[oscill8-info] Oscill8, pre-release 1.0.14

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

All,

Very briefly, I fixed a few minor bugs that people had noticed and have 
released a cleaner version of this ALPHA release. There is now an 
installer .exe to ease the installation. There are also example ode 
files (to try creating your own workspace) and a prebuilt workspace to 
try out.

(Sorry Kathy, AUTO constants aren't yet exposed to the user!!).

REMINDER: The first official release, v1.1, will be on April, 1, which 
will include the features previously mentioned and will have user 
documentation! FYI, I will be releasing several more 1.0.x version 
before April 1, but only for those who really want to use it right now. 
Most will probably want wait until the April 1st unless you'd just like 
a quick look.

For those of you who didn't receive the first mailing on this list, it 
is contained below (several people were added after the first mailing).

Enjoy,

Emery

--------------------------------------

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