after a longer time I downloaded the latest version of JDesigner (2.0.30) and tested it on SBW2.5 under win2k. It really has improved a lot over the latest version I used (1.936). The tree view of the SBML model is very helpful and also the option to design new icons for the species.
However, there are also some problems and I wonder if they are known and will be fixed in a new release.
1)
If I add formated text to the canvas it is saved in the SBML file (including formatting information), but when I read the model file, the formatting ist lost.
2)
When I create a PNG file via ExportBitmap there are problems if the canvas contains alias nodes that have outgoing regulator arrows. In that case the alias nodes AND the original nodes have outgoing regulator arrows the PNG picture. This bug also occurs during printing.
Furthermore, if I display the reaction name labels and then try to export the model to a PNG I get the error message: "Not enough storage is available to process this command".
3)
It is great that I can create new icon shapes and add them to the list of available icon shapes. But is there also a way to delete shapes from the list ?
4)
The "view model equations" command is not working :-(
5)
The layout information is not backward compatible to 1.980 ?!
6)
When I try to copy a node that has alias nodes via Ctrl-V I get the message box
"Node is a parent node with one or more alias nodes, deleting the parent node will delete all alias nodes. Are you sure you want this?"
But it doesn't matter if I press yes or no, the message box does not disappear. I have to kill JDesigner from the TaskManager :-(
Furthermore, I did not want to delete the node in the first place. I tried to copy it!
If these problems could be fixed soon, I would be a happy user of JDesigner.
Best regards,
Axel Kowald
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Thanks for your message, it is very useful to get any feedback.
We are looking into the issues you raised.
Issues 2) and 4) have been fixed and will go out with version 2.0.31. In issue 2) we weren't able to reproduce the error message about out of space when saving a PNG file with reaction names visible. Can you reproduce this problem with only a single reaction and two nodes?
Ww weren't able to reproduce Issue 6) probably because we're not following your description properly. For example we place one node on the canvas and create an alias node from it. We select the parent node and Ctrl-C followed by Ctrl-V, we don't get the message you indicate, can you confirm this?
Issue 5) is a difficult one to address. I think the only thing we could do is save the layout in the basic SBML layout that is being proposed on the SBML forum. This layout information only has position information, no rendering information. I assume this would be sufficient?
Issue 1) needs to be addressed, thank you for pointing it out.
Issue 3), to delete from the icon list, select the icon from the left had list and press the delete key. This isn't obvious so you probably wouldn't have spotted it.
Thanks again for the message. I think in the next release we can get issues 1), 2), 3), 4), and 6) resolved. Issue 5) (backward compatibility) may take a litte more time.
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I downloaded SBW latest version. installed on WinXp tried running Jarnak from JDesigner. It gives error.
Only version 2.3 works on XP SP2.
So I wanted it to try it on linux. Even worse, although installation was succesful. I could not figure out how to run JDesigner or Jarnac. It appears there is absolutely no documentation for running sbw and its associated programs in linux.
Has any body succeed running latest simultion service with in JDesigner of sbw 2.4/later on xp?
if so please indicate if any tweaks needed while installing or after installation configuration.
If some one has suceeded kindly let me know: my email is pradeeps_20002000@yahoo.com.
Thanks in advance.
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i just wanted to point out, that SBW will definitely work on XP ... please let me know about any problems you had with it.
A couple of minutes ago i released a bugfix version of 2.5.5 that takes care of minor glitches. Still ... JDesigner & Jarnac were written for windows. Thus the only way to get them running on Linux would be using Wine ...
The linux installer currently comes only with a handfull of tools. Mainly SBML conversion & simulation modules.
Sorry for that
Frank
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Hello everybody,
after a longer time I downloaded the latest version of JDesigner (2.0.30) and tested it on SBW2.5 under win2k. It really has improved a lot over the latest version I used (1.936). The tree view of the SBML model is very helpful and also the option to design new icons for the species.
However, there are also some problems and I wonder if they are known and will be fixed in a new release.
1)
If I add formated text to the canvas it is saved in the SBML file (including formatting information), but when I read the model file, the formatting ist lost.
2)
When I create a PNG file via ExportBitmap there are problems if the canvas contains alias nodes that have outgoing regulator arrows. In that case the alias nodes AND the original nodes have outgoing regulator arrows the PNG picture. This bug also occurs during printing.
Furthermore, if I display the reaction name labels and then try to export the model to a PNG I get the error message: "Not enough storage is available to process this command".
3)
It is great that I can create new icon shapes and add them to the list of available icon shapes. But is there also a way to delete shapes from the list ?
4)
The "view model equations" command is not working :-(
5)
The layout information is not backward compatible to 1.980 ?!
6)
When I try to copy a node that has alias nodes via Ctrl-V I get the message box
"Node is a parent node with one or more alias nodes, deleting the parent node will delete all alias nodes. Are you sure you want this?"
But it doesn't matter if I press yes or no, the message box does not disappear. I have to kill JDesigner from the TaskManager :-(
Furthermore, I did not want to delete the node in the first place. I tried to copy it!
If these problems could be fixed soon, I would be a happy user of JDesigner.
Best regards,
Axel Kowald
Thanks for your message, it is very useful to get any feedback.
We are looking into the issues you raised.
Issues 2) and 4) have been fixed and will go out with version 2.0.31. In issue 2) we weren't able to reproduce the error message about out of space when saving a PNG file with reaction names visible. Can you reproduce this problem with only a single reaction and two nodes?
Ww weren't able to reproduce Issue 6) probably because we're not following your description properly. For example we place one node on the canvas and create an alias node from it. We select the parent node and Ctrl-C followed by Ctrl-V, we don't get the message you indicate, can you confirm this?
Issue 5) is a difficult one to address. I think the only thing we could do is save the layout in the basic SBML layout that is being proposed on the SBML forum. This layout information only has position information, no rendering information. I assume this would be sufficient?
Issue 1) needs to be addressed, thank you for pointing it out.
Issue 3), to delete from the icon list, select the icon from the left had list and press the delete key. This isn't obvious so you probably wouldn't have spotted it.
Thanks again for the message. I think in the next release we can get issues 1), 2), 3), 4), and 6) resolved. Issue 5) (backward compatibility) may take a litte more time.
I downloaded SBW latest version. installed on WinXp tried running Jarnak from JDesigner. It gives error.
Only version 2.3 works on XP SP2.
So I wanted it to try it on linux. Even worse, although installation was succesful. I could not figure out how to run JDesigner or Jarnac. It appears there is absolutely no documentation for running sbw and its associated programs in linux.
Has any body succeed running latest simultion service with in JDesigner of sbw 2.4/later on xp?
if so please indicate if any tweaks needed while installing or after installation configuration.
If some one has suceeded kindly let me know: my email is pradeeps_20002000@yahoo.com.
Thanks in advance.
Hi,
i just wanted to point out, that SBW will definitely work on XP ... please let me know about any problems you had with it.
A couple of minutes ago i released a bugfix version of 2.5.5 that takes care of minor glitches. Still ... JDesigner & Jarnac were written for windows. Thus the only way to get them running on Linux would be using Wine ...
The linux installer currently comes only with a handfull of tools. Mainly SBML conversion & simulation modules.
Sorry for that
Frank