[oscill8-info] Oscill8, v1.1.3 released

[Emery C. <ec...@vt...>]

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