBL-European Bioinformatics Institute
Cambridge, UK
                .        .' '.             _
                 .        .   .           (_\
                  .         .         . -{{((|8<
                    ' .  . ' ' .  . '     (_/

[Ecell-users] E-Cell 3.1.106rc2 now available

[Moriyoshi K. <mo...@sf...>]

Hi all,

The E-Cell developers are proud to annouce the second release
candidate of the upcoming release, 3.1.106. A few bugs were fixed for
better compatibility with older systems like rhel5.

We are not going to place binary packages this time, as now we have
set up the repository that can be directly specified in the
configuration files of your package manager (wow!)

Instructions for the packages are explained in a separate page:
http://dev.e-cell.org/wiki/ecell3/install/packages

Hope you will enjoy them and wish your merry christmas!

Changelog:
* Avoided resetting LD_LIBRARY_PATH in ecell-python for the sake of
inter-platform operability. This was also problematic in combination
with multiple ldconfig paths. (Moriyoshi)
* Fixed sample installation rule so that samples would get installed
in sample-per-directory manner. (Moriyoshi)
* Fixed configure scripts for dmtool and dynamic modules so that
modules they produce would have right extensions that follows the
libltdl's convention. (Moriyoshi)

-- 
Moriyoshi Koizumi <mor...@gm...>
(also reachable on <mo...@sf...>)

Re: [Ecell-users] Fwd: Help!

[Yuri M. <yu...@sf...>]

Hi Sushil,

I got your mail forwarded by Moriyoshi.
What is the unit of "R" in your model?
is it particles / sec ?
I've made a model in that the unit of "R"
  is particles / second, though it is not
likely what you are expecting.

Yuri Matsuzaki

Re: [Ecell-users] Fwd: Help!

[Moriyoshi K. <mo...@sf...>]

It looks like sf.net rejects attachments of unknown file types. Sorry
for cluttering.

Moriyoshi

2007/12/11, Moriyoshi Koizumi <mo...@sf...>:
> Hi,
>
> Sorry, but I didn't manage to figure out what you are trying to do
> here. I created a sample model based on the description. Would you try
> it to see if it is what you want?
>
> Moriyoshi
>
> 2007/12/8, sushil ronghe <ron...@gm...>:
> >
> >
> > ---------- Forwarded message ----------
> > From: sushil ronghe <ron...@gm...>
> > Date: Dec 8, 2007 6:12 PM
> > Subject: Help!
> > To: e-c...@e-...
> >
> >
> >
> > Dear all,
> >
> > I am modeling a reaction with E-Cell where reagent (R)
> > is added to the system say M (infinitely).
> > Rate of addition of R to M is known.
> >
> > The rate of conversion of R to R2 is given.
> > I want to calculate the concentration of R
> > In M whose volume is also given.
> > Concentration in M is calculated as
> >
> >  C = [Concentration of R in M] / Volume of M;
> >
> > and Concentration of R in M is calculated as
> >  - [Rate of Conversion of R to R2] + [Rate of Addition of R]
> >
> > I want to simulate this equation:
> >
> >  d/dt [M] =  - [Rate of Conversion of R to R2] + [Rate of Addition of R]
> >
> > My Em file looks like this.I am not very much sure about the selection of
> > stepper
> > and process.
> >
> > Constant are as fallows :
> >
> >  [Concentration of R in M]  (initially) =0;
> >  [Rate of Conversion of R to R2] = 7.2
> >  [Rate of addition]= 600
> >
> >
> > >
> > >
> > >
> > > Stepper ODE45Stepper( DT_1 )
> > > {
> > >        StepInterval 0.01;
> > > }
> > >
> > >
> > > System System( / ){
> > >    StepperID DT_1;
> > >
> > >    Process ExpressionFluxProcess(C0){
> > >        Expression "M0.MolarConc/14";
> > >        VariableReferenceList [C0:./compartment:C 1]
> > > [M0:./compartment:M];
> > >        }
> > >
> > >    Process ExpressionFluxProcess(M0){
> > >        Expression "-(7.2*C0.MolarConc) +R0.Value";
> > >        VariableReferenceList [M0:./compartment:M -1]
> > > [C0:./compartment:C][R0:./compartment:R];
> > >        }
> > >    }
> > > System System( /compartment ){
> > >    StepperID DT_1;
> > >
> > >    Variable Variable(Size){
> > >        Value 1;
> > >        Fixed 1;
> > >    }
> > >
> > >    Variable Variable(M){
> > >        Value 0.0;
> > >        }
> > >
> > >    Variable Variable(R){
> > >        Value 600;
> > >        }
> > >
> > >    Variable Variable(C){
> > >        Value 0.0;
> > >        }
> > > }
> >
> > I am expecting a graph starting from 0 and reaching 600,
> >
> > what i am getting is Concentration of C is dropping and also
> > the simulation is stopped because of infinite numbers.
> >
> > Any help is really appreciated
> >
> >
> >
> > --
> > ********************************
> > sushil ronghe
> > *********************************
> >
> > --
> > ********************************
> > sushil ronghe
> > *********************************
> > -------------------------------------------------------------------------
> > SF.Net email is sponsored by:
> > Check out the new SourceForge.net Marketplace.
> > It's the best place to buy or sell services for
> > just about anything Open Source.
> > http://sourceforge.net/services/buy/index.php
> > _______________________________________________
> > Ecell-users mailing list
> > Ece...@li...
> > https://lists.sourceforge.net/lists/listinfo/ecell-users
> >
> >
>
>
> --
> Moriyoshi Koizumi <mor...@gm...>
> (also reachable on <mo...@sf...>)
>
>


-- 
Moriyoshi Koizumi <mor...@gm...>
(also reachable on <mo...@sf...>)

[Ecell-users] Fwd: Help!

[sushil r. <ron...@gm...>]

---------- Forwarded message ----------
From: sushil ronghe <ron...@gm...>
Date: Dec 8, 2007 6:12 PM
Subject: Help!
To: e-c...@e-...


Dear all,

I am modeling a reaction with E-Cell where reagent (R)
is added to the system say M (infinitely).
Rate of addition of R to M is known.

The rate of conversion of R to R2 is given.
I want to calculate the concentration of R
In M whose volume is also given.
Concentration in M is calculated as

 C = [Concentration of R in M] / Volume of M;

and Concentration of R in M is calculated as
 - [Rate of Conversion of R to R2] + [Rate of Addition of R]

I want to simulate this equation:

 d/dt [M] =  - [Rate of Conversion of R to R2] + [Rate of Addition of R]

My Em file looks like this.I am not very much sure about the selection
of stepper
and process.

Constant are as fallows :

 [Concentration of R in M]  (initially) =0;
 [Rate of Conversion of R to R2] = 7.2
 [Rate of addition]= 600


>  Stepper ODE45Stepper( DT_1 )
> {
>        StepInterval 0.01;
> }
>
>
> System System( / ){
>    StepperID DT_1;
>
>    Process ExpressionFluxProcess(C0){
>        Expression "M0.MolarConc/14";
>        VariableReferenceList [C0:./compartment:C 1]
> [M0:./compartment:M];
>        }
>
>    Process ExpressionFluxProcess(M0){
>        Expression "-(7.2*C0.MolarConc) +R0.Value";
>        VariableReferenceList [M0:./compartment:M -1]
> [C0:./compartment:C][R0:./compartment:R];
>        }
>    }
> System System( /compartment ){
>    StepperID DT_1;
>
>    Variable Variable(Size){
>        Value 1;
>        Fixed 1;
>    }
>
>    Variable Variable(M){
>        Value 0.0;
>        }
>
>    Variable Variable(R){
>        Value 600;
>        }
>
>    Variable Variable(C){
>        Value 0.0;
>        }
> }
>
I am expecting a graph starting from 0 and reaching 600,

what i am getting is Concentration of C is dropping and also
the simulation is stopped because of infinite numbers.

Any help is really appreciated



-- 
********************************
sushil ronghe
*********************************


-- 
********************************
sushil ronghe
*********************************

[Ecell-users] test, please ignore.

[Moriyoshi K. <mo...@sf...>]

test.

-- 
Moriyoshi Koizumi <mor...@gm...>
(also reachable on <mo...@sf...>)