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Description
Motivation
- user interface bugs place VCell in a bad light - leading the user to judge the quality of the underlying product with suspicion.
Completion Criteria
- all VCell UI bugs that are likely to be encountered should be fixed or otherwise accommodated (e.g. remove functionality)
- all VCell UI enhancements implemented or moved to other Epics.
Tasks (bugs)
- Results Graphing Functions errors for Moving Boundary Simulations #146
- Copy and Paste does not paste multiple reactions #150
- Scan parameter menu does not automatically pop up on Macs #157
- Expand identification of catalysts with dashed line to situations where catalyst species is part of a gobal parameter #176
- Include species with D=0 in "Post Processing Stats Data" #179
- ODE solver selection menu - change default solver to "Autoselect IDA or CVODE" #183
- Geometry editor bug: padding to add background pixels at edges of domain adds new "background" compartment if original background was renamed in the geometry. #194
- Ensure go back to original location in Model pane after clicking within database pane #203
- Bug when creating geometry if change subdomain name error window pops up that is subsequently ingnored when name entered. #289
- Defining new Volume Spatial Process in Kinematics always associated with first listed volume Spatial Object #290
- Opening VCell brings prompt to save previously exported sim results. #304
- Local sim results window pops behind the main VCell window #429
- Orphaned shapes remain after deleting species / reactions. #574
- Orphaned metadata remains after deleting species / reactions with RDF annotations. #575
- Global parameters are not listed under the Kinetics tab of a Rule-based Reaction #611
- Movie files from surface view not opened by windows player #772
- Smart Copy/Paste behavior with multiple reactions redesign and implement #792
- Multiple stochastic runs are not displayed #832
- Bug reported: ArrayIndexOutOfBounds in FunctionRangeGenerator.getFunctionStatistics() #858
- Bug with sharing permissions dialog box #869
- Display of simulation results for spatial does not redraw properly when using auto scale at all times #898
- Curator access to database needs fixes, specifically to flags #936
- Local run Par Scan doesn't show full results #950
- Parameter Estimation Window retains old values when switching to a new application in a Biomodel #1024
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Tasks (minor enhancements)
- Make molecular composition layout default in rule-based models #153
- Refine copy and paste for rule-based models #154
- Create annotation fields for Application elements #175
- Allow choice of concentrations or counts for observables and generated species for RBM #182
- Add right click to search reactions for Reaction Table under add a new reaction #184
- Allow assignment of .vcml files to open in VCell in macs #187
- When "Force Continuous" applied in spatial stochastic application, don't allow species to be displayed as number of particles #181
- Need warning when users enter circular expressions #214
- Control Click does not work on Mac when adding states to molecules #219
- Add progress bar or hourglass to time plot to indicate something is happening #221
- Allow right click to paste into initial conditions #222
- Expand search to include annotations #223
- Revive SabioRK using their native search tools #224
- Allow other panes besides reaction diagram to tear off from main workspace #225
- Client Side Annotations Search #751
- Online Annotations Search Window #752
- Error Reports from Contact-Us improvements #835
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Tasks (major enhancements)
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Pool