[Oscill8-info] Oscill8, pre-release 1.0.11

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

All,

I've just set up a mail list at sourceforge for announcements concerning 
Oscill8. The first official release (v1.1) will be made on April 1st, 
but I have placed an alpha pre-release v1.0.11 up there for those of you 
who have asked for it (Windows only). The input right now is a 
simplified ODE file. This file can only have velocities, right-hand side 
equations "param" and "init" statements; i.e., no functional 
definitions. Also, there is NO user documentation with it; this will 
wait until April 1st (sorry). In other words, this pre-release is a 
use-at-your-own-risk; many of the feature were just implemented in the 
last few days and aren't thoroughly tested (hence, April 1st for the 
official release). There is however, an oscill8/examples/ode directory 
with two simple ODE files that work so that you can try them out (as 
well as an oscill8/examples/workspaces directory with a workspace for 
the chap10_serious.ode model). These are for the "toy" and "serious" 
models in Chapter 10 of "Computational Cell Biology, Fall et. al. To 
install, read the brief README.txt in the oscill8/doc directory. There 
are bunch of hotkeys enabled, but I'll let you try to figure them out!!! 
(I'll tell you two... in the graph area--make sure the run history tree 
isn't highlighted--you can press "R" to reset the graph boundaries to 
the data and "P" for plot properties; there is also a mouse zoom feature 
where you make a box and zoom--but the trick is that the zoom box 
doesn't show up, although it works--I'll implement the box in the 1.1 
release!!)

The release on April 1st will allow functional definitions in the ODE 
file and will be distributed with an SMBL --> ODE converter that can be 
used by modelers. It will also include two parameter continuation and 
limit cycle continuation (which are currently disabled), in addition to 
a number of other features. I will announce this all on April 1st.

BTW, I will only use this list for brief announcements concerning 
releases etc; low traffic! If you're interested, you can subscribe to 
the "oscill8-help" list (see mailing lists at 
http://sourceforge.net/projects/oscill8) which we can use for discussing 
user issues. Also, I will be using the bug tracker and feature request 
tools at sourceforge.net for Oscill8, so (after April 1st) you can 
report you bugs and your wishes there!

Enjoy,

Emery Conrad