This document introduces E-Cell 3.2, a new version of the E-Cell biochemical simulation software. It provides bug fixes and new features, including improvements to stability, support for additional platforms, and the ability to implement processes and variables in Python. The document outlines changes in E-Cell 3.2 and discusses plans for E-Cell 4 to have increased rule-based modeling capabilities and scriptability.

1. Introducing E-Cell 3.2
Moriyoshi Koizumi <mozo@riken.jp>
Biochemical Simulation Research Team,
Advanced Science Institute,
RIKEN

2. Summary
• About E-Cell 3.2
• 3.2.0 just got out of the door
• What's new in 3.2?
• Towards E-Cell 4

3. E-Cell 3.2.0 released

4. E-Cell 3.2.0
• The very first release of 3.2 series
• Many major and minor bugs have been
fixed since 3.1.107
• New features that may draw some
attention
• All users are encouraged to upgrade to
3.2.0

5. Bugfixes
• Through overhaul of DM facility
• There were major design issues that
had caused instability.
• Lots of API change involved.
• Binary compatibility has been lost!
• You need to recompile DM's.

6. Bugfixes
• A Long-standing differential stepper
problem
• Velocity was not correctly calculated
right after (re)initialization
• DifferentialStepper API has been
changed
• StepInterval ➡ NextTime
• updateInternalState()

7. Bugfixes
• Reimplementation of session manager
• Much more stability
• especially used on the local
machine
• Support for Globus 4
• LSF support (by Giuseppe Aprea)

8. t=0
before stop
3.2.0 restart
3.2.0 stop
restart

9. Other changes
• Many API functions are now
deprecated.
• VariableReference::getValue() etc.
• libemc is declared obsolete
• Polymorph class was refactored to be
more efficient
• Added Model::deleteEntity() to support
dynamically generated reaction rules

10. Other changes
• Python code was updated to use
modern library functions
• Improvements on Python binding
• Optimization of Logger to NumPy
interface
• Providing interface to directly
manipulate C++ objects
• Now users can implement Processes,
Variables and Systems in Python!

11. from ecell.ecs import Process, Variable
class MyProcess(Process):
IsContinuous = True
def initialize(self):
pass
def fire(self):
return 1
class MyVariable(Variable):
def initialize(self):
pass
def onValueChanging(self, val):
return val
theSimulator.addPythonDM(MyProcess)
theSimulator.addPythonDM(MyVariable)
loadModel('mymodel.eml')
run(100)

12. Other changes
• Official support for the following
platforms:
• Mac OS X
• 64bit Windows
• Removed dependency on glade in favor
of GtkBuilder

13. Towards E-Cell 4
• E-Cell 4 will be highly rule-based and
also highly scriptable
• Script-based modeling is already
covered in 3.2
• migration from EmPy
• Rule-based modeling will be supported
in 3.3

14. rootSystem = sim.getEntity('System::/')
S = sim.createVariable('Variable')
P = sim.createVariable('Variable')
E = sim.createProcess('MassActionFluxProcess')
rootSystem.registerEntity(S)
rootSystem.registerEntity(P)
rootSystem.registerEntity(E)
S.ID = 'S'
P.ID = 'P'
E.ID = 'E'
E.k = .3
E.VariableReferences.add('S0', S, -1)
E.VariableReferences.add('P0', P, 1)
sim.run()

15. Acknowledgements
• JST CREST
• KEIO University
Masaru Tomita, Takeshi Sakurada, Kazunari Kaizu, Taiko Nishino, Ayako
"Kinoshita" Yachie and many kind students.
• RIKEN
Koichi Takahashi, Satya Nanda Vel Arjunan
• Mitsubishi Space Software
Sachio Nohara, Chihiro Okada, Yasuo Ohara, Gen Ishikawa and
Takeshi Yuasa