An Accelerated Biochemical Brownian Dynamics Code Released
Changelog
Changelog
Changes for E-Cell System version 3.1.105 from version 3.1.103
libecs/emc:
- update currenttime in interrupt(), because this procedure is effectively a stepping (shafi)
- new design for FluxProcess. this class of Processes no longer change Variable values, but simply uses Activity property to let Steppers know derivative values. Process::TotalVelocity was removed. (kaizu/shafi)
- Logger bug 1287630 (gabor)
- Scheduling mechanism refactoring and performance tuning (shafi)
DM:
- Step size selection bugfix in ODE Steppers (kaizu)
- Updates on FluxDistribution Steppers/Processes (tomo)
- Deprecated NRStepper, use DiscreteEventStepper instead (shafi)
- Deprecated Process classes: - RapidEquilibrium, - CatalyzedMassActionFlux - IsoUniUniFlux - OrderedFlux - RandomFlux. Use ExpressionFluxProcess or PythonFluxProcess instead. (shafi)
- Deprecated CompartmentSystem, use System instead. (shafi)
pyecs/pyecell:
- Bug #1235119, No error message when system structure is broken (shafi)
- Improvements in session-manager (sugi)
- SBML bug fixes, use of annotation tags (kaizu)
- Upgraded em.py to version 3.3 (addy)
GUI:
- Massive updates in the model editor (gabor et. al)
- Support for pygtk-2.6 (satya)
Build mechanism / overall coding issues:
- Support for freebsd (libdl detection, VVector.h etc.) (Hisham Zarka)
- Boost-related things is now treated as regular stuff. (shafi)
- Support for Linux/x86-64 (shafi)
- Support for gcc4.x (shafi)
- Switch from python-numeric to numpy (shafi)
- Changes in installation paths (PREFIX/lib/ecell-3.1 etc) (shafi)
Sample models:
- ODEStepper is now the default in all ODE models. (kaizu)
Miscellaneous:
- Program name changes: - toollauncher -> ecell3-toollauncher, - gecell -> ecell3-session-monitor, - gecell3-session -> ecell3-session-gui (shafi)
- Many other cleanups, small fixes.
