SemBioProcess SemGen issues

SemBioProcess / SemGen

A tool for semantics-based annotation and composition of biosimulation models

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issues

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Current JxBrowser version doesn't support Windows 11

#336 maxneal opened 1 year ago
0
Use ORCID URI as the RDF resource (or OWL individual) for model creators/contributors, if provided

#335 maxneal closed 2 years ago
1
Update DC terms namespace to match OMEX metadata spec

#334 maxneal closed 2 years ago
1
BioModels searches in Project tabs no longer functioning

#333 maxneal closed 3 years ago
1
Use concise form for physical entity composites OMEX metadata files

#332 maxneal closed 3 years ago
1
How to preserve identity annotations on SBML reactions?

#331 maxneal closed 2 years ago
1
Cannot load CellML models from the same OMEX archive in separate Annotator tabs

#330 maxneal closed 3 years ago
1
Variables with annotations in the groups of "encapsulation" are not detected by SemGen for auto-mapping while merging.

#329 Niloofar-Sh closed 4 years ago
5
Merging multiple models at once

#328 Niloofar-Sh opened 4 years ago
0
File open dialog appears behind main SemGen window on Mac

#327 maxneal closed 3 years ago
1
For resources in OMEX metadata files that are not resolvable in model code, only use fragment for URI

#326 maxneal closed 3 years ago
1
Error when launching SemGen on linux (ubuntu 18.04)

#325 matthiaskoenig opened 5 years ago
4
Integration with ontology lookup service

#324 matthiaskoenig closed 2 years ago
3
SG becomes unresponsive after mutliple uses on Mac OS X Mojave

#323 maxneal closed 3 years ago
2
Model classification should be based on file contents, not just file extension

#322 maxneal closed 5 years ago
1
Single-clicking off of hull after selecting nodes with bounding box selects nodes

#321 maxneal closed 5 years ago
1
The hulls of submodels within submodels cannot be moved independently

#320 maxneal closed 5 years ago
0
Incorrect nodes selected when clicked after using bounding box

#319 maxneal closed 5 years ago
0
Update force property annotations for models in the "examples" folder

#318 maxneal closed 5 years ago
0
Participants in physical processes not being displayed in Project Tab right fly-out panel

#317 maxneal closed 5 years ago
1
Sneyd and Kapela models not loading

#316 maxneal closed 5 years ago
1
Show human readable name instead of (or in addition to) model ID for BioModels search

#315 GrahamKim opened 5 years ago
1
Javascript error when retrieving abstract for BioModel search result

#314 GrahamKim closed 5 years ago
0
Add button to show abstract from BioModel search

#313 GrahamKim closed 5 years ago
0
Search progress bar

#312 GrahamKim closed 5 years ago
0
Re-support annotation against UniProt

#311 maxneal closed 5 years ago
1
Do not write out a new version of a model's source code when generating an OMEX file

#310 maxneal opened 5 years ago
0
ModelAccessor for string?

#309 0u812 closed 5 years ago
2
Add flag for writing Casa annotations

#308 0u812 closed 5 years ago
1
Making AbstractRDFWriter methods public

#307 0u812 closed 5 years ago
0
SemGen looks low-res on high resolution display

#306 GrahamKim closed 3 years ago
2
Determine how to recognize synonymous custom physical entities whose names are given in different languages

#305 maxneal opened 6 years ago
0
Support exporting merged models into SBML Comp package format

#304 maxneal opened 6 years ago
0
Nodes occasionally become unresponsive

#303 GrahamKim opened 6 years ago
2
Visualization error on submodel extraction with "fix nodes" on

#302 maxneal closed 6 years ago
0
If a Project Tab visualization is going to display a large number of nodes, prompt user to continue

#301 maxneal closed 6 years ago
2
Display alerts when an error occurs during model save out

#300 maxneal closed 6 years ago
1
Add progress indicator when saving models

#299 maxneal closed 6 years ago
1
Add progress indicator when loading models into a Project Tab

#298 maxneal closed 6 years ago
1
Ensure that curational metadata in models is preserved on roundtrips

#297 maxneal opened 6 years ago
3
Hide "Save", "Save As" and "Export" file menu items when user is on a Project Tab

#296 maxneal closed 6 years ago
1
Alert users to unsaved extractions on Project Tab close.

#295 maxneal closed 6 years ago
1
If "Fix Nodes" is on, keep nodes fixed when the user turns on/off node types

#294 maxneal closed 6 years ago
0
Nodes in visualizations should always be "on top"

#293 maxneal closed 6 years ago
0
Allow users to specify sources and sinks for force properties

#292 maxneal closed 6 years ago
0
Decide how to visualize SBML functions in dependency maps and implement changes

#291 maxneal opened 6 years ago
2
When attempting to write a model with SBML-style function definitions to a CellML model, abort and show error

#290 maxneal closed 6 years ago
0
Preserve curational and ad hoc model-level annotations in OMEX annotation files

#289 maxneal closed 5 years ago
1
Allow user to re-run OPB auto-annotation process at any time

#288 maxneal opened 6 years ago
0
Merger needs to recognize equivalent processes and forces that differ only in their polarity

#287 maxneal opened 6 years ago
0