From: Emery C. <ec...@vt...> - 2005-05-11 17:52:26
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All, In response to suggestions at the recent Bio-COMP meeting, I've fixed several bugs in Oscill8 and added a number of new convenient features, the main ones being that you can start Oscill8 from the command line using an ODE or SBML file as input (and a workspace will be transparently created in the local Oscill8 workspace cache directory) and the SBML --> ODE file conversion is now automatic (if you have JigCell installed in the default directory). Not all SBML files will work; in particular, functional expressions aren't yet supported in the model parser for Oscill8, so if you have functional expressions in your SBML, you'll need to use JigCell to convert to ODE, then use Oscill8's ode_clean.pl utility to make a valid Oscill8 ODE file. This should be remedied in a future release. In addition, I've switched the license over to CDDL (from LGPL) to better accommodate the community at large. Recall that you can find Oscill8 at http://sourceforge.net/projects/oscill8. Other updates since v1.1.0 include: 1) migration to CDDL (from LGPL), removed dependence on GSL. 2) added in minpack for jacobian calculations and later optimization functionality 3) fixed barf on @ symbol in XPPAUT ODE files 4) fixed another error in the parser that was getting incorrect operator precedence for / vs. * in certain cases. 5) fixed continuation parameters being properly passed to two parameter continuation 6) added SBML/XML and ODE start (without having to explicitly create the workspace--a workspace gets created in the local workspace cache) 7) added command-line start with .o8w, .ode, and .sbml/.xml files as input (which utilizes the auto-creation of workspaces) 8) added JigCell SBML->ODE conversion (JigCell install dir is hard-coded right now to the default JigCell install dir--NOTE: Oscill8's model parser doesn't yet accept functional expressions, so not all SBML files will work!! This feature is forthcoming. [REQUIRES JigCell version >= 5.0.1]. 9) added PATH update to registy/code section of windows exe installer 10) removed annoying "Not implemented yet" messages (for you Nick Allen!) Enjoy, Emery Conrad |