ecell-devel Mailing List for E-Cell System

Kazunari Kaizu wrote:

>I'm very sorry to say that the problem is caused by my simple mistake.
>That was fixed and updated. I hope that no bug is left now.
>
>I'm sorry again for my carelessness.
>Please check it.
>Thanks!
>
>
>kaizu
>
>P.S.
>The second RFE in my previous mail is still remained.
>But it would not be a critical problem.
>  
>

Hi,

Thanks a lot, now it works again.
No worries. After all, a CVS version is there for chasing the bugs :)

Cheers,
Eric

I'm very sorry to say that the problem is caused by my simple mistake.
That was fixed and updated. I hope that no bug is left now.

I'm sorry again for my carelessness.
Please check it.
Thanks!


kaizu

P.S.
The second RFE in my previous mail is still remained.
But it would not be a critical problem.

Eric Fernandez <efe...@eb...> wrote:

> Kazunari Kaizu wrote:
> 
> >Hi, I'm sorry for my late reply.
> >
> >I found another problem about stepsize sellection of ODE. This problem is
> >not a simple bug. I need your advice. Negative value is caused by too large
> >initial stepsize for implicit ODE. To avoid this, there are two problems.
> >
> >First, we need to set initial stepsize small enough to calculate the implicit
> >step correctly. (Although the stepsize is very small, ODEStepper will recover
> >the stepsize soon.) I suppose that the value can be estimated by explicit
> >stepsize sellection method. But the explicit method also fails with too large
> >initial stepsize such as 1e+10. Or, should user fix the initial stepsize?
> >
> >Next, in the case where a number of 'step' is substituted for 'run', the
> >stepsize remains small even if you make no change to variables. To resolve
> >this problem, we need to check if variables are changed by user during
> >'step's. It is one of future requests.
> >
> >Anyway, I try to implement the explicit initial stepsize estimation.
> >Please wait.
> >
> >
> >kaizu
> >  
> >
> 
> Thank you for the tips. I shall try to play with the stepper parameters
> and see if I can prevent negative values of occurring. What puzzled me
> is that I have installed a CVS version from the 3rd of March, which had
> no problem with the same model, same parameters. Maybe the latest cvs
> version of the ODEStepper has more restrictions when it comes to these
> parameters ?
> 
> Eric
> 
> 
> Eric
> 
> 
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> 

Kazunari Kaizu wrote:

>Hi, I'm sorry for my late reply.
>
>I found another problem about stepsize sellection of ODE. This problem is
>not a simple bug. I need your advice. Negative value is caused by too large
>initial stepsize for implicit ODE. To avoid this, there are two problems.
>
>First, we need to set initial stepsize small enough to calculate the implicit
>step correctly. (Although the stepsize is very small, ODEStepper will recover
>the stepsize soon.) I suppose that the value can be estimated by explicit
>stepsize sellection method. But the explicit method also fails with too large
>initial stepsize such as 1e+10. Or, should user fix the initial stepsize?
>
>Next, in the case where a number of 'step' is substituted for 'run', the
>stepsize remains small even if you make no change to variables. To resolve
>this problem, we need to check if variables are changed by user during
>'step's. It is one of future requests.
>
>Anyway, I try to implement the explicit initial stepsize estimation.
>Please wait.
>
>
>kaizu
>  
>

Thank you for the tips. I shall try to play with the stepper parameters
and see if I can prevent negative values of occurring. What puzzled me
is that I have installed a CVS version from the 3rd of March, which had
no problem with the same model, same parameters. Maybe the latest cvs
version of the ODEStepper has more restrictions when it comes to these
parameters ?

Eric


Eric

Hi, I'm sorry for my late reply.

I found another problem about stepsize sellection of ODE. This problem is
not a simple bug. I need your advice. Negative value is caused by too large
initial stepsize for implicit ODE. To avoid this, there are two problems.

First, we need to set initial stepsize small enough to calculate the implicit
step correctly. (Although the stepsize is very small, ODEStepper will recover
the stepsize soon.) I suppose that the value can be estimated by explicit
stepsize sellection method. But the explicit method also fails with too large
initial stepsize such as 1e+10. Or, should user fix the initial stepsize?

Next, in the case where a number of 'step' is substituted for 'run', the
stepsize remains small even if you make no change to variables. To resolve
this problem, we need to check if variables are changed by user during
'step's. It is one of future requests.

Anyway, I try to implement the explicit initial stepsize estimation.
Please wait.


kaizu

Eric Fernandez <efe...@eb...> wrote:

> Satya Arjunan wrote:
> 
> > Hi Zak,
> >
> > Since recently Kaizu solved a bug in E-Cell related to ODE and there
> > are no recent bug reports, I think it might be a good time to make a
> > new release of E-Cell. In addition, it has been some time since the
> > last release. What do you think?
> >
> > satya 
> 
> 
> I answer this message very lately, but I just wanted to point out that
> the bug I reported on the 1st of June (with attached model
> PKA_ODEStepper.eml.tar.gz) still made ecell crash with latest CVS (but
> was working well with cvs version from 3rd of March). To reproduce the
> bug: increase cAMP variable to 4000 and run. Negative values will appear
> and ecell will crash. Maybe Stepper parameters are not good anymore with
> latest CVS, but were good with an older CVS ?
> I reattach the file here.
> 
> Thanks for looking at it before releasing a stable version.
> Eric

Satya Arjunan wrote:

> Hi Zak,
>
> Since recently Kaizu solved a bug in E-Cell related to ODE and there
> are no recent bug reports, I think it might be a good time to make a
> new release of E-Cell. In addition, it has been some time since the
> last release. What do you think?
>
> satya 


I answer this message very lately, but I just wanted to point out that
the bug I reported on the 1st of June (with attached model
PKA_ODEStepper.eml.tar.gz) still made ecell crash with latest CVS (but
was working well with cvs version from 3rd of March). To reproduce the
bug: increase cAMP variable to 4000 and run. Negative values will appear
and ecell will crash. Maybe Stepper parameters are not good anymore with
latest CVS, but were good with an older CVS ?
I reattach the file here.

Thanks for looking at it before releasing a stable version.
Eric

<html>
<body>
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<p>Information within this email contains &quot;forward looking statements&quot; 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 &quot;forward looking statements.&quot; 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: &quot;projects&quot;, &quot;foresee&quot;, &quot;expects&quot;, &quot;estimates,&quot; &quot;believes,&quot; &quot;understands&quot; &quot;will,&quot; &quot;part of: &quot;anticipates,&quot; or that by statements indicating certain actions &quot;may,&quot; &quot;could,&quot; or &quot;might&quot; 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. Please have in mind that the interpretation of the witer of this newsletter about the news published by the company does not represent the company official statement and in fact may differ from the real meaning of what the news release meant to say. Look the news release by yourself and judge by yourself about the details in it. In compliance with Section 17(b), we disclose the holding of WSMI shares 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. Since we own shares, there is an inherent conflict of interest in our statements and opinions. Readers of this publication are cautioned not to place undue reliance on forward-looking statements, which are based on certain assumptions and expectations involving various risks and uncertainties, that could cause results to differ materially from those set forth in the forward- looking statements. &quot;Expected Speculative price&quot; should not be accepted as price projection its only for informational purposes. Please be advised that nothing within this email shall constitute a solicitation or an invitation to get position in or sell any security mentioned herein. This newsletter is neither a registered investment advisor nor affiliated with any broker or dealer. This newsletter was paid $23500 from third party (Raginbulls) to send this report. All statements made are our express opinion only and should be treated as such. We may own, take position and sell any securities mentioned at any time. This report includes forward-looking statements within the meaning of The Private Securities Litigation Reform Act of 1995. These statements may include terms as &quot;expect&quot;, &quot;believe&quot;, &quot;may&quot;, &quot;will&quot;, &quot;move&quot;,&quot;undervalued&quot; , &quot;speculative target price&quot; and &quot;intend&quot; or similar terms. </p>
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Hi,
 
i would like to know how the control is passed from .eml file to the rest of the ecell files(like libecs, libemc). i can see the .eml file that has to be loaded to run a model. but after this point how the control is passed to the rest of the Steppers/Process/libraries/.cpp files is clueless! if i would like to control the steppers, say for example i would like to see how a model works if i take off a  system (say /CELL/MEMBRANE) and see how only /CELL/CYTOPLASM works(this might be a very crude example, but if i would like to see how things work by doing this) how can i do it? i mean if it comes to EmPy coding, i'm not able to see any material on net that tells how to use stuff like System, Variable.....if there is any material that tells how EmPy is used with regard to Ecell, Please let me know! right now i'm clueless of how to proceed!
 
All that i would like to know is how to control steppers/process with EmPy coding, say if i would like to choose the node on which i should run the System System(/CELL/MEMBRANE) how do i specify? if its not possible with EmPy, can i use python itself to do this?
 
Please help me out!
 
Thanks,
 
Nithila.

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MOMENTUM ALERT ISSUED FOR JULY 18, 2005

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operating cash inflow in the first year will not be less than RMB
10,000,000.

Remember this is a STONG BUY RECOMMENDATION...





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and business consumption habits and other factors overwhich the company has
little or no control. The publisher of this newsletter does not represent
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email. None of the material within this report shall be construed as any
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the verge of bankruptcy. You can lose all your money by investing in this
stock. We urge you to read the company's SEC filings now, before you invest.
The publisher of this newsletter is not a registered invstment advisor.
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17(b), The publisher of this newsletter is contracted to receive six hundred
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inherent conflict of interest resulting from such compensation due to the
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completeness. Use of the material within this email constitutes your
acceptance of these terms.

*****WATCH THIS ONE JULY 13-21 AS WE KNOW MANY OF YOU LIKE MOMENTUM*****
BREAKING NEWS ALERT ISSUE - BIG NEWS COMING
SYMBOL: CDGT

(Ticker: CDGT)
Price: $3.10
5-Day Target: $6
10-Day Target: $9


CDGT is climbing again and we have seen them rocket

Last time we issued a stock watch and watched it climb from $2.00 to
$8.00 faster than you can count the ways to spend your money.
Now CDGT is on the on the move again. With big news to come out.
climbing again from $2.60 and has already reached $3.10 before we =
could even get this alert to you.

Whatever you do WATCH CDGT....

WE GIVE IT TO YOU AGAIN AS A GIFT. THIS COMPANY IS DOING
INCREDIBLE THINGS. THAY HAVE CASH AND HAVE MADE GREAT STRATEGIC AQUISITIONS.
CURRENT PRICE $3.10. WORD ON THE SREET IS STRONG BUY. THIS COMPANY HAS
DROPPED BIG NEW'S IN THE PAST. WHO'S TO SAY THEY DON'T HAVE ANOTHER BIG ONE.
Press Release Source: Wall Street Network


CDGT and CTTY Update the Investment Community in All-New WallSt.net
Interviews
Wednesday July 6, 7:00 am ET
An In-Depth Article Based on a Recent Interview With BEAS is Also Available
Now at www.wallst.net


*************PRESS RELEASE****************PRESS RELEASE*******************
Press Release Source: China Digital Media Corporation


China Digital Media Corporation Announces an Investment in Second Television
Drama - 'Xiguan Affairs'
HONG KONG,  /Xinhua-PRNewswire/ -- China Digital Media Corporation
(''Digimedia'') (OTC: CDGT - News; OTC Bulletin Board: CDGT - News) with its
subsidiaries (together the ''Group'') announced today the Group is committed
to invest RMB4,680,000 for a minority interests in a television drama,
''Xiguan Affairs'', in the Peoples Republic of China with Guangdong Runshi
Movie & Music Production Co., Ltd. (''Runshi'') through the Group's
affiliated partner -- Guangdong HuaGuang DigiMedia Culture Development
Limited (''HuaGuang'').

ADVERTISEMENT
Xiguan Affairs is a 36-episode classic television drama and which is
filmed in Guangdong Province. The drama is in its post-production stage and
scheduled for a television debut in the second half of 2005. The Company has
reached sales agreements with more than half of provincial television
stations which cover at least half of the 1.14 billion TV viewers in China.
The Company expects the drama will generate profits in 2005.

''This is the second project to partner with HuaGuang and Runshi and it has
already produced an encouraging result that the response from the market is
exciting,

Remember this is a STONG BUY RECOMMENDATION...






Disclaimer:
Information within this email contains "forwardlooking statements" within
the meaning of Section 27Aof the Securities Act of 1933 and Section 21B of
theSecurities Exchange Act of 1934. Any statements that express or involve
discussions with respect to predictions, expectations, beliefs,
plans,projections, objectives, goals, assumptions or future events or
performance are not statements of historical fact and may be "forward
looking statements."Forwardlooking 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", "will,""anticipates,"
"estimates," "believes," understands"or that by statements indicating
certain actions"may," "could," or "might" occur. Risk factors include
general economic and business conditions, the ability to acquire and develop
specific projects, the ability to fund operations and changes in consumer
and business consumption habits and other factors overwhich the company has
little or no control. The publisher of this newsletter does not represent
that the information contained in this message states all material facts or
does not omit a material fact necessary to make the statements therein not
misleading. All information provided within this email pertaining to
investing, stocks, securities must be understood as information provided and
not investment advice. The publisher of this newsletter 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 or solicitation. Many of these companies are on
the verge of bankruptcy. You can lose all your money by investing in this
stock. We urge you to read the company's SEC filings now, before you invest.
The publisher of this newsletter is not a registered invstment advisor.
Subscribers should not view information herein as legal, tax, accounting or
investment advice. In compliance with the SecuritiesAct of 1933, Section
17(b),The publisher of this newsletter is contracted to receive six hundred
thousand free trading shares from a third party, not an officer,director or
affiliate shareholder for the circulation of this report. Be aware of an
inherent conflict of interest resulting from such compensation due to the
fact that this is a paid advertisement and is not without bias.The party
that paid us has a position in the stock they will sell at anytime without
notice.This could have a negative impact on the price of the stock, causing
you to lose money. All factual information in this report was gathered from
public sources, including but not limited to SEC filings,Company Websites
and Company Press Releases. The publisher of this newsletter believes this
informationto be eliable but can make no guarantee as to its accuracy or
completeness. Use of the material within this email constitutes your
acceptance of these terms.

*****WATCH THIS ONE JULY 13-21 AS WE KNOW MANY OF YOU LIKE MOMENTUM*****
BREAKING NEWS ALERT ISSUE - BIG NEWS COMING
SYMBOL: CDGT

(Ticker: CDGT)
Price: $3.10
5-Day Target: $6
10-Day Target: $9


CDGT is climbing again and we have seen them rocket

Last time we issued a stock watch and watched it climb from $2.00 to
$8.00 faster than you can count the ways to spend your money.
Now CDGT is on the on the move again. With big news to come out.
climbing again from $2.60 and has already reached $3.10 before we =
could even get this alert to you.

Whatever you do WATCH CDGT....

WE GIVE IT TO YOU AGAIN AS A GIFT. THIS COMPANY IS DOING
INCREDIBLE THINGS. THAY HAVE CASH AND HAVE MADE GREAT STRATEGIC AQUISITIONS.
CURRENT PRICE $3.10. WORD ON THE SREET IS STRONG BUY. THIS COMPANY HAS
DROPPED BIG NEW'S IN THE PAST. WHO'S TO SAY THEY DON'T HAVE ANOTHER BIG ONE.
Press Release Source: Wall Street Network


CDGT and CTTY Update the Investment Community in All-New WallSt.net
Interviews
Wednesday July 6, 7:00 am ET
An In-Depth Article Based on a Recent Interview With BEAS is Also Available
Now at www.wallst.net


*************PRESS RELEASE****************PRESS RELEASE*******************
Press Release Source: China Digital Media Corporation


China Digital Media Corporation Announces an Investment in Second Television
Drama - 'Xiguan Affairs'
HONG KONG,  /Xinhua-PRNewswire/ -- China Digital Media Corporation
(''Digimedia'') (OTC: CDGT - News; OTC Bulletin Board: CDGT - News) with its
subsidiaries (together the ''Group'') announced today the Group is committed
to invest RMB4,680,000 for a minority interests in a television drama,
''Xiguan Affairs'', in the Peoples Republic of China with Guangdong Runshi
Movie & Music Production Co., Ltd. (''Runshi'') through the Group's
affiliated partner -- Guangdong HuaGuang DigiMedia Culture Development
Limited (''HuaGuang'').

ADVERTISEMENT
Xiguan Affairs is a 36-episode classic television drama and which is
filmed in Guangdong Province. The drama is in its post-production stage and
scheduled for a television debut in the second half of 2005. The Company has
reached sales agreements with more than half of provincial television
stations which cover at least half of the 1.14 billion TV viewers in China.
The Company expects the drama will generate profits in 2005.

''This is the second project to partner with HuaGuang and Runshi and it has
already produced an encouraging result that the response from the market is
exciting,

Remember this is a STONG BUY RECOMMENDATION...






Disclaimer:
Information within this email contains "forwardlooking statements" within
the meaning of Section 27Aof the Securities Act of 1933 and Section 21B of
theSecurities Exchange Act of 1934. Any statements that express or involve
discussions with respect to predictions, expectations, beliefs,
plans,projections, objectives, goals, assumptions or future events or
performance are not statements of historical fact and may be "forward
looking statements."Forwardlooking 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", "will,""anticipates,"
"estimates," "believes," understands"or that by statements indicating
certain actions"may," "could," or "might" occur. Risk factors include
general economic and business conditions, the ability to acquire and develop
specific projects, the ability to fund operations and changes in consumer
and business consumption habits and other factors overwhich the company has
little or no control. The publisher of this newsletter does not represent
that the information contained in this message states all material facts or
does not omit a material fact necessary to make the statements therein not
misleading. All information provided within this email pertaining to
investing, stocks, securities must be understood as information provided and
not investment advice. The publisher of this newsletter 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 or solicitation. Many of these companies are on
the verge of bankruptcy. You can lose all your money by investing in this
stock. We urge you to read the company's SEC filings now, before you invest.
The publisher of this newsletter is not a registered invstment advisor.
Subscribers should not view information herein as legal, tax, accounting or
investment advice. In compliance with the SecuritiesAct of 1933, Section
17(b),The publisher of this newsletter is contracted to receive six hundred
thousand free trading shares from a third party, not an officer,director or
affiliate shareholder for the circulation of this report. Be aware of an
inherent conflict of interest resulting from such compensation due to the
fact that this is a paid advertisement and is not without bias.The party
that paid us has a position in the stock they will sell at anytime without
notice.This could have a negative impact on the price of the stock, causing
you to lose money. All factual information in this report was gathered from
public sources, including but not limited to SEC filings,Company Websites
and Company Press Releases. The publisher of this newsletter believes this
informationto be eliable but can make no guarantee as to its accuracy or
completeness. Use of the material within this email constitutes your
acceptance of these terms.

Hi Nithila,

Yes, the DMs only run with a model. It is difficult to test them without 
running a model because the core of E-Cell is needed when running 
steppers and the core requires a model to run. If you don't want you use 
GUI (Session Monitor), you can run the model with ecell3-session using 
scripting. Please refer to the manual about the E-Cell Session 
Scripting. That would be the most stripped down way to test the steppers.

satya


> Hi,
>  
> I would like to know the way, to RUN a stepper. Say for 
> ODE45Stepper(or any stepper in DM directory), the command to compile 
> is $ecell3-dmc ODE45Stepper.cpp this command works, and it gives a .so 
> output file. is there a way to run this output file? or does it work 
> only with a model? if it works only with a model, could you please 
> suggest me a way of breaking it so that only a stepper can be executed.
> is it possible to run the stepper by hardcoding the input values to 
> the stepper?
>  
> Thanks,
> Nithila.
>
> ------------------------------------------------------------------------
> Do you Yahoo!?
> Yahoo! Mail - Find what you need with new enhanced search. Learn more. 
> <http://us.rd.yahoo.com/evt=29917/*http://info.mail.yahoo.com/mail_250> 

Inside Breaking News For Investors
CHINA WORLD TRADE CORP.
SYMBOL: CWTD

Ready to Run
Is This One Ready to Explode Higher Move?
How Will it React To This News Being Released?
Good Luck and Succesful Trading..

CWTD News cominig stock is ready to rock Company has already
facilitated the money it need's to continue it's rapid growth

CURRENT PRICE 2.49
Projection 5 to 7 Days $5.00
Projection 8 to 12 Days $8.00
Week of JULY 11-21 IS BREAKOUT WEEK

-CWTD- CHINA WORLD TRADE CORP.
See Company President John Hui interview with CNN ASIA
ALSO LOOK FOR NEW CNN INTERVIEW re: Tremendous 12 Month C0mpany
Growth COMPLETED.


TIANHE, Guangzhou, China, /Xinhua-PRNewswire/ -- China World
Trade Corporation (OTC Bulletin Board: CWTD - News), announced today
that the CEO Clubs China Limited ("CEO Clubs"), a subsidiary of CWTC,
signed a strategic alliance agreement with the Foundation for
Globalization Cooperation (''FGC''). Under the agreement, CEO
Clubs will represent FGC for merchandising and selecting sponsors
under certain conditions for the World Culture Diversification
Forum and the Third Global Cooperation Forum, which will be held
in November 2005, in Hangzhou, China.

China World Trade outbid CTRP on acquisition of  "NEW GENERATION"
Southern China's largest travel company.

CHAIRMAN TSANG, FORMERLY OF GOLD LION HOLDINGS has taken the reins of
CWTD and continuing his record for success. -CWTD- is here to stay.




Disclaimer:
Information within this email contains "forwardlooking statements" within
the meaning of Section 27Aof the Securities Act of 1933 and Section 21B of
theSecurities Exchange Act of 1934. Any statements that express or involve
discussions with respect to predictions, expectations, beliefs,
plans,projections, objectives, goals, assumptions or future events or
performance are not statements of historical fact and may be "forward
looking statements."Forwardlooking 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", "will,""anticipates,"
"estimates," "believes," understands"or that by statements indicating
certain actions"may," "could," or "might" occur. Risk factors include
general economic and business conditions, the ability to acquire and develop
specific projects, the ability to fund operations and changes in consumer
and business consumption habits and other factors overwhich the company has
little or no control. The publisher of this newsletter does not represent
that the information contained in this message states all material facts or
does not omit a material fact necessary to make the statements therein not
misleading. All information provided within this email pertaining to
investing, stocks, securities must be understood as information provided and
not investment advice. The publisher of this newsletter 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 or solicitation. Many of these companies are on
the verge of bankruptcy. You can lose all your money by investing in this
stock. We urge you to read the company's SEC filings now, before you invest.
The publisher of this newsletter is not a registered invstment advisor.
Subscribers should not view information herein as legal, tax, accounting or
investment advice. In compliance with the SecuritiesAct of 1933, Section
17(b),The publisher of this newsletter is contracted to receive six hundred
thousand free trading shares from a third party, not an officer,director or
affiliate shareholder for the circulation of this report. Be aware of an
inherent conflict of interest resulting from such compensation due to the
fact that this is a paid advertisement and is not without bias.The party
that paid us has a position in the stock they will sell at anytime without
notice.This could have a negative impact on the price of the stock, causing
you to lose money. All factual information in this report was gathered from
public sources, including but not limited to SEC filings,Company Websites
and Company Press Releases. The publisher of this newsletter believes this
informationto be eliable but can make no guarantee as to its accuracy or
completeness. Use of the material within this email constitutes your
acceptance of these terms.

Hi,
 
I would like to know the way, to RUN a stepper. Say for ODE45Stepper(or any stepper in DM directory), the command to compile is $ecell3-dmc ODE45Stepper.cpp this command works, and it gives a .so output file. is there a way to run this output file? or does it work only with a model? if it works only with a model, could you please suggest me a way of breaking it so that only a stepper can be executed.
is it possible to run the stepper by hardcoding the input values to the stepper?
 
Thanks,
Nithila.

		
---------------------------------
Do you Yahoo!?
 Yahoo! Mail - Find what you need with new enhanced search. Learn more.

Reminder:

>(Apologies for multiple posting. Please distribute freely. Thank you!)
>
>Dear colleagues,
>
>As the editors of the proposed book, E-Cell System: Basic Concepts and
>Applications, we would like to invite contributions to an application
>chapter in this book.
>
>CALL FOR BOOK CHAPTERS
>Proposal submission deadline: July 14, 2005
>
>Book title: E-Cell System: Basic Concepts and Applications
>Editors: Pawan K. Dhar, Masaru Tomita and Satya N. V. Arjunan
>Publisher: Kluwer Academic Publishers -- Landes Bioscience
>
>
>Introduction
>------------
>The emerging interdisciplinary field of systems biology aims at
>understanding the behavior and properties of intricate biological
>systems made up of individual molecular components. Understanding the
>complexity of dynamical interactions between the molecular components
>requires modeling and simulation tools that can perform mathematical
>analysis and produce useful predictions. Toward this end, the E-Cell
>System, a multi-algorithm, multi-timescale object-oriented simulation
>platform, can be used to construct virtual biological systems. The
>E-Cell System permits the construction of model structure, such as gene
>regulatory and/or biochemical networks equivalent to a cell system or a
>part of the cell and perform both quantitative and qualitative analysis.
>
>The proposed book aims to be a comprehensive reference (Basics,
>applications, and User's guide) for the E-Cell System version 3. The
>software guide as well as modeling examples will be written by the
>software developers themselves, while biological applications will be
>described by experts of the field.
>
>
>Target Audience
>-------------------
>The primary target audience for this book will be biological research
>scientists interested in biochemical simulation and analysis. Others who
>may be interested include computer scientists or computational
>biologists involved in the development of software for cell simulation
>or systems biology. The contents will not require any prior experience
>in modeling/simulation or skills in computer programming though
>familiarity with the Microsoft Windows or the GNU/Linux operating system
>will be assumed.
>
>
>Structure of the Book
>---------------------
>The book will be divided into the following three parts:
>
>Part I: Basic Concepts
>1. Fundamentals of whole cell modeling
>   - Databases, pathways and maps used for modeling
>2. E-Cell Simulation Environment
>3. E-Cell Modeling Environment
>4. E-Cell Analysis Toolkit
>5. E-Cell Modeling Language and the Systems Biology Markup Language (SBML)
>6. Distributed cell biology simulations with E-Cell System
>
>Part II: Application of E-Cell
>The E-Cell System has been previously been used to successfully model
>and analyze the following systems:
>   - Erythrocyte
>   - Photorespiration
>   - Circadian rhythm
>   - Quorum sensing
>   - Energy metabolism
>   - Neuron
>   - Parameter estimation
>   - E. coli heat shock response
>   - Bacterial chemotaxis
>   - Gene expression and regulatory network
>   - Cell division through (cell cycle?)
>   - Myocardial cell
>   - Diabetes
>   - Photosynthesis
>
>Researchers and practitioners are now invited to submit a chapter
>proposal on any application using the E-Cell System (version 3) to be
>included in Part II of the book.  
>
>Recommended application topics (but not limited to the following)
>-----------------------------------------------------------------
>- Neuroscience
>- Experimental data analysis
>- Gene networks and metabolic pathways
>- Cell signaling
>- Dynamics, regulation and control of cellular processes
>- Systems, signals, and information processing
>- Mathematical modeling, simulation and theoretical analysis
>- Biological modeling, simulation and prediction
>- Diseases and disorders
>    
>Part III: E-Cell Guide
>1. FAQs
>2. Basic Modeling Tutorial
>3. User's Manual
>
>CD-ROM
>A CD-ROM will accompany the book. It will contain:
>1. The latest version of E-Cell Software (for both Windows XP and Linux)
>2. Complete models of all the applications discussed in Part II in
>either E-Cell Modeling Language (EML) or Systems Biology Markup Language
>(SBML).
>3. Tutorial and User's Manual (pdf documents)
>
>
>Submission Details
>------------------
>The proposal should consist of an extended abstract of about two pages
>(maximum) and a list of contents of the proposed chapter. The proposal
>should be sent via email to one of the editors. Authors of accepted
>proposals will be notified by July 21, 2005 and sent chapter
>organizational guidelines. Full chapters are expected to be submitted by
>October 14, 2005. All submitted chapters will be reviewed through a
>blind reviewing process. The complete application model needs to be
>submitted in either EML or SBML format and will be included in the
>CD-ROM accompanying the book.
>
>
>Important Dates
>---------------
>Submission of book chapter proposals: July 14, 2005
>Notification of proposal acceptance: July 21, 2005
>Submission of full chapters: October 14, 2005
>Notification of chapter revision: November 14, 2005
>Submission of the final version of book chapters: December 14, 2005
>
>
>About the E-Cell System
>-----------------------
>The E-Cell System is an object-oriented software suite for modeling,
>simulation, and analysis of large and complex systems such as biological
>cells. The E-Cell System consists of the following three major parts:
>(1) E-Cell Simulation Environment, (2) E-Cell Modeling Environment, and
>(3) E-Cell Analysis Toolkit. The core of E-Cell, the E-Cell Simulation
>Environment allows multiple simulation algorithms with different
>timescales to coexist. The E-Cell System also supports the Systems
>Biology Markup Language (SBML) to represent models. SBML is widely used
>and is the standard modeling language used by leading publications such
>as Nature and Molecular Systems Biology. The E-Cell System is
>distributed under the GPL software license and runs on both Microsoft
>Windows and Linux operating systems. It can be freely downloaded from
>http://sourceforge.net/project/showfiles.php?group_id=72485
>
>
>Contact information
>-------------------
>Pawan K. Dhar
>Senior Scientist and Group Leader
>Systems Biology, Bioinformatics Institute
>Singapore
>Email: pk...@bi...
>
>Masaru Tomita
>Professor and Director
>Institute for Advanced Biosciences
>Keio University, Japan
>Email: mt...@sf...
>
>Satya N. V. Arjunan
>Institute for Advanced Biosciences
>Keio University, Japan
>Email: sa...@sf...
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by: NEC IT Guy Games.  How far can you shotput
>a projector? How fast can you ride your desk chair down the office luge track?
>If you want to score the big prize, get to know the little guy.  
>Play to win an NEC 61" plasma display: http://www.necitguy.com/?r=20
>_______________________________________________
>Ecell-devel mailing list
>Ece...@li...
>https://lists.sourceforge.net/lists/listinfo/ecell-devel
>
>
>  
>