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From: luli <lu...@eb...> - 2012-03-20 06:18:21
|
Dear Yasuhiro, Thank you for your reply. However, while running "make" for ecell3.1, I got the following error -- ...(I only displayed the part when error start) make[5]: Entering directory `/home/luli/bin/ecell-ecell3-ed9c78e-ecell3.1source/ecell/libecs' /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../.. -I/home/luli/bin/ecell-ecell3-ed9c78e-ecell3.1source -I../../libltdl -I/usr/include -g -O2 -g -O2 -MT libecs.lo -MD -MP -MF .deps/libecs.Tpo -c -o libecs.lo libecs.cpp mv -f .deps/libecs.Tpo .deps/libecs.Plo mv: cannot stat `.deps/libecs.Tpo': No such file or directory ... -- Cheers Lu On 20/03/12 06:21, Yasuhiro Naito wrote: > Dear Lu, > > Another way is downgrading E-cell to ver 3.1.x. > > You can download the latest version of E-Cell 3.1.x from GitHub [ecell/ecell3 branch:ecell-3.1]. > https://github.com/ecell/ecell3/tree/ecell-3.1 (ZIP download) > > You should run ./autogen.sh before ./configure . > I installed it just now on the latest Ubuntu, and successfully run the model including PythonProcess. > > We are sorry for the inconvenience. > > Regards, > Yasuhiro > > > On 2012/03/20, at 11:21, Yasuhiro Naito wrote: > >> Dear Lu, >> >> I'm not a developer but a modeler with E-Cell project. >> As you pointed out, both of PythonFluxProcess and PythonProcess in ver 3.2.x don't work correctly at present. E-Cell3 developers work to fix the problems. >> Temporarily, I use custom Processes wrote in C++ instead of using Python(Flux)Process. >> Some built-in Processes such as MichaelisUniUniFluxProces (/ecell/dm/MichaelisUniUniFluxProcess.cpp) are good samples to develop custom Process. >> >> Regards >> Yasuhiro >> >> >> On 2012/03/20, at 2:56, luli wrote: >> >>> Dear ECell3 developers, >>> >>> I just installed ecell-3.2.3pre2, however, encountering the following >>> problems. >>> >>> 1) PythonFluxProcess does not allow any "attribute" appear in the >>> expression. >>> For instance: >>> >>> Process PythonFluxProcess( test ) >>> { >>> k 0.5; >>> StepperID DE1; >>> Expression "k*S1.MolarConc*self.getSuperSystem().SizeN_A"; >>> VariableReferenceList [S1 Variable:/Spine:A] [P1 >>> Variable:/Spine:B]; >>> } >>> >>> When running ecell3-session..... ecell gives AttributeError, complaining >>> that there is no MolarConc attribute. >>> >>> 2) PythonProcess does not allo any "attribute" appear in the expression >>> either. >>> >>> Could you give an explanation please. >>> >>> BTW, the Ecell user manual is very incomplete and out of date (the last >>> modification is June 30th 2006). >>> Is it possible to update this manual, since ECell becomes more and more >>> popular now? >>> >>> Cheers >>> Lu >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF email is sponsosred by: >>> Try Windows Azure free for 90 days Click Here >>> http://p.sf.net/sfu/sfd2d-msazure >>> _______________________________________________ >>> Ecell-users mailing list >>> Ece...@li... >>> https://lists.sourceforge.net/lists/listinfo/ecell-users |
From: Yasuhiro N. <yn...@sf...> - 2012-03-20 05:21:18
|
Dear Lu, Another way is downgrading E-cell to ver 3.1.x. You can download the latest version of E-Cell 3.1.x from GitHub [ecell/ecell3 branch:ecell-3.1]. https://github.com/ecell/ecell3/tree/ecell-3.1 (ZIP download) You should run ./autogen.sh before ./configure . I installed it just now on the latest Ubuntu, and successfully run the model including PythonProcess. We are sorry for the inconvenience. Regards, Yasuhiro On 2012/03/20, at 11:21, Yasuhiro Naito wrote: > Dear Lu, > > I'm not a developer but a modeler with E-Cell project. > As you pointed out, both of PythonFluxProcess and PythonProcess in ver 3.2.x don't work correctly at present. E-Cell3 developers work to fix the problems. > Temporarily, I use custom Processes wrote in C++ instead of using Python(Flux)Process. > Some built-in Processes such as MichaelisUniUniFluxProces (/ecell/dm/MichaelisUniUniFluxProcess.cpp) are good samples to develop custom Process. > > Regards > Yasuhiro > > > On 2012/03/20, at 2:56, luli wrote: > >> Dear ECell3 developers, >> >> I just installed ecell-3.2.3pre2, however, encountering the following >> problems. >> >> 1) PythonFluxProcess does not allow any "attribute" appear in the >> expression. >> For instance: >> >> Process PythonFluxProcess( test ) >> { >> k 0.5; >> StepperID DE1; >> Expression "k*S1.MolarConc*self.getSuperSystem().SizeN_A"; >> VariableReferenceList [S1 Variable:/Spine:A] [P1 >> Variable:/Spine:B]; >> } >> >> When running ecell3-session..... ecell gives AttributeError, complaining >> that there is no MolarConc attribute. >> >> 2) PythonProcess does not allo any "attribute" appear in the expression >> either. >> >> Could you give an explanation please. >> >> BTW, the Ecell user manual is very incomplete and out of date (the last >> modification is June 30th 2006). >> Is it possible to update this manual, since ECell becomes more and more >> popular now? >> >> Cheers >> Lu >> >> >> ------------------------------------------------------------------------------ >> This SF email is sponsosred by: >> Try Windows Azure free for 90 days Click Here >> http://p.sf.net/sfu/sfd2d-msazure >> _______________________________________________ >> Ecell-users mailing list >> Ece...@li... >> https://lists.sourceforge.net/lists/listinfo/ecell-users > |
From: Yasuhiro N. <yn...@sf...> - 2012-03-20 02:21:19
|
Dear Lu, I'm not a developer but a modeler with E-Cell project. As you pointed out, both of PythonFluxProcess and PythonProcess in ver 3.2.x don't work correctly at present. E-Cell3 developers work to fix the problems. Temporarily, I use custom Processes wrote in C++ instead of using Python(Flux)Process. Some built-in Processes such as MichaelisUniUniFluxProces (/ecell/dm/MichaelisUniUniFluxProcess.cpp) are good samples to develop custom Process. Regards Yasuhiro On 2012/03/20, at 2:56, luli wrote: > Dear ECell3 developers, > > I just installed ecell-3.2.3pre2, however, encountering the following > problems. > > 1) PythonFluxProcess does not allow any "attribute" appear in the > expression. > For instance: > > Process PythonFluxProcess( test ) > { > k 0.5; > StepperID DE1; > Expression "k*S1.MolarConc*self.getSuperSystem().SizeN_A"; > VariableReferenceList [S1 Variable:/Spine:A] [P1 > Variable:/Spine:B]; > } > > When running ecell3-session..... ecell gives AttributeError, complaining > that there is no MolarConc attribute. > > 2) PythonProcess does not allo any "attribute" appear in the expression > either. > > Could you give an explanation please. > > BTW, the Ecell user manual is very incomplete and out of date (the last > modification is June 30th 2006). > Is it possible to update this manual, since ECell becomes more and more > popular now? > > Cheers > Lu > > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > _______________________________________________ > Ecell-users mailing list > Ece...@li... > https://lists.sourceforge.net/lists/listinfo/ecell-users |
From: luli <lu...@eb...> - 2012-03-19 17:57:06
|
Dear ECell3 developers, I just installed ecell-3.2.3pre2, however, encountering the following problems. 1) PythonFluxProcess does not allow any "attribute" appear in the expression. For instance: Process PythonFluxProcess( test ) { k 0.5; StepperID DE1; Expression "k*S1.MolarConc*self.getSuperSystem().SizeN_A"; VariableReferenceList [S1 Variable:/Spine:A] [P1 Variable:/Spine:B]; } When running ecell3-session..... ecell gives AttributeError, complaining that there is no MolarConc attribute. 2) PythonProcess does not allo any "attribute" appear in the expression either. Could you give an explanation please. BTW, the Ecell user manual is very incomplete and out of date (the last modification is June 30th 2006). Is it possible to update this manual, since ECell becomes more and more popular now? Cheers Lu |
From: luli <lu...@eb...> - 2012-03-19 17:39:43
|
Dear Yasuhiro, The problem listed in my previous e-mail has been solved by setting LD_LIBRARY_PATH to my local folder where Ecell has been installed (thanks to Michele Mattioni). Cheers Lu On 19/03/12 15:38, luli wrote: > Dear Yasuhiro, > > Thank you very much for your reply. > It seems ecell-3.2.3pre2 can be compiled, following the following commands: > ./configure --prefix=[myLocalFolder] > make > make install > > However, when I use ecell3-session to run a model (for instance, > ecell3-session run.py), I got the following error message: > > Traceback (most recent call last): > File "../bin/ecell3.2.3pre2/bin/ecell3-session", line 9, in<module> > import ecell.ecs > File > "/home/luli/bin/ecell3.2.3pre2/lib/python2.7/site-packages/ecell/ecs.py", line > 28, in<module> > import ecell._ecs > ImportError: libecs.so.2: cannot open shared object file: No such file > or directory > > > Could your please give some advice to fix this? > > The linux distribution I am using is: Ubuntu 11.10 (Oneiric Ocelot). > > Best Regards > Lu > > On 18/03/12 16:37, Yasuhiro Naito wrote: >> Dear Lu, >> >> Thank you for the report. >> >> Could you try ecell-3.2.3pre2? E-Cell 3.2.2 has some incompatibilities with recent boost C++ library. >> The source code of ecell-3.2.3pre2 is available at following: >> https://github.com/ecell/ecell3/downloads >> >> Please let me know your LINUX distribution and version. We'd like to reproduce your situation. >> >> Regards, >> >> ----- >> Yasuhiro Naito >> Institute for Advanced Biosciences, Keio University >> >> >>> I am trying to install the latest Ecell (3.2.2), but unsuccessfully. >>> >>> First of all, your repository of pre-built packages (for debian and >>> ubuntu) is down. >>> >>> Secondly, I tried to install the source from both sourceForge and >>> GitHub. During "make", I obtained the following logs: >> >> ------------------------------------------------------------------------------ >> This SF email is sponsosred by: >> Try Windows Azure free for 90 days Click Here >> http://p.sf.net/sfu/sfd2d-msazure >> _______________________________________________ >> Ecell-users mailing list >> Ece...@li... >> https://lists.sourceforge.net/lists/listinfo/ecell-users > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > _______________________________________________ > Ecell-users mailing list > Ece...@li... > https://lists.sourceforge.net/lists/listinfo/ecell-users |
From: luli <lu...@eb...> - 2012-03-19 14:38:29
|
Dear Yasuhiro, Thank you very much for your reply. It seems ecell-3.2.3pre2 can be compiled, following the following commands: ./configure --prefix=[myLocalFolder] make make install However, when I use ecell3-session to run a model (for instance, ecell3-session run.py), I got the following error message: Traceback (most recent call last): File "../bin/ecell3.2.3pre2/bin/ecell3-session", line 9, in <module> import ecell.ecs File "/home/luli/bin/ecell3.2.3pre2/lib/python2.7/site-packages/ecell/ecs.py", line 28, in <module> import ecell._ecs ImportError: libecs.so.2: cannot open shared object file: No such file or directory Could your please give some advice to fix this? The linux distribution I am using is: Ubuntu 11.10 (Oneiric Ocelot). Best Regards Lu On 18/03/12 16:37, Yasuhiro Naito wrote: > Dear Lu, > > Thank you for the report. > > Could you try ecell-3.2.3pre2? E-Cell 3.2.2 has some incompatibilities with recent boost C++ library. > The source code of ecell-3.2.3pre2 is available at following: > https://github.com/ecell/ecell3/downloads > > Please let me know your LINUX distribution and version. We'd like to reproduce your situation. > > Regards, > > ----- > Yasuhiro Naito > Institute for Advanced Biosciences, Keio University > > >> I am trying to install the latest Ecell (3.2.2), but unsuccessfully. >> >> First of all, your repository of pre-built packages (for debian and >> ubuntu) is down. >> >> Secondly, I tried to install the source from both sourceForge and >> GitHub. During "make", I obtained the following logs: > > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > _______________________________________________ > Ecell-users mailing list > Ece...@li... > https://lists.sourceforge.net/lists/listinfo/ecell-users |
From: Yasuhiro N. <yn...@sf...> - 2012-03-18 15:43:24
|
Dear Lu, Thank you for the report. Could you try ecell-3.2.3pre2? E-Cell 3.2.2 has some incompatibilities with recent boost C++ library. The source code of ecell-3.2.3pre2 is available at following: https://github.com/ecell/ecell3/downloads Please let me know your LINUX distribution and version. We'd like to reproduce your situation. Regards, ----- Yasuhiro Naito Institute for Advanced Biosciences, Keio University > I am trying to install the latest Ecell (3.2.2), but unsuccessfully. > > First of all, your repository of pre-built packages (for debian and > ubuntu) is down. > > Secondly, I tried to install the source from both sourceForge and > GitHub. During "make", I obtained the following logs: |
From: Yasuhiro N. <yn...@sf...> - 2012-03-18 15:37:12
|
Dear Lu, Thank you for the report. Could you try ecell-3.2.3pre2? E-Cell 3.2.2 has some incompatibilities with recent boost C++ library. The source code of ecell-3.2.3pre2 is available at following: https://github.com/ecell/ecell3/downloads Please let me know your LINUX distribution and version. We'd like to reproduce your situation. Regards, ----- Yasuhiro Naito Institute for Advanced Biosciences, Keio University > I am trying to install the latest Ecell (3.2.2), but unsuccessfully. > > First of all, your repository of pre-built packages (for debian and > ubuntu) is down. > > Secondly, I tried to install the source from both sourceForge and > GitHub. During "make", I obtained the following logs: |
From: luli <lu...@eb...> - 2012-03-17 18:23:57
|
Hi, I am trying to install the latest Ecell (3.2.2), but unsuccessfully. First of all, your repository of pre-built packages (for debian and ubuntu) is down. Secondly, I tried to install the source from both sourceForge and GitHub. During "make", I obtained the following logs: --- make all-recursive make[1]: Entering directory `/home/luli/bin/ecell-3.2.2' Making all in libltdl make[2]: Entering directory `/home/luli/bin/ecell-3.2.2/libltdl' make all-am make[3]: Entering directory `/home/luli/bin/ecell-3.2.2/libltdl' /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -g -O2 -c -o ltdl.lo ltdl.c /bin/bash ./libtool --tag=CC --mode=link gcc -g -O2 -o libltdlc.la ltdl.lo -ldl make[3]: Leaving directory `/home/luli/bin/ecell-3.2.2/libltdl' make[2]: Leaving directory `/home/luli/bin/ecell-3.2.2/libltdl' Making all in dmtool make[2]: Entering directory `/home/luli/bin/ecell-3.2.2/dmtool' make all-am make[3]: Entering directory `/home/luli/bin/ecell-3.2.2/dmtool' make[3]: Leaving directory `/home/luli/bin/ecell-3.2.2/dmtool' make[2]: Leaving directory `/home/luli/bin/ecell-3.2.2/dmtool' Making all in ecell make[2]: Entering directory `/home/luli/bin/ecell-3.2.2/ecell' make all-recursive make[3]: Entering directory `/home/luli/bin/ecell-3.2.2/ecell' Making all in libecs make[4]: Entering directory `/home/luli/bin/ecell-3.2.2/ecell/libecs' Making all in scripting make[5]: Entering directory `/home/luli/bin/ecell-3.2.2/ecell/libecs/scripting' /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I.. -I../.. -I/home/luli/bin/ecell-3.2.2 -I../../../libltdl -I/usr/include -g -O2 -g -O2 -MT ExpressionCompiler.lo -MD -MP -MF .deps/ExpressionCompiler.Tpo -c -o ExpressionCompiler.lo ExpressionCompiler.cpp mv -f .deps/ExpressionCompiler.Tpo .deps/ExpressionCompiler.Plo mv: cannot stat `.deps/ExpressionCompiler.Tpo': No such file or directory make[5]: *** [ExpressionCompiler.lo] Error 1 make[5]: Leaving directory `/home/luli/bin/ecell-3.2.2/ecell/libecs/scripting' make[4]: *** [all-recursive] Error 1 make[4]: Leaving directory `/home/luli/bin/ecell-3.2.2/ecell/libecs' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/luli/bin/ecell-3.2.2/ecell' make[2]: *** [all] Error 2 make[2]: Leaving directory `/home/luli/bin/ecell-3.2.2/ecell' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/luli/bin/ecell-3.2.2' make: *** [all] Error 2 -- It seems that the .deps/ExpressionCompiler.Tpo can not be generated.... Could you please give some advice and help? Best Regards Lu |
From: Kozo N. <kni...@ri...> - 2011-06-01 11:08:37
|
E-Cell's source code repository has moved to GitHub! E-Cell has been developed using SourceForge's subversion repository since its inception, but we think that now is a good time to switch to a distributed version control system, and we chose GitHub. All the source code from E-Cell project is now available on https://github.com/ecell. You will also find the source code of the E-Cell 3 project under the same organization. The development of E-Cell now continues on GitHub. The previous Subversion repository will be abandoned. We think that migration to GitHub will make it much easier for users to contribute to our project and also help us reach our next milestone more gracefully. -- Kozo Nishida Laboratory for Biochemical Simulation OLABB, Osaka University 6-2-3, Furuedai, Suita, Osaka 565-0874, JAPAN kni...@ri... |
From: Bin Hu <hub...@gm...> - 2010-10-29 17:07:21
|
Thanks for sharing. I have been enjoying using ipython and matplotlib for processing my simulation tasks too. By the way, is the deb distribution for ecell3 still working? I tried one for Ubuntu 10.04 but got time out warnings. Regards, Bin On Fri, Oct 29, 2010 at 4:21 AM, Michele Mattioni <mat...@eb...> wrote: > Dear all, > > I've made a really simple python script to integrate ecell with > matplotlib from an ipython console. > > You can find the code here: > http://github.com/mattions/QuickEcell > > The latest release is this one: > http://github.com/mattions/QuickEcell/archives/0.0.2 > > Maybe it useful to some of you for quick tests. > > Regards, > Michele. > > ------------------------------------------------------------------------------ > Nokia and AT&T present the 2010 Calling All Innovators-North America contest > Create new apps & games for the Nokia N8 for consumers in U.S. and Canada > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store > http://p.sf.net/sfu/nokia-dev2dev > _______________________________________________ > Ecell-users mailing list > Ece...@li... > https://lists.sourceforge.net/lists/listinfo/ecell-users > |
From: Koichi T. <sha...@gm...> - 2010-10-29 10:30:40
|
Dear Michele, Great contribution! Thank you! Koichi > Dear all, > > I've made a really simple python script to integrate ecell with > matplotlib from an ipython console. > > You can find the code here: > http://github.com/mattions/QuickEcell > > The latest release is this one: > http://github.com/mattions/QuickEcell/archives/0.0.2 > > Maybe it useful to some of you for quick tests. > > Regards, > Michele. > > ------------------------------------------------------------------------------ > Nokia and AT&T present the 2010 Calling All Innovators-North America contest > Create new apps& games for the Nokia N8 for consumers in U.S. and Canada > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store > http://p.sf.net/sfu/nokia-dev2dev > _______________________________________________ > Ecell-users mailing list > Ece...@li... > https://lists.sourceforge.net/lists/listinfo/ecell-users |
From: Michele M. <mat...@eb...> - 2010-10-29 10:22:05
|
Dear all, I've made a really simple python script to integrate ecell with matplotlib from an ipython console. You can find the code here: http://github.com/mattions/QuickEcell The latest release is this one: http://github.com/mattions/QuickEcell/archives/0.0.2 Maybe it useful to some of you for quick tests. Regards, Michele. |
From: Michele M. <mat...@eb...> - 2010-06-14 10:32:15
|
Dear all, I've updated Ecell to the latest release for the series 3.1 --> 3.1.108. Unfortunately my model does not run properly anymore and I receive this error: gsl: lu.c:147: ERROR: matrix is singular Default GSL error handler invoked. Aborted Any idea how to go about this? Thanks, Michele. |
From: Erin <she...@um...> - 2010-04-05 21:46:50
|
Hello, I am currently using E-Cell for a number of modeling projects but I'm finding the "logger" functions in my ess files are very tedious to write and keep track of. Is there a function that will log ALL variables in a model rather than having to specify each variable individually? Thank you, Erin Shellman -- Erin Rachael Shellman The University of Michigan Bioinformatics PhD Candidate http://www.erinshellman.com she...@um... (937) 321.1129 |
From: Erin <she...@um...> - 2010-03-18 18:49:32
|
Hello, I think there is a bug in the ECD file writing code. After running a simulation via an ess file, I get the following errors: erin@bobby:~/modelingFiles$ ecell3-session experiment.py Running for a minute Simulation complete! Traceback (most recent call last): File \"/usr/bin/ecell3-session\", line 234, in <module> main() File \"/usr/bin/ecell3-session\", line 229, in main aConsole.loadScript( anEssFile, aParameters ) File \"/usr/bin/ecell3-session\", line 56, in loadScript execfile( ecsFile, aContext ) File \"experiment.py\", line 68, in <module> malateResults.save( \'malateResults.ecd\' ) File \"/usr/lib/python2.6/dist-packages/ecell/ECDDataFile.py\", line 91, in save TableIO.writeArray( self.theFileName, self.theData, 1 ) File \"/usr/lib/python2.6/dist-packages/ecell/TableIO.py\", line 79, in writeArray t[\'rows\'] = data.shape[0] AttributeError: \'ecell._ecs.DataPointVector\' object has no attribute \'shape\' The file "malateResults" is created however, it contains only headers and no data. I am using E-Cell 3.2.0p1 on Ubuntu 9.10. Thanks, Erin -- Erin Rachael Shellman The University of Michigan Bioinformatics PhD Candidate http://www.erinshellman.com she...@um... (937) 321.1129 |
From: Moriyoshi K. <mo...@sf...> - 2010-02-11 09:53:34
|
Hi, We are pleased to announce the immediate availablity of E-Cell System, 3.2.0p1. This is a maintainance release of 3.2.0, with the following bugfixes addressed: * Fixed the build system so that resource files for the GUI tools are correctly installed under the package data directory. * Fixed FileSelection combatibility wrapper so that they can present the text box for the filename entry. Because of this bug, models could not be saved in session-monitor or model editor. * Fixed a bug in System::detach() that causes random segfault on cleanup. * Fixed infinite recursion in ecell._ecs.Simulator.getDMSearchPath(). We apologize the inconveniences caused by these bugs. Moriyoshi Koizumi E-Cell 3 RM |
From: shahin s. <sha...@gm...> - 2010-02-10 07:05:29
|
---------- Forwarded message ---------- From: shahin shaj <sha...@gm...> Date: Feb 9, 2010 9:47 PM Subject: help me To: ecellusermailinglist <ece...@li...> Respected sir, I am shahin.I am doing II-m.sc bioinformatics.I have interested to do work in simulation work.so i have chosen ecell software.I tried out some of the models such drosophila and LTD.It was interesting. i have planned to simulate small pathway using ecell.but not yet decided the pathway.Is it possible to complete my work within this month.And what are the prior knowledge i require to do simulation in ecell. What i have to learn to do simulation in ecell.I am just a learner.Help me to complete my work. and i want to know "In what basis steppers and process are selected?Which stepper is easy to work? Thanking you, Yours faithfully, S.Shahin |
From: shahin s. <sha...@gm...> - 2010-02-09 16:18:05
|
Respected sir, I am shahin.I am doing II-m.sc bioinformatics.I have interested to do work in simulation work.so i have chosen ecell software.I tried out some of the models such drosophila and LTD.It was interesting. i have planned to simulate small pathway using ecell.but not yet decided the pathway.Is it possible to complete my work within this month.And what are the prior knowledge i require to do simulation in ecell. What i have to learn to do simulation in ecell.I am just a learner.Help me to complete my work. and i want to know "In what basis steppers and process are selected?Which stepper is easy to work? Thanking you, Yours faithfully, S.Shahin |
From: Moriyoshi K. <mo...@sf...> - 2010-02-05 06:15:54
|
We are proud to announce the release of the latest version of E-Cell System, 3.2.0 and 3.1.108. The highlights of these releases are as follows: - Thorough refactoring for the sake of stability - Improved differential steppers for more accuracy - Migration to gtk.Builder. GUI frontends no longer require libglade / pyglade. - x86_64 support on Windows (XP, Vista and 7) 3.1.108 is a maintenance release of 3.1 series and it is terminated as of this release. Users are strongly encouraged to migrate to 3.2.0 if possible. You can download the source code and precompiled binaries from the following page: http://sourceforge.net/projects/ecell/ Enjoy! Moriyoshi Koizumi E-Cell 3 release master |
From: Michele M. <mat...@eb...> - 2009-12-01 23:05:04
|
Hello list, I'm trying to compile the final version of Ecell on a Ubuntu Karmic (9.10) and unfortunaly the compilation fail: cc -fPIC -g -O2 -g -O2 -Wno-pmf-conversions -g -O2 -Wno-pmf-conversions -D_ECELL3_DM_CLASSNAME=GillespieProcess -I/usr/include -I../libecs -I../.. -I.. -I../../libltdl -I/usr/include/python2.6 -c GillespieProcess.cpp -o GillespieProcess.o In file included from GillespieProcess.cpp:28: GillespieProcess.hpp: In static member function ‘static void GillespieProcess::initializePropertyInterface(libecs::Type2Type<TT>)’: GillespieProcess.hpp:59: error: ‘getc’ is not a member of ‘GillespieProcess’ GillespieProcess.hpp:59: error: ‘getc’ is not a member of ‘GillespieProcess’ dmcompile: failed to compile the specified source files: CompileError(DistutilsExecError("command 'cc' failed with exit status 1",),) ecell3-dmc: ../../dmtool/dmcompile returned error status: 1 make[4]: *** [GillespieProcess.so] Error 1 make[4]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell/dm' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell' make[2]: *** [all] Error 2 make[2]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.107/ecell' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/mattions/Work/progs/ecell/ecell-3.1.107' make: *** [all] Error 2 The problem seems to be the line 59 of the ecell/dm/GillespieProcess.hpp file, which is: PROPERTYSLOT_GET_NO_LOAD_SAVE( Real, c ); Any idea what's wrong? (are you thinking to provide deb package for karmic? (maybe using launchpad... :) ) Regards, Michele |
From: Bin Hu <hub...@gm...> - 2009-08-04 05:55:52
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Hi, Will anyone attend ICSB this year? Maybe we should have a gathering for beer? Bin |
From: Bin Hu <hub...@gm...> - 2009-08-04 05:54:58
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Hi, I am having a problem in installing 3.1.107 on a virtual machine running Ubuntu. Configure and compile looked fine, but got the following error in sudo make install: Making install in doc make[1]: Entering directory `/home/hu/bak/ecell-3.1.107/doc' Making install in users-manual make[2]: Entering directory `/home/hu/bak/ecell-3.1.107/doc/users- manual' rm -f -rf users-manual mkdir users-manual make[3]: Entering directory `/home/hu/bak/ecell-3.1.107/doc/users- manual' make[3]: Nothing to be done for `install-exec-am'. rm -f -rf users-manual mkdir users-manual test -z "/usr/local/share/doc/ecell/users-manual" || /bin/mkdir -p "/ usr/local/share/doc/ecell/users-manual" /usr/bin/install -c -m 644 './users-manual/*' '/usr/local/share/doc/ ecell/users-manual/*' /usr/bin/install: cannot stat `./users-manual/*': No such file or directory make[3]: *** [install-_htmlDATA] Error 1 make[3]: Leaving directory `/home/hu/bak/ecell-3.1.107/doc/users-manual' make[2]: *** [install-am] Error 2 make[2]: Leaving directory `/home/hu/bak/ecell-3.1.107/doc/users-manual' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/home/hu/bak/ecell-3.1.107/doc' make: *** [install-recursive] Error 1 Executing ecell3-session generates the following error: Traceback (most recent call last): File "/usr/local/bin/ecell3-session", line 8, in <module> import ecell.config ImportError: No module named ecell.config $ ecell3-python Python 2.6.2 (release26-maint, Apr 19 2009, 01:56:41) [GCC 4.3.3] on linux2 Type "help", "copyright", "credits" or "license" for more information. Can anyone show me how to solve the problem? Thanks. Regards, Bin |
From: Michele M. <mat...@eb...> - 2009-04-30 06:30:49
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Ok, thanks. One question, Why are you guys still using the old libtool and didn't switch to the new one? Is it so hard to recompile ecell everytime.... :) Do you think you will get rid of it in the future or not? If you really need it, can you please write somewhere how to compile it? ./configure make doesn't work. Cheers, Michele. On Thu, Apr 30, 2009 at 3:59 AM, Moriyoshi Koizumi <mor...@gm...> wrote: > I completely removed the part of Session class in which the current > working directory is changed to the place the given script is located. > You'll find it not bothering with 3.1.107 or later versions. > > Thanks for the report and the patch. > > -- moriyoshi > > > > 2009/4/20 Michele Mattioni <mat...@eb...>: >> Hello list, >> >> I modified the SessionManager class so it doesn't change always the >> directory, but it has a true/false switch to do it. >> >> Patch attached (against the last revision of the svn) >> Default is False. (Not as normal) >> >> Cheers, >> Michele >> >> ------------------------------------------------------------------------------ >> Stay on top of everything new and different, both inside and >> around Java (TM) technology - register by April 22, and save >> $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. >> 300 plus technical and hands-on sessions. Register today. >> Use priority code J9JMT32. http://p.sf.net/sfu/p >> _______________________________________________ >> Ecell-users mailing list >> Ece...@li... >> https://lists.sourceforge.net/lists/listinfo/ecell-users >> >> > |
From: Moriyoshi K. <mor...@gm...> - 2009-04-30 02:59:33
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I completely removed the part of Session class in which the current working directory is changed to the place the given script is located. You'll find it not bothering with 3.1.107 or later versions. Thanks for the report and the patch. -- moriyoshi 2009/4/20 Michele Mattioni <mat...@eb...>: > Hello list, > > I modified the SessionManager class so it doesn't change always the > directory, but it has a true/false switch to do it. > > Patch attached (against the last revision of the svn) > Default is False. (Not as normal) > > Cheers, > Michele > > ------------------------------------------------------------------------------ > Stay on top of everything new and different, both inside and > around Java (TM) technology - register by April 22, and save > $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. > 300 plus technical and hands-on sessions. Register today. > Use priority code J9JMT32. http://p.sf.net/sfu/p > _______________________________________________ > Ecell-users mailing list > Ece...@li... > https://lists.sourceforge.net/lists/listinfo/ecell-users > > |