E-Cell 3.1.105 Released

Release Notes

E-Cell Simulation Environment

Version 3.1.105 E-Cell Project June 2006

We are pleased to announce the release of E-Cell Simulation Environment Version 3.1.105, after more than a year of work since the last release(3.1.103) in January 2005. Version 3.1.104 was skipped.

Here I note some major changes that most of the users may want to know.

For more details, please see Changelog and ecell-cvs archives, or post a question on ecell-devel mailing list.

• We switched from Numeric (python-numeric) to numpy. Numpy is available from http://www.scipy.org. If you are a Fedora Core user, you can find numpy rpms in Fedora Extras.
• Some command names were changed for better consistency: 'gecell' command is now called 'ecell3-session-monitor'. 'gecell' still works with a warning message, but will be removed in future versions. Also, toollauncher was renamed to ecell3-toollauncher, and gecell3-session is now ecell3-session-gui.
• We now recommend ODEStepper for all ODE models, and DAEStepper for DAE models. ODE45 and ODE23 Steppers are still there, but ODEStepper will perform (at least equally) better in most situations, especially on 'stiff' models.
• Some Process classes were deprecated: CatalyzedMassActionFlux, IsoUniUniFlux, Ordered*Flux, Random*Flux. Use ExpressionFluxProcess or PythonFluxProcess instead.
• NRStepper was removed. Use DiscreteEventStepper instead, which is identical.
• The empy parser that controls interpretation of em files was upgraded from version 3.1 to version 3.3. As a result, the em.py hook 'after_substitute' is no longer available.