ecell-devel Mailing List for E-Cell System

I'm very sorry for my late reply.

Now I attached two em and eml files. They were checked on
E-Cell 3.1.103 on Windows XP, which is found at sourceforge.

In test1.eml, CatalyzedMassActionFluxProcess is used.
On the other hand, in test2.eml, ExpressionFluxProcess is used
instead of CatalyzedMassActionFluxProcess.

CatalyzedMassActionFluxProcess calculates its activity by the
"concentration" of variables. In your latest model,  the concentration
of variables are too small. (When Value of Variable "A" is 150,
its MolarConc is 2.5e-22.) So the activity is also very small but is
not equal to zero. If you want to use CatalyzedMassAction, inclease
the molecular number of Variables or declease the size(volume) of
System which contains Variables and Processes.

Next, using ExpressionFluxProcess, you can define the equation as
you want. Set "Expression". For example, in test2.eml, Expression-
FluxProcess is designed as calculating the activity by the value of
Variables, not by the concentration.

Please test the attached files and report the result.
regards.

P.S.
I'm very sorry to say that I'm not "Doctor " yet:-)

kaizu

2005/9/22, S.Krishnaswamy <kr...@mr...>:
>
> Dear Dr. Kaizu
>
> We have tried the syntax in the way you have described. But still
> the activity of the reactor is nil. The substrate and product
> do not change and remain constant. Can you please help us sort
> this out. If you can send us a sample input (.em file) which
> works this will help us. We are using ecell version 3.0 on
> Windows.
>
> regards
>
> krishnaswamy
>
> On Tue, 9 Aug 2005, Kazunari Kaizu wrote:
>
> >
> > 'C0' is an ID for VariableReference. Set it in the following way.
> >
> > Process CatalysedMassActionFluxProcess( c1c2c3omprp_envzk_ompc )
> > {
> >       Name    A_B_C;
> >       k       1.0;
> >       VariableReferenceList   [ S0 :.:A-1 ]
> >                               [ C0 :.:B 0 ] # the enzymatic substrate
> >                               [ P0 :.:C1 ];
> > }
> >
> > CatalysedMassActionFluxProcess allows only one enzymatic substrate C0.
> > If you want to use two or more enzymes, substitute ExpressionFlux-
> > Process.
> >
> >
> > kaizu
> >
> > Srividhya K.V. wrote:
> > >
> > > We replaced the CatalysedMassActionFluxProcess file with the new vers=
ion of the same file you had sent us.But still the reactor doesnt seem to w=
ork.we would like to know the syntax for giving
> > > variable reference list in eml file .
> > > Say for mass action process we specify substrates and products.
> > > Process MassActionFluxProcess( c1c2c3omprp_envzk_ompc )
> > > {
> > >     Name    A_B_C;
> > >     k       1;
> > >     VariableReferenceList   [ S0 :.:A-1 ] [ S1 :.:B] [ P0 :.:C1 ];
> > >
> > > }
> > >
> > > How do we specify C0  for CatalysedMassActionFluxProcess.
> > >
> > > Regards
> > > vidhya
> > >
> > >
> > >>Hi, thank you for your report.
> > >
> > >
> > >>As you said, CatalysedMassActionFluxProcess did not work.
> > >>It was a bug about CatalysedMassActionFluxProcess itself.
> > >>I fixed and updated it. Please try again with the latest
> > >>CVS or the attached cpp file.
> > >
> > >
> > >
> > >>kaizu
> > >
> > >
> > > 2005/8/3, S.Krishnaswamy <kr...@mr...>:
> > >
> > >>We want to use the catalysed mass action reactor
> > >>in Ecell 3.0 but find it does not work.
> > >>The mass action reactor works.
> > >>Are we giving the input in the wrong syntax or
> > >>does the catalysed mass action reactor not working.
> > >>If it is working can someone give us the eml file
> > >>showing how it is used.
> > >>
> > >>regards
> > >>
> > >>krishnaswamy
> > >>
> > >>
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > On Thu, 04 Aug 2005 Kazunari Kaizu wrote :
> > >
> > >>#include "libecs.hpp"
> > >>
> > >>#include "ContinuousProcess.hpp"
> > >>
> > >>USE_LIBECS;
> > >>
> > >>LIBECS_DM_CLASS( CatalyzedMassActionFluxProcess,
> > >>ContinuousProcess )
> > >>{
> > >>
> > >> public:
> > >>
> > >>  LIBECS_DM_OBJECT( CatalyzedMassActionFluxProcess,
> > >>Process )
> > >>    {
> > >>      INHERIT_PROPERTIES( Process );
> > >>      PROPERTYSLOT_SET_GET( Real, k );
> > >>    }
> > >>
> > >>
> > >>  CatalyzedMassActionFluxProcess()
> > >>    {
> > >>      ; // do nothing
> > >>    }
> > >>
> > >>  SIMPLE_SET_GET_METHOD( Real, k );
> > >>
> > >>  virtual void initialize()
> > >>    {
> > >>      Process::initialize();
> > >>
> > >>      C0 =3D getVariableReference( "C0" );
> > >>    }
> > >>
> > >>  virtual void fire()
> > >>    {
> > >>      Real velocity( k );
> > >>      velocity *=3D C0.getValue();
> > >>      for( VariableReferenceVectorConstIterator
> > >>         i ( theVariableReferenceVector.begin() );
> > >>           i !=3D theZeroVariableReferenceIterator ; ++i )
> > >>    {
> > >>      VariableReferenceCref aVariableReference( *i );
> > >>      const Real aConcentration(
> > >>aVariableReference.getMolarConc() );
> > >>
> > >>      Integer j( aVariableReference.getCoefficient() );
> > >>      do
> > >>        {
> > >>          velocity *=3D aConcentration;
> > >>          ++j;
> > >>        } while( j !=3D 0 );
> > >>    }
> > >>
> > >>      setFlux( velocity );
> > >>    }
> > >>
> > >> protected:
> > >>
> > >>  Real k;
> > >>  VariableReference C0;
> > >>
> > >>};
> > >>
> > >>LIBECS_DM_INIT( CatalyzedMassActionFluxProcess, Process
> > >>);
> > >
> > >
> > >
> > > Srividhya ,K.V.
> > > Junior Research Fellow
> > > C/O Dr.S.Krishnaswamy
> > > Department of Genetic Engineering
> > > School of Biotechnology
> > > Madurai Kamaraj University
> > > Madurai-625 021
> > > CONTACT No. 2459931 , 2459141
> > >
> > >
> > >
> >
>
> --
> S.Krishnaswamy
> Professor
> School of Biotechnology
> Madurai Kamaraj University
> Madurai 625 021, India
>
> mku...@gm...    mku...@re...   kr...@mr....i=
n
> 91-452-2458638 (res) 91-452-2459931 (lab) 91-452-2459141 (bioinfo office)
>
>
>

Dear Dr. Kaizu

We have tried the syntax in the way you have described. But still
the activity of the reactor is nil. The substrate and product
do not change and remain constant. Can you please help us sort 
this out. If you can send us a sample input (.em file) which
works this will help us. We are using ecell version 3.0 on 
Windows. 

regards

krishnaswamy

On Tue, 9 Aug 2005, Kazunari Kaizu wrote:

> 
> 'C0' is an ID for VariableReference. Set it in the following way.
> 
> Process CatalysedMassActionFluxProcess( c1c2c3omprp_envzk_ompc )
> {
> 	Name	A_B_C;
> 	k	1.0;
> 	VariableReferenceList	[ S0 :.:A-1 ]
> 				[ C0 :.:B 0 ] # the enzymatic substrate
> 				[ P0 :.:C1 ];
> }
> 
> CatalysedMassActionFluxProcess allows only one enzymatic substrate C0.
> If you want to use two or more enzymes, substitute ExpressionFlux-
> Process.
> 
> 
> kaizu
> 
> Srividhya K.V. wrote:
> > 
> > We replaced the CatalysedMassActionFluxProcess file with the new version of the same file you had sent us.But still the reactor doesnt seem to work.we would like to know the syntax for giving 
> > variable reference list in eml file . 
> > Say for mass action process we specify substrates and products. 
> > Process MassActionFluxProcess( c1c2c3omprp_envzk_ompc )
> > {
> > 	Name	A_B_C;
> > 	k	1;
> > 	VariableReferenceList	[ S0 :.:A-1 ] [ S1 :.:B] [ P0 :.:C1 ];
> > 
> > }
> > 
> > How do we specify C0  for CatalysedMassActionFluxProcess.
> > 
> > Regards
> > vidhya
> > 
> > 
> >>Hi, thank you for your report.
> > 
> > 
> >>As you said, CatalysedMassActionFluxProcess did not work.
> >>It was a bug about CatalysedMassActionFluxProcess itself.
> >>I fixed and updated it. Please try again with the latest
> >>CVS or the attached cpp file.
> > 
> > 
> > 
> >>kaizu
> > 
> > 
> > 2005/8/3, S.Krishnaswamy <kr...@mr...>:
> > 
> >>We want to use the catalysed mass action reactor
> >>in Ecell 3.0 but find it does not work.
> >>The mass action reactor works.
> >>Are we giving the input in the wrong syntax or
> >>does the catalysed mass action reactor not working.
> >>If it is working can someone give us the eml file
> >>showing how it is used.
> >>
> >>regards
> >>
> >>krishnaswamy
> >>
> >>
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > On Thu, 04 Aug 2005 Kazunari Kaizu wrote :
> > 
> >>#include "libecs.hpp"
> >>
> >>#include "ContinuousProcess.hpp"
> >>
> >>USE_LIBECS;
> >>
> >>LIBECS_DM_CLASS( CatalyzedMassActionFluxProcess, 
> >>ContinuousProcess )
> >>{
> >>
> >> public:
> >>
> >>  LIBECS_DM_OBJECT( CatalyzedMassActionFluxProcess, 
> >>Process )
> >>    {
> >>      INHERIT_PROPERTIES( Process );
> >>      PROPERTYSLOT_SET_GET( Real, k );
> >>    }
> >>
> >>
> >>  CatalyzedMassActionFluxProcess()
> >>    {
> >>      ; // do nothing
> >>    }
> >>  
> >>  SIMPLE_SET_GET_METHOD( Real, k );
> >>    
> >>  virtual void initialize()
> >>    {
> >>      Process::initialize();
> >>
> >>      C0 = getVariableReference( "C0" );
> >>    }
> >>
> >>  virtual void fire()
> >>    {
> >>      Real velocity( k );
> >>      velocity *= C0.getValue();
> >>      for( VariableReferenceVectorConstIterator
> >>	     i ( theVariableReferenceVector.begin() );
> >>           i != theZeroVariableReferenceIterator ; ++i )
> >>	{
> >>	  VariableReferenceCref aVariableReference( *i );
> >>	  const Real aConcentration( 
> >>aVariableReference.getMolarConc() );
> >>
> >>	  Integer j( aVariableReference.getCoefficient() );
> >>	  do
> >>	    {	   
> >>	      velocity *= aConcentration;
> >>	      ++j;
> >>	    } while( j != 0 );
> >>	}
> >>
> >>      setFlux( velocity );
> >>    }
> >>  
> >> protected:
> >>  
> >>  Real k;
> >>  VariableReference C0;
> >>
> >>};
> >>
> >>LIBECS_DM_INIT( CatalyzedMassActionFluxProcess, Process 
> >>);
> > 
> > 
> > 
> > Srividhya ,K.V.
> > Junior Research Fellow
> > C/O Dr.S.Krishnaswamy
> > Department of Genetic Engineering 
> > School of Biotechnology
> > Madurai Kamaraj University
> > Madurai-625 021
> > CONTACT No. 2459931 , 2459141
> > 
> > 
> > 
> 

-- 
S.Krishnaswamy
Professor
School of Biotechnology
Madurai Kamaraj University
Madurai 625 021, India

mku...@gm...    mku...@re...   kr...@mr...
91-452-2458638 (res) 91-452-2459931 (lab) 91-452-2459141 (bioinfo office)

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the above company.

Gabor,

Thanks for the urls. The problem is that when we release version 3.1.105 
for FC 3 (or CentOS 4) it won't work directly on those platforms. We 
need to ask the users to get the rpms. On the other hand, for FC 4, 
there is no problem with gnome-canvas, but there is a bug with gcc4.

Kaizu, do you think we should wait for the bug to be solved? Or should I 
just release now for FC 3?

satya


>You can download gnome-python2-canvas from here
>http://rpm.pbone.net/index.php3/stat/4/idpl/1533016/com/gnome-python2-
>canvas-2.6.0-3.i386.rpm.html
>or here
>http://rpm.pbone.net/index.php3/stat/4/idpl/1584466/com/gnome-python2-
>canvas-2.6.0-1.1.fc3.nr.i386.rpm.html
>Gabor
>
>On Tue, 2005-09-20 at 17:09 +0900, Satya Arjunan wrote:
>  
>
>>Hi all,
>>
>>I have tried building E-Cell on Fedora Core 3 for 3.1.105 release 
>>candidate but it fails because it doesn't have the required gnome-canvas 
>>for Model Editor. Next, I have tried on Fedora Core 4 but it fails also 
>>as a result of the bug 
>>http://sourceforge.net/tracker/index.php?func=detail&aid=1291476&group_id=72485&atid=534670) 
>>in either boost or libecs with gcc4. I have also tried upgrading boost 
>>from version 1.32 to version 1.33 in FC 4 but the bug persists. 
>>Currently we have two options:
>>
>>1. Release 3.1.105 with FC 3 as the target, but we need to find a 
>>workaround for gnome-canvas (gabor?)
>>2. Wait until this bug is solved and release for FC 4 (kaizu?)
>>
>>I would like to know your views on this. Thank you.
>>
>>satya
>>
>>
>>
>>    
>>

You can download gnome-python2-canvas from here
http://rpm.pbone.net/index.php3/stat/4/idpl/1533016/com/gnome-python2-
canvas-2.6.0-3.i386.rpm.html
or here
http://rpm.pbone.net/index.php3/stat/4/idpl/1584466/com/gnome-python2-
canvas-2.6.0-1.1.fc3.nr.i386.rpm.html
Gabor

On Tue, 2005-09-20 at 17:09 +0900, Satya Arjunan wrote:
> Hi all,
> 
> I have tried building E-Cell on Fedora Core 3 for 3.1.105 release 
> candidate but it fails because it doesn't have the required gnome-canvas 
> for Model Editor. Next, I have tried on Fedora Core 4 but it fails also 
> as a result of the bug 
> http://sourceforge.net/tracker/index.php?func=detail&aid=1291476&group_id=72485&atid=534670) 
> in either boost or libecs with gcc4. I have also tried upgrading boost 
> from version 1.32 to version 1.33 in FC 4 but the bug persists. 
> Currently we have two options:
> 
> 1. Release 3.1.105 with FC 3 as the target, but we need to find a 
> workaround for gnome-canvas (gabor?)
> 2. Wait until this bug is solved and release for FC 4 (kaizu?)
> 
> I would like to know your views on this. Thank you.
> 
> satya
> 
> 
> 
-- 
Bereczki Gabor <ga...@sf...>

What is the problem with gnome canvas?
Gabor

On Tue, 2005-09-20 at 17:09 +0900, Satya Arjunan wrote:
> Hi all,
> 
> I have tried building E-Cell on Fedora Core 3 for 3.1.105 release 
> candidate but it fails because it doesn't have the required gnome-canvas 
> for Model Editor. Next, I have tried on Fedora Core 4 but it fails also 
> as a result of the bug 
> http://sourceforge.net/tracker/index.php?func=detail&aid=1291476&group_id=72485&atid=534670) 
> in either boost or libecs with gcc4. I have also tried upgrading boost 
> from version 1.32 to version 1.33 in FC 4 but the bug persists. 
> Currently we have two options:
> 
> 1. Release 3.1.105 with FC 3 as the target, but we need to find a 
> workaround for gnome-canvas (gabor?)
> 2. Wait until this bug is solved and release for FC 4 (kaizu?)
> 
> I would like to know your views on this. Thank you.
> 
> satya
> 
> 
> 
-- 
Bereczki Gabor <ga...@sf...>

Hi all,

I have tried building E-Cell on Fedora Core 3 for 3.1.105 release 
candidate but it fails because it doesn't have the required gnome-canvas 
for Model Editor. Next, I have tried on Fedora Core 4 but it fails also 
as a result of the bug 
http://sourceforge.net/tracker/index.php?func=detail&aid=1291476&group_id=72485&atid=534670) 
in either boost or libecs with gcc4. I have also tried upgrading boost 
from version 1.32 to version 1.33 in FC 4 but the bug persists. 
Currently we have two options:

1. Release 3.1.105 with FC 3 as the target, but we need to find a 
workaround for gnome-canvas (gabor?)
2. Wait until this bug is solved and release for FC 4 (kaizu?)

I would like to know your views on this. Thank you.

satya

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---
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and developing new ones through the m-Wise technology. Installed locally, 
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---

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hoyden try wile some may sugar ! on goodwill !
in combine see or chromosphere in see andrew may and
shiny bebe abrogate and.
sperm see fest some in shoestring , and friedrich may
it's gulp ! see bookseller try be potentate some it
till thea goat see.

Hi all,

I would like to bring out the Release Candidate 1 of E-Cell version 
3.1.105 by Sept 19th (Monday) based on the current CVS. Version 3.1.104 
will be skipped. I will be tagging the CVS repository for this version 
on Sept 16th (Friday). If you have issues to fix before the release 
please let me know. Thank you.

satya

We want to congratulate all of our members who read our Trading Alert on AXCP. 
Did their due diligence and then acted and are now up over $3.00. 
We know you are GLAD you did.

On THURSDAY Sept, 8 we are issuing a Trading Alert on ALLIXON INTL CORP (AXCP), 
today it is currently trading at $5.70, NEED WE SAY MORE !!!!

But we think the fun is just beginning with this stock. 
It has been showing a steady move up on increasing volume. 
The chart on AXCP is a thing of beauty as it shows what we mentioned earlier slow 
and steady upward movement. It appears to us that the stock is in an accumulation phase 
and might be ready for a big pop to new highs. That would be well over a 300-500% gain 
from these levels. So if you haven't done your DD yet, you better hurry 
because it appears that the huge move is about to start.

Symbol: AXCP
Price: $5.70
Week Target: $10

Buy: Strong
Expectations: 300-500%


*************************************************************************************
Allixon Provides Update on RFID Middleware Seminar for SMB (Small and Medium Business) 
in Cooperation With IBM Korea

We have seen big news before and we feel that ALLIXON INTL CORP 
can drop a bomb at anytime. Don't get caught just looking...

SEOCHO-KU, SEOUL, Korea, (PRIMEZONE) -- Allixon International Corporation 
(Other OTC:AXCP.PK - News) is pleased to announce that it's first RFID Seminar 
in conjunction with IBM Korea to introduce IBM RFID middleware with the demonstration 
of Warehouse Management System (WMS) at Millennium Hilton Hotel was a success. 
With over 250 customers in attendance at this year's event, IBM introduced Allixon 
as the RFID Middleware solution and business partner to IBM Korea customers. 
During the seminar, Allixon participated in, as a partner for RFID business, 
to demonstrate the Warehouse Management System application, developed by EXE, 
based on the IBM RFID middleware.

IBM Korea and Allixon prepared a stage that materialized a part of a warehouse 
and shop to demonstrate the practical applications of the IBM RFID Middleware. 
Many of the IBM invitees and potential SMB customers expressed their approval 
in regards to the seminar and the possibilities that RFID middleware could bring. 
As a result, many of IBM's invitees have subsequently contacted Allixon 
to investigate how their organizations could adopt the RFID system.

"Our primary goal is to improve RFID applications for all our customers - 
consumers and businesses, regardless of size - through a balance 
of technology innovation, guidance and industry leadership," said Mr. Lee, 
CEO of Allixon International Corporation. He also added, "We're committed 
to continued innovation in RFID application and laying the groundwork 
for future growth in this industry."

Few Allixon Partners: MICROSOFT, IBM, SUN, KOREA FIRST BANK, SAMSUNG, FUJITSU...











Disclaimer:
Information within this email contains "forward looking statements" within the meaning 
of Section 27A of the Securities Act of 1933 and Section 21B of the Securities Exchange 
Act of 1934. Any statements that express or involve discussions with respect to predictions, 
goals, expectations, beliefs, plans, projections, objectives, assumptions or future 
events or performance are not statements of historical fact and may be "forward 
looking statements."

Forward looking statements are based on expectations, estimates and projections 
at the time the statements are made that involve a number of risks and uncertainties 
which could cause actual results or events to differ materially from those presently 
anticipated. Forward looking statements in this action may be identified through 
the use of words such as: "projects", "foresee", "expects", "estimates," "believes," 
"understands" "will", "anticipates," or that by statements indicating certain actions 
"may," "could," or "might" occur. All information provided within this email 
pertaining to investing, stocks,securities must be understood as information 
provided and not investment advice. Emerging Equity Alert advises all readers 
and subscribers to seek advice from a registered professional securities 
representative before deciding to trade in stocks featured within this email. 
None of the material within this report shall be construed as any kind 
of investment advice.

In compliance with Section 17(b), we disclose the holding of shares of axcp prior 
to the publication of this report. Be aware of an inherent conflict of interest 
resulting from such holdings due to our intent to profit from the liquidation of 
these shares. Shares may be sold at any time, even after positive statements 
have been made regarding the above company.