problems running biotapestry

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Streit, Andrea

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Dec 9, 2011, 8:53:24 AM12/9/11
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Hi

I cannot run biotapestry on my Mac (OSx 10.6.8) anymore neither locally nor from the biotapestry site (used to work fine, works fine on PC)
error: "unable to launch the application:
Could not parse launch file. error at line 1."
Any idea?
Thanks
Andrea

Andrea Streit, PhD
Department of Craniofacial Development
King's College London
Guy's Tower Wing, Floor 27
London SE1 9RT
UK
andrea...@kcl.ac.uk
Tel 44-20-71881802
Fax 44-20-71881674

William Longabaugh

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Dec 9, 2011, 7:02:56 PM12/9/11
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Andrea:

Thanks for the bug report. This is the first I have heard about this,
so more info would be useful.

Did you just recently do a software update on your Mac? I'm guessing
that perhaps the recent release (Java for Mac OS X 10.6 Update 6)
has broken things.

If you do the following:

1) Click on the Apple menu
2) Click on "About this Mac"
3) Click on "More Info"
4) Select Software > Frameworks
5) Look at the "JavaVM" version.

What does it say? Mine is slightly older, and reads as 13.5.0.

Is it possible to send me a screen shot of the error dialog?

I will start tracking this down...

Sorry for the inconvenience.

Bill

William Longabaugh

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Dec 9, 2011, 7:29:05 PM12/9/11
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Andrea:

I have just updated my Mac to the latest Java release
from Apple, and I can't seem to reproduce the problem
yet. Has there been any other recent software updates
on your Mac since BioTapestry last worked for you
(e.g. Safari update, installing a new Web browser)?

Another thing to check is to use the Finder to go to
Applications::Utilities::Java Preferences to run
that program. A screen shot of the "General" tab
would be useful. Depending on what I found out from
that, I might have you do the "Delete Files..." off
the "Network" tab, or have you select "Show console"
under the Java console setting on the "Advanced" tab,
then try to run the program, and send me the results.

You can email me directly with the various screen
shots, instead of using this mailing list. I will
post the outcome of the troubleshooting back to this
list.

Thanks,

Bill

zuo

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Dec 20, 2011, 5:04:56 AM12/20/11
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Dear  Biotapestryer, 

maybe I missed some points, but a quick answer would be very helpful. 

Regarding 'Experimental Data for a link', it sounds only show user's text, not even well for a pubmed abstract link. Unfortunately we have some expression images of embryos for the link. is there any way to use a browser (IE, FF or Chrome etc.) for showing experimental data or is any method to link this with external data, saying, a web link?

many thanks.     

Kind Regards

 
jié zuo 
 
Email: po_...@yahoo.com
Tel: +44 (0)1865 222470
Fax: +44 (0)1865 222501

William Longabaugh

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Dec 20, 2011, 12:50:58 PM12/20/11
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Currently, the experimental data for a link is presented using
Java's build-in HTML rendering engine. Because of this, the
types of web pages you can show are pretty limited. The idea
is that you could create a simple set of pages on a local web
server that would be referenced to present the data for each link.

Given this framework, images are easy to support, as your
set of simple html pages would also include <img> tags that
reference the images you need that are also hosted on the server.

While it would be nice to be able to use the user's web
browser to display the data, there is a significant reason that
is not supported at the moment. This is because the BioTapestry
Viewer, used to publicly share networks on the web, is designed
to operate as an _unsigned_ Java Web application, so that
the casual user is not put off by having to accept that the
Java program wants special permissions to access the user's
computer. This introduces restrictions on what resources
BioTapestry can access, and what web sites it can visit. And
while the BioTapestry Editor is signed and able to do these
things, somebody setting up a network for public read-only
access using the Viewer could be lured into setting up a
complex set of evidence pages that would break the moment
they went to share the results over the web.

Sorry there is this restriction, but the thinking is that
it is not impractical to create and host a set of web pages
to present the evidence supporting the network. Perhaps
we could try to make this somewhat more flexible in future
releases, but it will take some effort.

Bill

zuo wrote:
> Dear Biotapestryer,
>
> maybe I missed some points, but a quick answer would be very helpful.
>
> Regarding 'Experimental Data for a link', it sounds only show user's
> text, not even well for a pubmed abstract link. Unfortunately we have
> some expression images of embryos for the link. is there any way to use
> a browser (IE, FF or Chrome etc.) for showing experimental data or is
> any method to link this with external data, saying, a web link?
>
> many thanks.
>
> Kind Regards
>
>

> ji� zuo

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zuo

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Dec 21, 2011, 6:10:48 AM12/21/11
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Thanks a lot for the clarification. Bill. We do have a local server for the expression image data. I'll try to link that. 

Merry Xmas and Happy New Year 

Kind Regards

 
jié zuo
--- On Tue, 12/20/11, William Longabaugh <wlong...@systemsbiology.org> wrote:
>  jié zuo  Email: po_...@yahoo.com

> Tel: +44 (0)1865 222470
> Fax: +44 (0)1865 222501
>
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