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Re: [Oscill8-devel] Re: inspector
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From: Emery C. <ec...@vt...> - 2005-06-07 12:52:38
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Herb,<br>
<br>
I agree. Technically, the bsam branch isn't for release; this is my
testing branch for the new features I'm currently developing. It wasn't
actually intended for anyone to use, but a few folks asked me to
release it on sourceforge so I did. I'll release it officially later in
June and it should be stable and working at that time.<br>
<br>
Also, I'm going to switch the installation over to a USER installation,
rather than an ADMIN install. This will make things less dependent on
security; there are students who want to use Oscill8, but can't because
they don't have admin privileges on their machines. I will change this
for the next "real" release.<br>
<br>
About it's fragility for model input, that's for sure. If you get the
model just right, everything works smoothly (most of the time). But
that step isn't yet made simple for the user. I plan on making that a
bit more straight-forward in the future.<br>
<br>
If you guys have spare time and would like to, an SBW module that
converts SBML --> ODE would be nice... You basically have that in
Jarnac already, except you don't remove differential eqs for dependent
species. All you'd need to do would be to remove ODEs for those
dependent species, and then you'd have a bifurcation ready model.<br>
<br>
Anyway, I'm in the process of adding a few fundamental new features
right now; the bsam branch is going to remain rather unstable for
another week or two at least. At that point, I would really like to
finalize the SBW connection so that we can all use things smoothly
through JDesigner etc. If you have the time and/or the desire, adding a
Jarnace getReducedODEList() would be nice... that would do it for
bifurcation analysis.<br>
<br>
Take it easy,<br>
<br>
Emery<br>
<br>
<br>
Herbert Sauro wrote:
<blockquote
cite="mid...@DE..."
type="cite">
<pre wrap="">Emery, version 1.9.7 is not well, it's quite a difficult version to get
running. The dependence on jigcell is one issue, I don't think many
users would realize that they must install jigcell. Also it's quite
picky about models, some work some don't (I think it's the jigcell bit
which is having problems). Also on machines which are connected to the
network there are security issues with using program files to sort
temporary information, i.e it won't let your software save files to this
area (I have the same problem with my software).
If there is anything we can do let me know.
Herbert
-----Original Message-----
From: Emery Conrad [<a class="moz-txt-link-freetext" href="mailto:ec...@vt...">mailto:ec...@vt...</a>]
Sent: Monday, June 06, 2005 11:15 AM
To: <a class="moz-txt-link-abbreviated" href="mailto:osc...@li...">osc...@li...</a>
Subject: [Oscill8-devel] Re: inspector
Herb,
1.9.7 is on the bsam branch, which is unstable at this point; the HUH?
error happens when Oscill8 doesn't know where the install directory
is... Frank said he was having this trouble too... it might work if you
reboot (did you install Oscill8 to a different directory than previous
installs... this might cause it as well). Otherwise, make a c:/log
directory; that should be a temporary fudge.
This SBW interface relies on JigCell right now, which is broken for sbml
conversion. Best way for now is to get the ODEs from JDesigner or
something, and remove the conservation relations by hand, defining extra
"total" parameters as needed.
Sorry I couldn't be more helpful... after next week Monday I'll put
effort into getting things running smoothly with SBW.
Emery
Herbert Sauro wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Frank just showed me the lastest source under the bsam branch.
However, I still get a crash when I call oscill8 from sbw.
Herbert
</pre>
</blockquote>
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