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SemBioProcess
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SemGen
A tool for semantics-based annotation and composition of biosimulation models
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Support specifying sources and sinks for force properties
#286
maxneal
closed
5 years ago
0
Support showing/hiding certain types of codewords in the Annotator interface
#285
maxneal
opened
6 years ago
0
Hide classes that should not be used for annotation when searching the OPB
#284
maxneal
opened
6 years ago
0
rice_winslow_jafri_1999 example model doesn't load in Project Tab or Annotator
#283
maxneal
closed
5 years ago
1
When writing out to SBML, need to ensure that unit names are SBML-valid
#282
maxneal
closed
6 years ago
1
Names of SBML compartments that are custom physical entities are being written out in CASA file which duplicates info
#281
maxneal
closed
5 years ago
1
Add indicator to node key to show they can be toggled
#280
GrahamKim
closed
6 years ago
0
Entering a space in the Project Tab search bar moves visualization nodes even if "fix nodes" is selected
#279
maxneal
closed
6 years ago
0
Incorrect sinks and mediators shown in "Node Info" box of right fly-out panel in Project Tab
#278
maxneal
closed
6 years ago
0
Hierarchical visualization for PhysioMaps
#277
GrahamKim
opened
6 years ago
0
Annotator fails to open
#276
GrahamKim
closed
6 years ago
1
Need a better way to highlight node search results on the Stage
#275
GrahamKim
closed
6 years ago
0
Make sure that example models can be loaded into Project Tab
#274
maxneal
closed
6 years ago
1
SBML and CellML need to be written out in UTF-8 format
#273
maxneal
closed
6 years ago
3
Opening a submodel while nodes are fixed should only redraw the necessary nodes.
#272
GrahamKim
closed
6 years ago
0
Errors in CellML units when translating from a source JSim model description
#271
nickerso
opened
6 years ago
1
Need to make sure that all FMA IDs used in previously annotated models are up to date
#270
maxneal
closed
6 years ago
2
Clicking on node type circle icons in upper right fly-out should show/hide nodes
#269
maxneal
closed
6 years ago
0
No search when making new custom term that is not a rate variable
#268
carlsonbrian
opened
6 years ago
1
window pop under
#267
carlsonbrian
closed
6 years ago
1
Source code panel in Annotator scrolls when attempting to highlight multiple lines
#266
maxneal
closed
6 years ago
0
Support read/write of SBML models with function definitions
#265
maxneal
closed
6 years ago
2
Should be able to draw a bounding box starting within a model's hull
#264
maxneal
closed
6 years ago
1
Read/write COMBINE archives and associated semantics files
#263
maxneal
closed
6 years ago
1
"Error javascript: undefined" when you close multiple models, perform an extraction, then perform a merge
#262
maxneal
closed
6 years ago
1
"Select Node Inputs" doesn't seem to do anything when viewing a PhysioMap
#261
maxneal
closed
6 years ago
3
Extraction following a merge performs multiple extractions
#260
maxneal
closed
6 years ago
1
Closing a model in a Project Tab that is used in an Active Task throws Null Pointer Exception
#259
maxneal
closed
6 years ago
1
Remove extraction scissors from Project Tab GUI
#258
maxneal
closed
6 years ago
2
Can't close merged model after adding it to project
#257
maxneal
closed
6 years ago
1
CV+BARO merge doesn't save out
#256
maxneal
closed
6 years ago
1
Nodes should remain highlighted after extraction and graph shouldn't move
#255
maxneal
closed
6 years ago
7
Attempting to select all nodes with bounding box leaves one node unselected
#254
maxneal
closed
6 years ago
0
Cancelling merge save-out should just close the save dialog
#253
maxneal
closed
7 years ago
4
PhysioMap Extract sometimes fails if the term has a '+'
#252
thompsct
closed
7 years ago
1
Manual mapping during semantic resolution throws IndexOutOfBoundsException
#251
maxneal
closed
7 years ago
3
Extracting a mix of submodels and dependency nodes sometimes fails with "Uncaught TypeError: Cannot read property 'graph' of null" in dependencyNode.js:78
#250
maxneal
closed
7 years ago
3
Extracting unselected nodes in a physiomap extracts entire model
#249
maxneal
closed
6 years ago
7
The auto-copy button doesn't appear in the annotation panel for the current codeword when you toggle the "Auto-copy annotations to mapped variables" button.
#248
maxneal
closed
5 years ago
1
Hiding Entity nodes on Physiomap breaks the visualization. Hiding Unspecified ndoes on Physiomap doesn't actually hide Unspecified nodes.
#247
maxneal
closed
7 years ago
3
Toggling "Center Graph" then moving the hull causes nodes and links to misalign.
#246
maxneal
closed
7 years ago
2
Dependency visualizations don't show model-model connections for Pandit-Hinch merge
#245
maxneal
closed
7 years ago
2
Can't load models into project tab after cancelling out of a merge
#244
maxneal
closed
7 years ago
0
"Replace and Remove" on a physical process doesn't replace the old process in composites
#243
maxneal
closed
7 years ago
0
Show confirmation message when user adds custom entity or process to term library
#242
maxneal
closed
7 years ago
0
Cannot save out model after removing a composite annotation
#241
maxneal
closed
7 years ago
0
Legacy code for CV and BARO models no longer at their URLs
#240
maxneal
closed
7 years ago
1
Save, Save As and Export items in File menu should be disabled on startup, and should only be enabled when they can actually be used
#239
maxneal
closed
7 years ago
0
Unspecified source/sink node is grayed-out in visualization key by default
#238
maxneal
closed
7 years ago
0
Extractions produce empty models
#237
maxneal
closed
7 years ago
5
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