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From: Jason Z. <jz...@gm...> - 2011-01-20 22:34:37
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Dear Oscill8 Users, Oscill8 is now available on Windows 7 and Vista! If you have one of these platforms, download Oscill8 at http://sourceforge.net/projects/oscill8/ -- Jason Zwolak |
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From: Emery C. <em...@um...> - 2007-03-05 21:53:36
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All,
A few bug fixes and a feature or two have been added, and since several of
you have been requesting related fixes, I thought I'd send notice to the
general list.
Enjoy,
Emery
#====================================================================
# release 2.0.9 notes (2007/3/5)
#====================================================================
Updates are:
* Fixed bug #1674084 for model view behavior (cancel, escape work,
and there is a new Save As button).
* Fixed bug #1348552 for improper treatment of run IDs for
limit cycle continuation (actually, this was fixed some
iterations ago).
* Fixed bug #1284235 regarding log scale reset malfunction.
Everything can now be set separately.
--
Emery Conrad
Department of Mathematics
University of Michigan
4827 East Hall
Ann Arbor, MI 48109-1043
(734) 936-9973
http://www-personal.umich.edu/~emeryc
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From: Emery C. <em...@um...> - 2007-02-23 20:40:10
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All, I've just released a new version of Oscill8 at the usual place ( http://sf.net/projects/oscill8) with a few bug fixes and enhancements... FYI Oscill8 version 2 now requires .NET framework 2.0 (if you don't have this, the installer will tell you this). In the next month, there will be several new releases with bug fixes, but for those interested, there is a temporary bug fix for the "aux" variable/continuation problem... you cannot view aux variables in the bifurcation diagrams, but it won't return with MX every time. More to come soon, Emery Conrad #==================================================================== # release 2.0.8 notes (2007/2/23) #==================================================================== Updates are: * Got most of SBW SimAPI done. * Fixed bifurcation search output (crash on writing files). * Fixed color bug in graphics interface (named colors work now). * Fixed limit cycle minor ID number issue (limit cycle continuation is no longer considered a sub run...) * Fixed bifurcation match crash for empty-garbage population. * Fixed non-refresh bug in par twiddler. * Fixed aux variable bug in continuation (for now, no aux vars are displayed in continuation output, but it won't just return an MX). -- Emery Conrad Department of Mathematics University of Michigan 4827 East Hall Ann Arbor, MI 48109-1043 (734) 936-9973 http://www-personal.umich.edu/~emeryc |
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From: Emery C. <ec...@vt...> - 2006-02-16 21:43:58
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All,
After a little hiatus (job searched for, job found!), I'm back to
Oscill8 development. Although I expect to have the full 2.0 release out
in the next month or two (with bifurcation matching etc in the
interface), I will probably give many small incremental updates,
starting with today's.
(Tongli Zhang, pay attention to the last one!)
Updates are:
* Add xy data from file adds a black curve now.
* Fixed handling of ' and '' on parameter names.
* Fixed memory leak in Dataset.
* Fixed infinite loop on repeated mxnil error in CVode.
* Enabled random walk bifurcation search to o8core (type
"o8core --help" and look at the bifurcation search opts).
Enjoy,
Emery
|
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From: Emery C. <ec...@vt...> - 2005-11-18 20:24:29
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All, An update for the holiday! I'll refrain from calling this the "Turkey" Release... see notes below for details if you're interested. You need the latest version of the XPPTranslator, v1.04, in order to take advantage of the updates. (The updates only relate to SBW simulation). Also, I've started a little Oscill8 documentation project or devblog, you might call it, to keep track of the trials and tribulation of developing the software. If you're interested, point your browser here http://oscill8.biol.vt.edu/blogs. This is were I'll cull a bunch of the documentation from in the future, as I keep track of new features etc there. Enjoy the holidays, gobble gobble, Emery #==================================================================== # release 1.18.0 notes (2005/11/18) #==================================================================== Updates are: * Implemented more of the SBW sim interface... * Added in "#o8> dep" syntax in the ODE file to store the next velocity name as a dependent species. This is important for SBW interoperability. * Added in "#o8> reaction name vel" syntax to store reaction names that are associated with a particular velocity. Again, this is for SBW interop. |
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From: Emery C. <ec...@vt...> - 2005-11-16 14:32:18
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All,
A couple of (long-awaited) useful features have been added to Oscill8,
including:
* Added aux variable plotting capability. That is, anything marked
with the ODE file syntax "aux x1px2 = x1+x2" will be an extra
variable which you can plot.
* Added SBW simulator interface to o8core; can be run from
SimDriver and JDesigner now.
* Alt-click run TimeSeries is now implemented for TimeSeries,
OneParameter, and TwoParameter runs. This loads the initial conditions
and parameter settings from the clicked-on point into the new run.
Enjoy,
Emery
|
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From: Emery C. <ec...@vt...> - 2005-11-09 21:15:31
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All, There is a new version of Oscill8 available at the usual place. There are a number of new convenient features, including alt-click TimeSeries generation from TimeSeries, OneParameter, and TwoParameter diagrams that will automatically load the initial conditions and parameter settings from the point clicked on so that you can see wave forms associated with particular parameter values (or continue TimeSeries runs). Enjoy, Emery |
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From: Emery C. <ec...@vt...> - 2005-10-20 19:57:05
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All,
Sorry to spam you, but I forgot to mention a few new things from the
last release and I have a nice new release with fully functional
progress bar (so waiting for that limit cycle run to finish doesn't have
to be so painful). In addition, I've added,
1) a tutorial (see documentation in the Help-->General menu under
tutorials)--this was with v1.12.1
2) ignore case feature for model init (converts everything to lowercase
for compatibility with XPP ODE files)
3) right click node selection works properly now.
4) a few other tidbits, see below if you're interested.
Thanks,
Emery
#====================================================================
# release 1.15.0 notes (2005/10/20)
#====================================================================
Updates are:
* Added very fine grained progress indication to all runs types.
#====================================================================
# release 1.14.1 notes (2005/10/20)
#====================================================================
Updates are:
* Added "ignore case" check box to model creation dialog, which
converts everything to lower case. This avoids
case-sensitivity for the symbols defined in the ODE text, and
improves compatibility with XPP.
* Right-click selection actually works now in the run history.
This means that a right click on a node will actually bring
up a context menu for the newly right-clicked node, rather than
the previously selected node, as before.
* Updates to the progress bar (finer grained updates, position).
#====================================================================
# release 1.14.0 notes (2005/10/19)
#====================================================================
Updates are:
* Added rerun mode for ALL runs. This means you can just take
your .o8w file with you (without the data) and rerun the
particular runs you are interested in.
* Changed default NTST to 15 for faster default limit cycle
continuation.
* Fixed runset run config reload (correctly loads previously
stores values).
* Fixed no-log-directory crash error.
* Adjusted GUI look and feel again (DockPadding 12 --> 8).
#====================================================================
# release 1.13.0 notes (2005/10/17)
#====================================================================
Updates are:
* Got o8core running under linux and cygwin (need to check
MacOSX). It doesn't pass 100% of parser tests, but I'll
look into that later.
* Change GUI look and feel (ala Herbert Sauro)
#====================================================================
# release 1.12.1 notes (2005/10/12)
#====================================================================
Updates are:
* Fixed another GUI run hang issue.
* Enabled XP windows sytle (the SEHException has gone away).
* Added a tutorial for the chap10_serious.ode model.
|
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From: Emery C. <ec...@vt...> - 2005-10-20 04:03:27
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All,
Oscill8 has had a few minor changes, but it just might be worth
updating. Highlights of new features include rerunning any run (which
allows you to just take the .o8w file and regenerate runs of importance
without zipping up the entire directory structure--helps with sharing
workspace files), increased speed of default limit cycle continuation
(NTST = 15 by default now, increase if numerical problems result), fixed
RunSet reload run parameters on edit, and adjusted the look and feel to
make things easier to navigate.
Enjoy,
Emery
#====================================================================
# release 1.14.0 notes (2005/10/19)
#====================================================================
Updates are:
* Added rerun mode for ALL runs. This means you can just take
your .o8w file with you (without the data) and rerun the
particular runs you are interested in.
* Changed default NTST to 15 for faster default limit cycle
continuation.
* Fixed runset run config reload (correctly loads previously
stores values).
* Fixed no-log-directory crash error.
* Adjusted GUI look and feel again (DockPadding 12 --> 8).
|
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From: Emery C. <ec...@vt...> - 2005-10-11 17:14:49
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All, Some significant enhancements to the graphics capabilities have finally been made. They include 1) settable line properties (via a right click on the legend)--color, width, alt-width (for stable curves) etc. (style is currently not implemented). 2) settable font size for the plot (from the plot properties dialog) 3) settable legend placement and visibility (from the plot properties dialog--visibility can also be toggled with "l" inside the graphic) Many of you have been asking for these features, and I finally found a few minutes to get it done. Enjoy. Emery |
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From: Emery C. <ec...@vt...> - 2005-10-06 17:06:21
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All,
There are many, many new user-convenience features added to Oscill8 in
v1.11, and I thought it appropriate to say this is a very good time to
update! See details if you like below, but the features generally fall
into these categories:
1) Much improved logging and error handling: helping the user know what
went wrong (see "View->Log Window" for full logs)
2) Data integrity: automatic workspace backups, md5 digest checks on
data, workspace overwrite confirmations, etc
3) Ease of input: input through "Open" now includes ODE/XML/SBML as
valid "openable" file types (workspace is created automatically)
4) Various annoying bugs: increased xpp ODE format compliance, FIXED \
character for line continuation.
I highly recommend a refresh/upgrade now.
Enjoy,
Emery
#====================================================================
# release 1.11.0 notes (2005/10/06)
#====================================================================
Updates are:
* Auto set directory in "New" after file load (last release).
* Auto conversion of ODE file to readable form (\n-->\r\n conv).
* Fixed \ continuation of lines for DOS/Windows \r\n line end
(Bug #1313228).
* Added overwrite confirm when you try to create a new
workspace that will overwrite an old one.
* Added auto backup feature (for data recovery in an emergency).
Your workspace directory now has a "backup" directory which
contains a sequence of last known good workspaces. In the
future, this will only contain a maximum number of files, but
for now (in this oscill8 version), there will be an unlimited
number of copies here... you may want to purge the older ones
if you have disk space problems.
* Added ODE/XML/SBML file to valid "File->Open" options... this will
pass you off to the workspace creation interface.
#====================================================================
# release 1.10.3 notes (2005/10/05)
#====================================================================
Updates are:
* Fixed error handling for model init (o8core properly exits)
(Bug #1313228).
* Added o8core log output to GUI log.
* Changed the look/feel of log form; need to add convenient
highlighting etc.
#====================================================================
# release 1.10.2 notes (2005/10/04)
#====================================================================
Updates are:
* Fixed minor silliness with an extra data point (in very rare
cases).
* Added parsing and model speed test cases to o8core_tests.
#====================================================================
# release 1.10.1 notes (2005/10/04)
#====================================================================
Updates are:
* Addressed mutiple problems with simulator re: xpp simulation
test suite (thanks Nick); only one of the remaining failing
tests (arcsin) is a real fail, the rest are unimplemented
features.
* Fixed error in global flag parser (which was introduced in
v1.10.0 when I added a slightly sloppier syntax variant).
|
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From: Emery C. <ec...@vt...> - 2005-09-30 16:29:43
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All,
Several additions and fixes of interest:
* Added heav(x) function.
* Added a sloppier syntax for global to accommodate XPP users!
* Added implicit "t" symbol for time. Now you can include time
dependent terms in your ODEs and discrete events!
* Fixed @dt parse from ODE file to read floats, not ints.
* Added data corruption protection; there is now an md5 hash
produced for output; if the output changes from its first run, a "Bad
Data" message shows up in the plot and you need to rerun to refresh the
data. (Rerun currently only works for RunSets, though... I'll enable it
for regular runs later).
* Fixed XY data load to be more robust (you can have separate
columns by spaces, tabs, commas, and a few other characters)!
* Added right click to run time series from a time series graph.
* Fixed time series run to include the FINAL point.
* Fixed -ts:out to give TIME only ONCE!!
* Fixed time series run from command line to parse out XPP-style @
options in place of the command line options (you must, however, specify
"-ts:format xpp" if you choose to leave out the -ts:output option).
* updated error message passing between o8core and GUI, now you get
some kind of semi-useful message!
Enjoy,
Emery
#====================================================================
# release 1.10 notes (2005/09/30)
#====================================================================
Updates are:
* Fixed @dt parse from ODE file to read floats, not ints.
* Added less/greater than functions to valid operators,
ONLY WITH PROPERLY PARENTHESIZED EXPRESSIONS!! That is,
2+2>2+1=2+(2>2)+1=2+0+1=3, not 0 for false!!
Also note that this doesn't include <= and >=. I'll fix this
in the future.
* Added heav(cond) function.
* Added conversion for certain special character sequences,
including > and <.
* Added a sloppier syntax for global to accommodate XPP users!
* Added implicit "t" symbol for time. Now you can include time
dependent terms in your ODEs and discrete events!
#====================================================================
# release 1.9.32 notes (2005/09/29)
#====================================================================
Updates are:
* Added data corruption protection; there is now an md5 hash
produced for output; if the output changes from its first run,
a "Bad Data" message shows up in the plot and you need to rerun
to refresh the data. (Rerun currently only works for RunSets,
though... I'll enable it for regular runs later).
#====================================================================
# release 1.9.31 notes (2005/09/28)
#====================================================================
Updates are:
* Fixed XY data load to be more robust (you can have separate
columns by spaces, tabs, commas, and a few other characters)!
* Added right click to run time series from a time series graph.
* Fixed time series run to include the FINAL point.
* Fixed -ts:out to give TIME only ONCE!!
* Fixed time series run from command line to parse out XPP-style
@ options in place of the command line options (you must,
however, specify "-ts:format xpp" if you choose to leave out
the -ts:output option).
#====================================================================
# release 1.9.30 notes (2005/09/28)
#====================================================================
Updates are:
* updated error message passing between o8core and GUI, now
you get some kind of useful message!
|
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From: Emery C. <ec...@vt...> - 2005-09-27 20:53:05
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All,
There have been significant enhancement to Oscill8's expression parser
over the last day or so. We now allow many common mathematical functions
(exp, log, etc... see list below) and arbitrary user defined functions
(for those of you using GK and BB, etc). In addition, the ODE/Expression
parser is smart enough to do each call to a user defined function ONLY
once, store the value and reuse it where possible to cut down on the
overhead.
In addition, you can now run TimeSeries from the command line using
o8core (see below for the relevant options). [Nick, this should be ready
for JigCell to use].
Enjoy,
Emery
#====================================================================
# release 1.9.29 notes (2005/09/27)
#====================================================================
Updates are:
* added some common functions to expression parser. This includes
exp, log, log10, ln, sin/cos/tan, asin/acos/atan,
sinh/cosh,tanh, abs. Use this some care... to keep speed high,
I don't check arguments to make sure they are valid (e.g,
acos(2)=#-1.IND or something ugly).
* added user definable functions to ODE spec. That is user,
can define MyFunc(x,y)=x^2+y and then use it in their ODE def.
Beware not to use valid parameters/state variables for the names
of the arguments to these functions...
* added capability to run a TimeSeries from the command line w/o
needing to write your own .o8r file. The relevant pars are
-ts:out, -ts:format, -ts:t_end, -ts:n_points, -ts:rtol,
and -ts:atol. Enjoy (you can output to xpp, o8p, columnar etc).
|
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From: Emery C. <ec...@vt...> - 2005-09-12 15:45:54
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All,
I've fixed several small bugs and annoyances; the highlights are that
graphs are prettier (intelligent choice of tic marks so that you get
nice labels on the axes) and the export/import data features are
enhanced (in addition to a number of bugs that have been causing
anomalies and crashes!).
Enjoy,
Emery
#====================================================================
# release 1.9.27 notes (2005/09/12)
#====================================================================
Updates are:
* Graphs are now sexier! Tic marks and ranges are intelligently
set and labels are nice round (minimal number of sig digits)
viewable numbers.
* Adjusted point tolerance (easier to get alt-click continuation
options).
* Renamed labels for LP bif points (SN and CF are distinguished).
* Fixed check boxes for active column in model data display.
* Fixed "close-to-zero" label snafu...
#====================================================================
# release 1.9.26 notes (2005/09/08)
#====================================================================
Updates are:
* Fixed bug #1284230 (graphs not representative of what AUTO
returned; problems was overflow errors in reading doubles
since AUTO was outputting 1e-320 type doubles; created
thresholding for output of double from AUTO).
* Fixed bug #1242323, the disappearing notes issue.
* Fixed annoying auto zoom bug on startup (after open and a
double click, the zoom lines would be there. Now though you
have to have the focus on the plot (double click in the plot)
to do zooming).
* Fixed bug #1284229, deleting a subrun of an instance of a
runset will not crash anymore... it is prohibited for the
time-being.
#====================================================================
# release 1.9.25 notes (2005/09/07)
#====================================================================
Updates are:
* Fixed Export/Add XY data to do ONLY first active curve. The
Export Raw Data will export all curve data in a plot, but
cannot be loaded right now.
|
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From: Emery C. <ec...@vt...> - 2005-09-07 18:31:20
|
All, I finally found a bit of time to fix limit cycle continuation (new version is 1.9.24); similar to the sample period/min/max feature, limit cycle continuation (right click on Hopf bifurcations to continue this way) returns the period and min/max of each component on the limit cycle. WARNING: the default tolerances etc for limit cycle continuation are quite low and will take a very long time for large models especially. Easing up on DS, NMX and possibly the EPS* constants will make your life easier. In a future release, I will set more reasonable default values for these parameters, but for now, better safe than sorry (but be patient!) Enjoy, Emery |
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From: Emery C. <ec...@vt...> - 2005-08-18 20:12:55
|
All, There was a rather serious bug in CVODE (derived from SUNDIALS v2.2.0) which caused (sometimes terrible) inaccuracies in integration, especially in models with discrete events. This has been patched pending an official fix from the developers of CVODE; things should been in order and (assuming I diagnosed the bug correctly) identical to any final fixes from LLNL. Those who are currently relying on results from Oscill8 should update as soon as possible. Thanks, Emery |
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From: Emery C. <ec...@vt...> - 2005-08-05 19:32:43
|
All,
Just a quick note: Oscill8 has reached a milestone of sorts. Oscill8
(the GUI, not the core) is now working well as an SBW module. You can
use it from JDesigner 1 or 2 to load up your models directly from the
SBW menu in JDesigner.
Enjoy,
Emery
P.S. Here's a complete list of bug fixes and updates since 1.9.18 (just
a few days ago).
* Fixed divide by zero error when a user forgets to input some
information and the expected number of outputs from a run is
zero.
* Compatible with JDesigner2.0.23+.
* Multiple loads possible from JDesigner (different models etc).
* Cleaned up plot wipe on new model load.
* Enhanced error handling for SBW interface to report propagated
errors from SBW.
* Fixed installer to run the sbwregister command for oscill8
and o8core.
* Added index, label, type to export of raw data from a graphic.
* NOTE: until the next release of SBW (which will include
the new XPP translator service), you can get the necessary
modules from http://public.kgi.edu/~rrao/XPP.
|
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From: Emery C. <ec...@vt...> - 2005-08-02 17:06:18
|
All,
There is a pre-release of Oscill8 v2 out (current version is
1.9.18--full v2 will be early in the fall). There are many new features
and enhancements, including SBML input, SBW module mode, bifurcation
matching and searching (command line version only right now--will be GUI
version in v2 release), print summary features, parameter twiddler and
run set functionality. The official v2 release will document all of the
new features in detail (none of these features are properly documented
yet), but here are some of the highlights of the latest:
* SBW module mode, i.e., run from JDesigner SBW menu passing SBML
version of model (this requires SBW and the XPP converter tools to be
installed, see next).
* SBML input (using SBML --> ODE conversion SBW utility thanks to V.
Ravi Rao of KGI)
* RunSet functionality with a parameter twiddler and real-time
multigraph view update (define set of runs and use a parameter twiddler
to see graphs update in real-time)
* Full discrete event support (via XPP "global" syntax in the ODE
file). This is still a bit buggy for a small set of models, but works
for many.
* Drag and drop plot combining (graph one run and drop it on the
graphic for another and they are combined)
* SamplePeriodMinMax feature (sample the period and amplitude of
limit cycles in oscillatory region of parameter space)
* Fixed edge interpolation in graphics
* Cntl-S save to bmp/png etc from a graphic.
* Added save to bmp and print features; run context menu has nice
print summary feature which encapsulates the graph and other info for a run.
* Many updates to matching... added relative matching, match classes
now allows multiple identical p-value matches, takes best.
* Fixed Cntl+S to bmp to 640,480 size for niceness.
* Added zoom lines.
* Fixed nit/nit1 infinite loop in AUTO.
* Added -c/--coreport command line option so user can run multiple
oscill8/o8core copies on a single machine.
* Bifurcation Matching is working nicely in core.
Enjoy,
Emery
|
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From: Emery C. <ec...@vt...> - 2005-05-11 17:52:26
|
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 |
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From: Emery C. <ec...@vt...> - 2005-05-02 18:05:34
|
All, I'm happy to announce the first official release of the Oscill8 Dynamical Systems Toolset, v1.1.0. Please see attached README.txt for installation instructions (windows only; linux version planned for June 2005). You may also visit http://oscill8.sourceforge.net/doc for more comprehensive user documentation. For those of you in the Bio-SPICE community, there is also an initial beta set of analyzers for the Dashboard which can be downloaded/installed via the Dashboard Update Center (it should be there shortly--you can also download the netbeans module file directly from the "oscill8 biospice" link at http://sourceforge.net/projects/oscill8). Still much work to do, but I hope you find Oscill8 to be useful!! I'm certainly enjoying it ;-) Cheers, Emery Conrad |
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From: Emery C. <ec...@vt...> - 2005-04-18 20:21:31
|
All, Oscill8, v1.0.22, includes many upgrades from v1.0.11 (last email sent); this is a milestone prior to the v1.1 release, which has been postponed until May 2nd to coincide with the BioCOMP meeting. Most importantly, there is 1) a bit of user documentation (first draft/outline--adding it in as we speak), 2) AUTO/CVODE numerical parameters are now exposed, 3) fixed bug in expression parser that was causing odd behavior for very isolated cases, and 4) limit cycle continuation (only works for small models, isolated cases... currently in the process of fixing this bug). There are a number of really cool new features being added in right now (bifurcation searches, matching, etc) and fixing many outstanding bugs/issues people have been running into. Enjoy, Emery Conrad |
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From: Emery C. <ec...@vt...> - 2005-03-21 21:54:27
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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 |
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From: Emery C. <ec...@vt...> - 2005-03-18 14:10:36
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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 |
