ecell-2 2.20 beta SP1 (exe)

Release notes:

Patch for CD-ROM distributed in ISMB2002.
Please see patch-220-1.txt for detail.

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Changelog:

ecell-2 2.20 beta SP1 (exe)

Release notes:

======== E-CELL2.20 beta release note in English ====
date : Aug. 3. 2002
version : 2.20 beta
author of this document : Mitsui Knowledge Industry Co., Ltd.
                          Bioscience Division 

*** Contents of this distribution :

 *standard directory
  * SRCC directory       --- C++ source files of the core
  * SRCJ directory       --- Java source files of the GUI
  * SRCR directory       --- standard-reactor source files
  * STDR directory       --- standard-reactor description files
  * GLIB directory       --- index and get option files
  * DLLR directory       --- dll files for the GUI mode of standard reactors
  * DLLRB directory      --- dll files for the batch mode of standard reactors
  * WIN-BCC directory    --- Core binary executables and Borland C++ Makefile
  * ECELL directory      --- Java class files for GUI
  * SAMPLE directory     --- rule templates and sample spread sheets,rule files and script files 
  * buildr.bat           --- the batch file to build Reactor source files
  * ecellstart.bat       --- the start-up batch file for the shortcut from the desktop
  * sample.eri           --- sample rule file (Toy model)
  * simple.eri           --- sample rule file (simple model)
  * sample.ecs           --- sample script file (Toy model)
  * simple.ecs           --- sample script file (simple model)
  * Ecanim2.gif          --- E-CELL's logo (animated GIF file)
  * ECELL2.BAT           --- the start-up batch file for the GUI mode
  * ECELL2B.BAT          --- the start-up batch file for the batch mode
  
 *erythrocyte directory
  * SRCC directory       --- C++ source files of the core
  * SRCJ directory       --- Java source files of the GUI
  * GLIB directory       --- index and get option files
  * DLLR directory       --- dll files for the GUI mode of erythrocyte model reactors
  * DLLRB directory      --- dll files for the batch mode of erythrocyte model reactors
  * WIN-BCC directory    --- Core binary executables and Borland C++ Makefile
  * ECELL directory      --- Java class files for the GUI
  * Erythrocyte_v236.eri --- erythrocyte model rule file
  * default.ecs          --- sample script file (for running automatically)
  * ALL.ecs              --- sample script file (whole metabolic pathway for the erythrocyte model)
  * NM.ecs               --- sample script file (nucleotide metabolism)
  * PPP.ecs              --- sample script file (pentose phosphate pathway)
  * Gly.ecs              --- sample script file (glycolysis)
  * Ecanim2.gif          --- E-CELL's logo (animated GIF file)
  * ECELL2.BAT           --- the start-up batch file for GUI mode
  * ECELL2B.BAT          --- the start-up batch file for batch mode

 *tools directory
  * reactor directory    --- the Perl scripts to convert reactor description files to
                             reactor source files (rd2ch)
  * rule directory       --- the binary executables and Perl scripts to convert
                             row rule files to executable rule files (ss2er?Aer2eri)

*** Verified environments to run :
* MS-Windows 98
* MS-Windows NT4.0
* MS-Windows 2000
* MS-Windows XP

*** System requirements :
Java(TM) 2 Runtime Environment (J2RE): 1.3.0_02 is recommended.
Cygwin(TM) 2.78 or newer (Perl 5.6 or newer)
Borland C++ Compiler 5.5.1 or Borland C++ Builder 5
  (It does not correspond to Borland C++ Builder 6 and Microsoft Visual C++ 6)

*** How to install and run the software :
* Please refer to an attached manual (IndexE.html).

*** Copyright and license :
  Copyright (C) 1996-2002 Keio University
  Copyright (C) 1998-2002 Japan Science and Technology Corporation (JST)
  Copyright (C) 2000-2002 Mitsui Knowledge Industry Co., Ltd. Bioscience Division
  GNU General Public License

*** Developers : 
* E-CELL 1 core : Kouichi TAKAHASHI
* E-CELL 1 GUI : Kouichi TAKAHAHI and Naota ISHIKAWA
* E-CELL 2 core improved parts : Naota ISHIKAWA
* E-CELL 2 GUI : Mitsui Knowledge Industry Co., Ltd. Bioscience Division
  http://bio.mki.co.jp/ (Only in Japanese)

*** Improvement : ECD file generated by the tracer :
An ECD file generated by E-CELL1 contains only the total running time and the present time,
while an ECD file generated by E-CELL2 contains the maximum, mean, and minimum values in addition.

*** Improvement : logger function is mounted:
The logger function, which performs a simulation without displaying any Tracer window, is mounted in E-CELL2

*** Improvement : Batch mode is mounted:
The batch mode which performs a simulation at high speed without displaying GUI is mounted in E-CELL2

*** Restriction : Operation during simulation execution:
In E-CELL2.20beta, if it operates closing Tracer during simulation execution (a control panel being the Run state), a system may fall rarely. Please perform operation in the Stop state as much as possible.

*** Restriction : Initial value of .ecd files:
In E-CELL2.20beta, the initial value may not be saved at .ecd files which Tracer and Logger output.

*** Restriction : Initial value of Reactor window:
In E-CELL2.20beta, a different value  may be displayed on the initial value of Reactor window. The right value will be displayed if simulation is performed.

*** Other resources :
* A user's manual
* Latest source codes for the E-CELL2
* Binary executables of the E-CELL2.0 or later
The items above can be downloaded at the following URL:
http://bioinformatics.org/project/?group_id=49

*** Acknowledgments :
This work is also supported in part by Japan Science and Technology Corporation (JST), The Ministry of Agriculture, Forestry and Fisheries of Japan (Rice Genome Project SY-2103), and New Energy and Industrial Technology Development Organization (NEDO) of the Ministry of Economy, Trade and Industry of Japan.  


======== end of release note ========

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Changelog: