Re: [SED-ML-discuss] A SED-ML visualizer/editor tool

[Robert P. <rp...@in...>]

Richard,

Did a Windows install and tried to load a file from the examples folder. Got
this exception:

java.lang.ClassCastException: org.eclipse.ui.ide.FileStoreEditorInput cannot
be cast to org.eclipse.ui.IFileEditorInput

Probably I just did something wrong during install, but I would like to look
at your tool. Any ideas?

Thanks.

Robert

On Tue, May 24, 2011 at 11:41 AM, Richard Adams <ric...@ed...>wrote:

> Dear SED-MLers,
>   I'd like to bring to your attention a new tool for editing, viewing and
> running SED-ML files - the SED-ED editor.   The main aims of the app are to
>   make it easier to view and understand the contents of SED-ML documents,
> to provide a UI for validation support, to help  with the generation of
>  XPath expressions accurately, and to provide tooling to support the
> proposed Sedx archive format.
>
>   Features include:
>
>    -  Create   new SED-ML files  from scratch.
>    -  Edit existing SED-ML files  using a graphical/form based editor.
>    -  Auto-generation of XPath expressions to identify selected elements
> and attributes in your model.
>    -  Previews of model changes.
>    -  Model agnostic, at least for editing (simulating  is SBML only ).
>    -  Create, edit, view and expand sedx archive files.
>    -  Graphical layout of SED-ML components (  including autolayout, align,
> zoom).
>    -  SED-ML validation and display of errors/warnings.
>
> Example SED-ML files and sedx archives  are included in the download to
> help you get started.
>
>
> This is an early, alpha release of the editor, which we've tested and
> believe to work on at least the example models, but we'd really appreciate
> any feedback on missing features / bugs to make the application more robust
> at an early stage.
>
> The download instructions and a screenshot are below, for those interested.
>
>  Thanks for your attention,
>
>  Best wishes
>
>      Richard
>
> Availability:
>
> The SED-ED editor is available in three forms:
> 1) As a standalone application for Windows/Mac/Linux, accessible from
> https://sourceforge.net/projects/jlibsedml/files/
>      To get started:
> 1.  Download, unzip, double-click the launch icon in the unzipped folder
> 2. When the application starts, click Window->Help to open the Help pages
> which tell you  how  to use the application and work with the included
> examples.
>
> 2) As a plugin for the SBSIVisual workbench. This has the same editing
> functionality as the standalone app but also enables simulation of  least
> ODE based SBML models, defined in SEDML. To get started:
> 1. Download and extract SBSIVisual from
> http://sourceforge.net/projects/sbsi/
> 2. Follow the instructions in the README file to launch the app for your
> platform.
> 3.  To install the SED-ED plugin,  go to Help->Install New Software, and in
> the ensuing dialog choose the 'Public SBSI' from the 'Work with'  drop down
> list.
> 4. In the list of plugins, select  the 'SEDML tools' and follow the prompts
> to install the plugin.
> 5. Once the plugin is installed you can create a new Project (
> File->New->SBSI system) and drag the examples folder into the new project.
> 6. The SED-ED help pages can be accessed from Window->Help. The example
> files will be put in your application folder.
>
> 3) As an Eclipse plugin. This is essentially the same installation as  2),
> step 3 onwards,  except you'll need to manually add the update site URL
> http://www.sbsi.ed.ac.uk/update in step 3. The example files will be put
> into the top-level folder of your Eclipse install.
>
>
>
>
>
>
>
>
>
>
> Dr Richard Adams
> Software Development Team Leader,
> Centre For Systems Biology Edinburgh
> University of Edinburgh
> Tel: 0131 651 9019
> email : ric...@ed...
> Web: http://csbe.bio.ed.ac.uk/adams.php
>
>
>
>
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
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-- 
Robert D Phair PhD  |  Chief Scientific Officer  |  Integrative
Bioinformatics Inc
Los Altos, CA
www.integrativebioinformatics.com

ProcessDB: Modeling for Biological Discovery