What's new in JSim 2.09 Beta
Oct 29, 2012
- Added new Save Every Nth Point feature, reducing the memory required for long model runs. Feature request JB.
- Texts in a model's "Debug" tab (e.g. standard units file) are now initially positioned at the beginning of the file. Previously, they were positioned at the end of the file. Change request JB.
- Added -builddirsfx switch to jsbatch and jsfim to enable running large numbers of simultaneous jobs on high-performance clusters. Feature request by AA.
- Added -ofinal switch to jsbatch, allowing printing of only the final values for model variables after a run.
- Added JSim.plan.XMMLTranslator class for light-weight MML to XMML translation. Feature request by MN.
- Due to internal engine changes, JSim release 2.09 will require a new compatible release of QPP (0.916) to work with it.
New in JSim 2.08 Beta (Aug 13, 2012)
- Fixed bug in LSFEA PDE solver in which problems with x-dependent source terms were not calculated correctly. Bug report by GR.
- A revised version of the LSFEA PDE solver is now available under the name LSFEA3. This is expected to replace the existing LSFEA solver, once users have had a chance to evaluate it. The algorithm change is as follows. The spatial resolution equals the number of grid points used by the other solvers (no longer restricted to just the odd integers) and the solution values at the endpoints of the spatial array are no longer used to store information needed for the next time step. This has resulted in more accurate spatial displays. The calculations for system transit time and mass balance are approximately the same with minor differences. New code thanks to GR.
- Fixed bug in MacIntosh version in which double-clicking on model or project files did not always launch the most recent version. Bug fix thanks to AS.
- Most tabs in the JSim GUI now have a "Help" menu. Selecting items from this menu causes the relevant documentation page to be loaded into your desktop web browser.
- JSim's Model Browser now retains any user edited layout between refreshes. The layout is also stored in the project file so it can be restored when reloaded. Selecting "Revert to default layout" from the Render menu abandons user edits and performs a fresh computer generated layout. Update thanks to BJ.
- Each JSim download and documentation page now has a button to send comments and questions to JSim support staff.
New in JSim 2.07 (Jun 13, 2012)
- More warnings for untranslateable bits.
- Bugs in variable stoichiometry translation were fixed.
- SBML conversion factors are now translated.
- Variable compartments are now correctly handled, both in terms of species amounts or concentrations varying in time, and in terms of species initial amounts/concentrations being set.
- Formulas that use SBML function definitions now correctly note that they vary in time.
- Reactions with local parameters with IDs that duplicate global parameters and/or other local parameters are now given unique global IDs for the translated version.
- Variable and unit names starting with and underscore are now properly mapped to JSim-safe names.
- All variables renamed due to JSim name-space considerations, are now tagged with property "sbmlName" mapping to the original SBML name or identifier. Bug report by MN.
New in JSim 2.06 (Apr 23, 2012)
- JSim's Monte Carlo analysis module is now available. This module, found in the new "Monte Carlo" tab in the JSim GUI, allows the user to estimate parameter confidence by running multiple optimizations on noisy data sets. Currently, this functionality is not available when using a remote server (e.g. running applets).
- JSim now allows export of models in CellML format using either the JSim GUI or jsbatch. Feature implementation thanks to LS.
- Fixed bug in the handling SBML models with time-varying compartment volumes. Bug fix by LS.
- JSim's Linux Makefiles now support both EL5 or EL6 releases of Redhat Linux. Previously, only EL5 was supported. This change only affects those building JSim from source. Additions thanks to BJ.
- Removed extraneous console messages when rendering graphics in a model's "Browser" tab. Change thanks to BJ.
- Fixed bug in UtilIO.readBytes(File) that caused