RuleBender-2.3.2

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Installation instructions

Minor changes

• Underlying BioNetGen version ticked up to the latest release (2.5.1)

Build Details

• Built with Eclipse Neon 3 for RCP and RAP developers (4.6.3, build id: 20170314-1500) for Linux 64-bit

RuleBender-2.3.1

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Minor changes

• Underlying BioNetGen version ticked up to the latest release (2.5.0)
• BioNetGen folder is now version agnostic
• Underlying BNG syntax parser updated to reflect recent additions to BNGL

Bug Fixes

• Fixed a bug where an exception that was thrown wasn't being caught correctly, leading to compiler errors
• Fixed a bug where if you selected recover workspace, you can't get switch workspace dialog again
• Attempts to fix a windows specific issue where the simulator path had an extra "/", leading to the RuleBender not being able to find the simulator

Build Details

• Built with Eclipse Neon 3 for RCP and RAP developers (4.6.3, build id: 20170314-1500) for Linux 64-bit

RuleBender-2.3.0

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New Features

• You can now highlight molecules from within BNGL editor and it will highlight the corresponding molecule in the contact map and every instance of the molecule in the editor. The selection has to either match the full molecule expression or the exact molecule name. If the highlighting doesn't seem to be working please try to click on the BNGL tab and re-try, especially for the Windows version of RuleBender.

Minor changes

• Underlying BioNetGen version ticked up to the latest release (2.4.0)
• Icons changed to PNG format from GIF format to comply with up-to-date Eclipse standards

Bug Fixes

• Fixed a bug where left clicking on a bond with a single rule definition caused a null pointer exception
• Fixed #200 where continuation line in observables section caused simulation failure
• Fixed #205 where a numberic line label caused the underlying BNG console to crash. If the BNG console crashes a new one should be opened, preventing future bugs of this type.

Notes

• There is a current known bug where the path to the simulator is incorrect by default, only observed in Windows version so far and it's not consistent. Sometimes there is an extra "" at the beginning of the simulator path. If your simulator doesn't seem to be working, please go to Window -> Preferences -> Simulator and if there is an extra "" at the beginning of your simulator path, remove it and click Apply and OK. If that doesn't work try to Browse and find the BioNetGen-2.4 folder under the installation folder.

Build Details

• Built with Eclipse Neon 3 for RCP and RAP developers (4.6.3, build id: 20170314-1500) for Linux 64-bit