/
whatIsNew.js
693 lines (693 loc) · 49.2 KB
/
whatIsNew.js
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
var jsonData = { "versions": [
{ "anchor": "latest", "description": "Latest snapshot", "day": 20, "month": 1, "year": 2020,
"categories": [
{ "name": "General",
"entries": [
{ "type": "improved", "description": "Rendering of the <a href=\"https://en.wikipedia.org/wiki/Graphical_user_interface\">GUI</a>." },
{ "type": "improved", "description": "Plugin framework." },
{ "type": "added", "description": "Support for <a href=\"https://python.org/\">Python</a>." }
]
},
{ "name": "Editing",
"entries": [
{ "type": "subCategory", "name": "CellML Annotation view",
"entries": [
{ "type": "fixed", "description": "Crash when a file has been rendered invalid." }
]
},
{ "type": "subCategory", "name": "CellML Text view",
"entries": [
{ "type": "improved", "description": "Unicode support." }
]
}
]
},
{ "name": "Editing",
"entries": [
{ "type": "subCategory", "name": "CellML Text view",
"entries": [
{ "type": "improved", "description": "Rendering of the <a href=\"https://en.wikipedia.org/wiki/Graphical_user_interface\">GUI</a>." },
{ "type": "fixed", "description": "Reading a <a href=\"https://cellml.org/\">CellML</a> file that has no <a href=\"https://w3.org/XML/\">XML</a> processing instruction." }
]
}
]
},
{ "name": "Organisation",
"entries": [
{ "type": "subCategory", "name": "PMR Workspaces window",
"entries": [
{ "type": "improved", "description": "Synchronisation dialog." }
]
}
]
},
{ "name": "Simulation",
"entries": [
{ "type": "subCategory", "name": "Simulation Experiment view",
"entries": [
{ "type": "added", "description": "Basic support for the import of external data." },
{ "type": "improved", "description": "Rendering of the <a href=\"https://en.wikipedia.org/wiki/Graphical_user_interface\">GUI</a>." },
{ "type": "improved", "description": "Plotting of simulations." },
{ "type": "fixed", "description": "Issue with handling the Graph Panel properties." },
{ "type": "fixed", "description": "Various issues with saving a file under a new name." },
{ "type": "fixed", "description": "Issue with reopening a remote <a href=\"https://cellml.org/\">CellML</a> file from a <a href=\"https://sed-ml.github.io/\">SED-ML</a> file." },
{ "type": "fixed", "description": "Issue with a <a href=\"https://sed-ml.github.io/\">SED-ML</a> file / <a href=\"https://co.mbine.org/documents/archive\">COMBINE archive</a> not necessarily saving all of a solver's properties." },
{ "type": "fixed", "description": "Issue with a <a href=\"https://sed-ml.github.io/\">SED-ML</a> file / <a href=\"https://co.mbine.org/documents/archive\">COMBINE archive</a> being considered modified after changing languages." }
]
}
]
},
{ "name": "Support",
"entries": [
{ "type": "subCategory", "name": "CellML support",
"entries": [
{ "type": "improved", "description": "Loading of <a href=\"https://cellml.org/\">CellML</a> files." }
]
},
{ "type": "subCategory", "name": "COMBINE support",
"entries": [
{ "type": "fixed", "description": "Files with a master attribute of \"1\" (rather than \"true\")." }
]
},
{ "type": "subCategory", "name": "<a href=\"https://sed-ml.github.io/\">SED-ML</a> support",
"entries": [
{ "type": "added", "description": "Support for left and right triangle symbols." }
]
},
{ "type": "subCategory", "name": "Simulation support",
"entries": [
{ "type": "improved", "description": "Accuracy of algebraic variables that depend on the value of some state variables." },
{ "type": "fixed", "description": "Issue with a remote <a href=\"https://sed-ml.github.io/\">SED-ML</a> file being run headless." }
]
}
]
},
{ "name": "Tools",
"entries": [
{ "type": "subCategory", "name": "CellML tools",
"entries": [
{ "type": "added", "description": "Validation of a <a href=\"https://cellml.org/\">CellML</a> file from the <a href=\"https://en.wikipedia.org/wiki/Command-line_interface\">CLI</a>." }
]
}
]
}
]
},
{ "anchor": "0.6", "description": "Version 0.6", "day": 11, "month": 12, "year": 2018,
"categories": [
{ "name": "General",
"entries": [
{ "type": "added", "description": "Preferences dialog." },
{ "type": "added", "description": "include/exclude plugins from the <a href=\"https://en.wikipedia.org/wiki/Command-line_interface\">CLI</a>." },
{ "type": "improved", "description": "Support for <a href=\"https://en.wikipedia.org/wiki/Microsoft_Windows\">Windows</a>." },
{ "type": "improved", "description": "Support for <a href=\"https://en.wikipedia.org/wiki/Linux\">Linux</a>." },
{ "type": "improved", "description": "Support for <a href=\"https://en.wikipedia.org/wiki/MacOS\">macOS</a>." },
{ "type": "improved", "description": "Plugins dialog." },
{ "type": "improved", "description": "Plugin framework." },
{ "type": "improved", "description": "Rendering of the <a href=\"https://en.wikipedia.org/wiki/Graphical_user_interface\">GUI</a>." },
{ "type": "improved", "description": "Support for <a href=\"https://en.wikipedia.org/wiki/Differential_algebraic_equation\">DAE</a> models." },
{ "type": "improved", "description": "Keyboard navigation in tree views." }
]
},
{ "name": "API",
"entries": [
{ "type": "added", "description": "<a href=\"https://github.com/NuML/NuML/\">NuML</a> API (via <a href=\"https://github.com/NuML/NuML/\">libNuML</a>)." }
]
},
{ "name": "Data store",
"entries": [
{ "type": "improved", "description": "Selection of data." },
{ "type": "subCategory", "name": "<a href=\"https://en.wikipedia.org/wiki/Comma-separated_values\">CSV</a> data store",
"entries": [
{ "type": "improved", "description": "Export of data." }
]
}
]
},
{ "name": "Editing",
"entries": [
{ "type": "subCategory", "name": "Text-based view",
"entries": [
{ "type": "added", "description": "Word wrap." },
{ "type": "added", "description": "Line numbers." },
{ "type": "added", "description": "Text highlighting." }
]
},
{ "type": "subCategory", "name": "CellML Annotation view",
"entries": [
{ "type": "improved", "description": "Rendering of the <a href=\"https://en.wikipedia.org/wiki/Graphical_user_interface\">GUI</a>." }
]
},
{ "type": "subCategory", "name": "CellML Text view",
"entries": [
{ "type": "improved", "description": "Conversion of <a href=\"https://cellml.org/\">CellML</a> files to the <a href=\"user/plugins/editing/cellmlTextView.html#plugins-editing-cellmltextview-cellmltextformat\">CellML Text format</a>." },
{ "type": "improved", "description": "Rendering of the <a href=\"https://en.wikipedia.org/wiki/Graphical_user_interface\">GUI</a>." }
]
}
]
},
{ "name": "Miscellaneous",
"entries": [
{ "type": "added", "description": "Web Browser window." }
]
},
{ "name": "Organisation",
"entries": [
{ "type": "added", "description": "<a href=\"user/plugins/organisation/pmrWorkspacesWindow.html\">PMR Workspaces window</a>." },
{ "type": "subCategory", "name": "PMR window",
"entries": [
{ "type": "improved", "description": "Initialisation." },
{ "type": "improved", "description": "Cloning of a workspace." }
]
}
]
},
{ "name": "Simulation",
"entries": [
{ "type": "subCategory", "name": "Simulation Experiment view (formerly known as the Single Cell view)",
"entries": [
{ "type": "added", "description": "Support for multiple runs." },
{ "type": "added", "description": "Ability to customise a graph." },
{ "type": "added", "description": "Support for logarithmic scales." },
{ "type": "added", "description": "Ability to customise a graph panel." },
{ "type": "added", "description": "Ability to show the legend of a graph panel." },
{ "type": "added", "description": "Support for pinch gestures to zoom in/out a graph panel." },
{ "type": "added", "description": "Export a graph panel to various formats (e.g. PDF, PNG, SVG)." },
{ "type": "improved", "description": "Rendering of the <a href=\"https://en.wikipedia.org/wiki/Graphical_user_interface\">GUI</a>." },
{ "type": "improved", "description": "Plotting of simulations." },
{ "type": "improved", "description": "Colour for a new graph." },
{ "type": "improved", "description": "Simulation time information." },
{ "type": "improved", "description": "Running of long simulations." },
{ "type": "improved", "description": "Resetting of model parameters." },
{ "type": "improved", "description": "Synchronisation of the X and/or Y axes of all the graph panels." },
{ "type": "fixed", "description": "<a href=\"https://computation.llnl.gov/projects/sundials/cvode\">CVODE</a> solver issue when modifying a model state." }
]
}
]
},
{ "name": "Solver",
"entries": [
{ "type": "subCategory", "name": "<a href=\"https://computation.llnl.gov/projects/sundials/kinsol\">KINSOL</a> solver",
"entries": [
{ "type": "added", "description": "Parametrisation of the solver." }
]
},
{ "type": "comment", "description": "The <a href=\"https://computation.llnl.gov/projects/sundials/ida\">IDA</a> solver was removed (in favour of <a href=\"https://computation.llnl.gov/projects/sundials/cvode\">CVODE</a>+<a href=\"https://computation.llnl.gov/projects/sundials/kinsol\">KINSOL</a>)." }
]
},
{ "name": "Support",
"entries": [
{ "type": "subCategory", "name": "CellML support",
"entries": [
{ "type": "improved", "description": "Generation of error messages." }
]
},
{ "type": "subCategory", "name": "<a href=\"https://sed-ml.github.io/\">SED-ML</a> support",
"entries": [
{ "type": "added", "description": "Customisation of graph panels." }
]
},
{ "type": "subCategory", "name": "ZIP support",
"entries": [
{ "type": "improved", "description": "decompression." }
]
}
]
}
]
},
{ "anchor": "0.5", "description": "Version 0.5", "day": 15, "month": 10, "year": 2016,
"categories": [
{ "name": "General",
"entries": [
{ "type": "added", "description": "Resetting all your settings from the <a href=\"https://en.wikipedia.org/wiki/Command-line_interface\">CLI</a>." },
{ "type": "added", "description": "Detection of changes to one or several file dependencies." },
{ "type": "added", "description": "Support for an OpenCOR-specific URL scheme." },
{ "type": "added", "description": "Default view to open a particular type of file." },
{ "type": "added", "description": "Reference to the <a href=\"https://tutorial-on-cellml-opencor-and-pmr.readthedocs.io/en/latest/\">official OpenCOR tutorial</a>." },
{ "type": "added", "description": "Use of a user's proxy settings." },
{ "type": "improved", "description": "Support for <a href=\"https://en.wikipedia.org/wiki/Microsoft_Windows\">Windows</a>." },
{ "type": "improved", "description": "Handling of files." },
{ "type": "improved", "description": "Rendering of the <a href=\"https://en.wikipedia.org/wiki/Graphical_user_interface\">GUI</a>." },
{ "type": "improved", "description": "Rendering of equations." },
{ "type": "improved", "description": "Editing of text-based files." },
{ "type": "improved", "description": "Retrieval of a Save File name." },
{ "type": "improved", "description": "Reopening of the most recent file." },
{ "type": "fixed", "description": "Rendering of equations." },
{ "type": "fixed", "description": "Copying of a rendered equation to the clipboard (on <a href=\"https://en.wikipedia.org/wiki/Microsoft_Windows\">Windows</a>)." },
{ "type": "fixed", "description": "Compiler engine crash due to an unfound external function (on <a href=\"https://en.wikipedia.org/wiki/Linux\">Linux</a>)." }
]
},
{ "name": "API",
"entries": [
{ "type": "added", "description": "<a href=\"http://sbml.org/\">SBML</a> API (via <a href=\"http://sbml.org/Software/libSBML/\">libSBML</a>)." },
{ "type": "added", "description": "<a href=\"https://sed-ml.github.io/\">SED-ML</a> API (via <a href=\"https://github.com/fbergmann/libSEDML/\">libSEDML</a>)." }
]
},
{ "name": "Data store",
"entries": [
{ "type": "added", "description": "BioSignalML data store." },
{ "type": "subCategory", "name": "<a href=\"https://en.wikipedia.org/wiki/Comma-separated_values\">CSV</a> data store",
"entries": [
{ "type": "added", "description": "Selection of model parameters prior to data export." },
{ "type": "improved", "description": "Export of data." }
]
}
]
},
{ "name": "Editing",
"entries": [
{ "type": "subCategory", "name": "CellML Annotation view",
"entries": [
{ "type": "improved", "description": "Rendering of the <a href=\"https://en.wikipedia.org/wiki/Graphical_user_interface\">GUI</a>." }
]
},
{ "type": "subCategory", "name": "Raw Text view (formerly known as the Raw view)",
"entries": [
{ "type": "improved", "description": "Support for text files." }
]
},
{ "type": "subCategory", "name": "Raw CellML view",
"entries": [
{ "type": "improved", "description": "Validation of <a href=\"https://cellml.org/\">CellML</a> files." },
{ "type": "fixed", "description": "Reformatting unescaped HTML entities." }
]
},
{ "type": "subCategory", "name": "CellML Text view",
"entries": [
{ "type": "added", "description": "Import/export of the <a href=\"user/plugins/editing/cellmlTextView.html#plugins-editing-cellmltextview-cellmltextformat\">CellML Text format</a> from/to <a href=\"https://cellml.org/\">CellML</a>." },
{ "type": "added", "description": "Support for the <code>min()</code>/<code>max()</code> and <code>gcd()</code>/<code>lcm()</code> functions." },
{ "type": "added", "description": "Offer to save the contents of the view to a text file if it cannot be saved as a <a href=\"https://cellml.org/\">CellML</a> file." },
{ "type": "improved", "description": "Syntax highlighting." },
{ "type": "improved", "description": "Support for comments." },
{ "type": "improved", "description": "Support for <code>cmeta:id</code>'s." },
{ "type": "improved", "description": "Saving of a <a href=\"https://cellml.org/\">CellML</a> file." },
{ "type": "fixed", "description": "Serialisation of a mathematical equation with a <code>cmeta:id</code> value." },
{ "type": "fixed", "description": "Serialisation of numbers that have an exponent." },
{ "type": "fixed", "description": "Serialisation of metadata." }
]
},
{ "type": "added", "description": "<a href=\"user/plugins/editing/rawSedmlView.html\">Raw SED-ML view</a>." }
]
},
{ "name": "Organisation",
"entries": [
{ "type": "subCategory", "name": "Physiome Model Repository window (formerly known as the CellML Model Repository window)",
"entries": [
{ "type": "improved", "description": "Listing of exposures and exposure files." },
{ "type": "added", "description": "Listing of <a href=\"https://sed-ml.github.io/\">SED-ML</a> files." },
{ "type": "added", "description": "Cloning of a workspace." },
{ "type": "added", "description": "Opening of an exposure file." }
]
}
]
},
{ "name": "Simulation",
"entries": [
{ "type": "subCategory", "name": "Single Cell view",
"entries": [
{ "type": "added", "description": "Basic <a href=\"https://sed-ml.github.io/\">SED-ML</a> support (both through a <a href=\"https://sed-ml.github.io/\">SED-ML</a> file and a <a href=\"https://co.mbine.org/documents/archive\">COMBINE archive</a>)." },
{ "type": "added", "description": "Creation of a new <a href=\"https://cellml.org/\">CellML</a> file or update of an existing one based on the results of a simulation." },
{ "type": "added", "description": "Specification of the minimum/maximum values of the axes of a graph panel." },
{ "type": "added", "description": "Synchronisation of the X and/or Y axes of all the graph panels." },
{ "type": "improved", "description": "Rendering of the <a href=\"https://en.wikipedia.org/wiki/Graphical_user_interface\">GUI</a>." },
{ "type": "improved", "description": "Plotting of simulation data." },
{ "type": "improved", "description": "Support for <a href=\"https://cellml.org/\">CellML</a> models." },
{ "type": "improved", "description": "Listing of <a href=\"https://cellml.org/\">CellML</a> 1.1 model parameters." },
{ "type": "fixed", "description": "Computing the initial value of a 'constant' algebraic variable." }
]
}
]
},
{ "name": "Solver",
"entries": [
{ "type": "subCategory", "name": "<a href=\"https://computation.llnl.gov/projects/sundials/cvode\">CVODE</a> solver",
"entries": [
{ "type": "improved", "description": "Parametrisation of the solver." }
]
},
{ "type": "subCategory", "name": "<a href=\"https://computation.llnl.gov/projects/sundials/ida\">IDA</a> solver",
"entries": [
{ "type": "improved", "description": "Parametrisation of the solver." }
]
}
]
},
{ "name": "Support",
"entries": [
{ "type": "added", "description": "Support for <a href=\"https://sed-ml.github.io/\">SED-ML</a>." },
{ "type": "added", "description": "Support for <a href=\"https://co.mbine.org/documents/archive\">COMBINE archive</a>." },
{ "type": "subCategory", "name": "<a href=\"https://riverbankcomputing.com/software/qscintilla/intro\">QScintilla</a> support",
"entries": [
{ "type": "improved", "description": "Support for Unicode." }
]
}
]
},
{ "name": "Tools",
"entries": [
{ "type": "subCategory", "name": "CellML tools",
"entries": [
{ "type": "improved", "description": "Export of a <a href=\"https://cellml.org/\">CellML</a> file." }
]
}
]
}
]
},
{ "anchor": "0.4.1", "description": "Version 0.4.1", "day": 20, "month": 5, "year": 2015,
"categories": [
{ "name": "Editing",
"entries": [
{ "type": "subCategory", "name": "Raw CellML view",
"entries": [
{ "type": "improved", "description": "Validation of <a href=\"https://cellml.org/\">CellML</a> files." }
]
},
{ "type": "subCategory", "name": "CellML Text view",
"entries": [
{ "type": "improved", "description": "Validation of <a href=\"https://cellml.org/\">CellML</a> files." }
]
}
]
},
{ "name": "Simulation",
"entries": [
{ "type": "subCategory", "name": "Single Cell view",
"entries": [
{ "type": "fixed", "description": "<a href=\"https://en.wikipedia.org/wiki/Mac_OS_X_Lion\">Mac OS X 10.7</a> (Lion) and <a href=\"https://en.wikipedia.org/wiki/OS_X_Mountain_Lion\">OS X 10.8</a> (Mountain Lion) issue with models that need to compute 10<sup>x</sup>." }
]
}
]
}
]
},
{ "anchor": "0.4", "description": "Version 0.4", "day": 29, "month": 4, "year": 2015,
"categories": [
{ "name": "General",
"entries": [
{ "type": "added", "description": "Checking for updates." },
{ "type": "added", "description": "<a href=\"howToGetStarted.html\">How to get started</a> section." },
{ "type": "improved", "description": "OpenCOR logo." },
{ "type": "improved", "description": "Binaries on <a href=\"https://en.wikipedia.org/wiki/OS_X\">OS X</a>." },
{ "type": "improved", "description": "<a href=\"https://nsis.sourceforge.io/\">NSIS</a> packaging on <a href=\"https://en.wikipedia.org/wiki/Microsoft_Windows\">Windows</a>." },
{ "type": "improved", "description": "<a href=\"https://en.wikipedia.org/wiki/Zip_(file_format)\">ZIP</a> packaging on <a href=\"https://en.wikipedia.org/wiki/OS_X\">OS X</a>." },
{ "type": "improved", "description": "Handling of files." },
{ "type": "improved", "description": "Display of numbers." },
{ "type": "improved", "description": "Rendering of equations." },
{ "type": "improved", "description": "Opening and reopening of files." }
]
},
{ "name": "Data store",
"entries": [
{ "type": "added", "description": "<a href=\"https://en.wikipedia.org/wiki/Comma-separated_values\">CSV</a> data store." }
]
},
{ "name": "Editing",
"entries": [
{ "type": "subCategory", "name": "CellML Annotation view",
"entries": [
{ "type": "added", "description": "Two new <a href=\"https://co.mbine.org/standards/qualifiers\">BioModels.net qualifiers</a> (<code>model:isInstanceOf</code> and <code>model:hasInstance</code>)." },
{ "type": "improved", "description": "Rendering of the <a href=\"https://en.wikipedia.org/wiki/Graphical_user_interface\">GUI</a>." },
{ "type": "improved", "description": "Responsiveness of the <a href=\"https://en.wikipedia.org/wiki/Graphical_user_interface\">GUI</a>." },
{ "type": "improved", "description": "Listing of component variables." },
{ "type": "improved", "description": "Translation of views for inactive <a href=\"https://cellml.org/\">CellML</a> files." },
{ "type": "improved", "description": "Setting of the modified state of the <a href=\"https://cellml.org/\">CellML</a> file." },
{ "type": "improved", "description": "Detection of direct ontological terms." },
{ "type": "improved", "description": "Retrieval of ontological terms." },
{ "type": "improved", "description": "Listing of ontological terms." },
{ "type": "fixed", "description": "Editing of malformed <a href=\"https://cellml.org/\">CellML</a> files." },
{ "type": "fixed", "description": "Further editing after saving a <a href=\"https://cellml.org/\">CellML</a> file." },
{ "type": "fixed", "description": "Risk of the same <code>cmeta:id</code> value being used for two different <a href=\"https://cellml.org/\">CellML</a> elements." }
]
},
{ "type": "subCategory", "name": "Raw view",
"entries": [
{ "type": "improved", "description": "Changes to file permissions." }
]
},
{ "type": "subCategory", "name": "Raw CellML view",
"entries": [
{ "type": "added", "description": "Reformatting of the contents of the editor." },
{ "type": "improved", "description": "Context menu." },
{ "type": "improved", "description": "Validation of <a href=\"https://cellml.org/\">CellML</a> files." },
{ "type": "improved", "description": "Changes to file permissions." },
{ "type": "fixed", "description": "Retrieval of view settings." }
]
},
{ "type": "added", "description": "<a href=\"user/plugins/editing/cellmlTextView.html\">CellML Text view</a>." }
]
},
{ "name": "Miscellaneous",
"entries": [
{ "type": "subCategory", "name": "Help",
"entries": [
{ "type": "improved", "description": "Printing." }
]
}
]
},
{ "name": "Organisation",
"entries": [
{ "type": "subCategory", "name": "CellML Model Repository window",
"entries": [
{ "type": "improved", "description": "Retrieval of <a href=\"https://cellml.org/\">CellML</a> files." },
{ "type": "improved", "description": "Listing of <a href=\"https://cellml.org/\">CellML</a> files." }
]
}
]
},
{ "name": "Simulation",
"entries": [
{ "type": "subCategory", "name": "Single Cell view",
"entries": [
{ "type": "improved", "description": "Export to <a href=\"https://en.wikipedia.org/wiki/Comma-separated_values\">CSV</a>." },
{ "type": "improved", "description": "Rendering of the <a href=\"https://en.wikipedia.org/wiki/Graphical_user_interface\">GUI</a>." },
{ "type": "fixed", "description": "Tracking of simulation properties." }
]
}
]
},
{ "name": "Support",
"entries": [
{ "type": "subCategory", "name": "CellML support",
"entries": [
{ "type": "improved", "description": "Generation of error messages." },
{ "type": "improved", "description": "Serialisation of <a href=\"https://cellml.org/\">CellML</a> files." },
{ "type": "improved", "description": "Reloading of <a href=\"https://cellml.org/\">CellML</a> files." },
{ "type": "fixed", "description": "Loading of <a href=\"https://cellml.org/\">CellML</a> files." }
]
}
]
}
]
},
{ "anchor": "0.3", "description": "Version 0.3", "day": 19, "month": 8, "year": 2014,
"categories": [
{ "name": "General",
"entries": [
{ "type": "added", "description": "Creation of a new blank file." },
{ "type": "added", "description": "Creation of a new <a href=\"https://cellml.org/\">CellML</a> 1.0 file." },
{ "type": "added", "description": "Creation of a new <a href=\"https://cellml.org/\">CellML</a> 1.1 file." },
{ "type": "added", "description": "Opening of a remote file." },
{ "type": "added", "description": "Duplication of a file." },
{ "type": "added", "description": "(Un)locking of a file." },
{ "type": "added", "description": "Closing of a file by pressing <code>Ctrl+W</code> on <a href=\"https://en.wikipedia.org/wiki/Microsoft_Windows\">Windows</a>." },
{ "type": "improved", "description": "Support for <a href=\"https://en.wikipedia.org/wiki/Command-line_interface\">CLI</a> on <a href=\"https://en.wikipedia.org/wiki/Linux\">Linux</a> and <a href=\"https://en.wikipedia.org/wiki/OS_X\">OS X</a>." },
{ "type": "improved", "description": "Rendering of the <a href=\"https://en.wikipedia.org/wiki/Graphical_user_interface\">GUI</a>." },
{ "type": "improved", "description": "Plugin framework." },
{ "type": "improved", "description": "Plugins dialog." },
{ "type": "improved", "description": "Handling of files." },
{ "type": "improved", "description": "Mode/view philosophy." },
{ "type": "improved", "description": "Keyboard navigation in tree views." },
{ "type": "improved", "description": "Saving of a file using any file extension." }
]
},
{ "name": "Development",
"entries": [
{ "type": "subCategory", "name": "Examples of <a href=\"developer/develop/plugins/index.html\">how to write plugins</a>",
"entries": [
{ "type": "added", "description": "<a href=\"developer/develop/plugins/sample.html\">Sample</a> plugin." },
{ "type": "added", "description": "<a href=\"developer/develop/plugins/sampleTools.html\">Sample tools</a> plugin." },
{ "type": "added", "description": "<a href=\"developer/develop/plugins/sampleView.html\">Sample view</a> plugin." },
{ "type": "added", "description": "<a href=\"developer/develop/plugins/sampleWindow.html\">Sample window</a> plugin." }
]
}
]
},
{ "name": "Editing",
"entries": [
{ "type": "subCategory", "name": "CellML Annotation view",
"entries": [
{ "type": "improved", "description": "Retrieval of possible ontological terms." },
{ "type": "fixed", "description": "Listing of some unrecognisable metadata." },
{ "type": "fixed", "description": "Listing of suggested ontological terms." }
]
},
{ "type": "added", "description": "<a href=\"user/plugins/editing/rawTextView.html\">Raw view</a>." },
{ "type": "added", "description": "<a href=\"user/plugins/editing/rawCellmlView.html\">Raw CellML view</a>." }
]
},
{ "name": "Miscellaneous",
"entries": [
{ "type": "subCategory", "name": "CellML tools",
"entries": [
{ "type": "added", "description": "Export of a <a href=\"https://cellml.org/\">CellML</a> file to a user-defined format." },
{ "type": "added", "description": "User-defined format for <a href=\"https://en.wikipedia.org/wiki/C_(programming_language)\">C</a>." },
{ "type": "added", "description": "User-defined format for <a href=\"https://en.wikipedia.org/wiki/Fortran#FORTRAN_77\">FORTRAN 77</a>." },
{ "type": "added", "description": "User-defined format for <a href=\"https://en.wikipedia.org/wiki/MATLAB\">MATLAB</a>." },
{ "type": "added", "description": "User-defined format for <a href=\"https://en.wikipedia.org/wiki/Python_(programming_language)\">Python</a>." }
]
}
]
},
{ "name": "Organisation",
"entries": [
{ "type": "subCategory", "name": "CellML Model Repository window",
"entries": [
{ "type": "improved", "description": "Retrieval of <a href=\"https://cellml.org/\">CellML</a> files." }
]
},
{ "type": "subCategory", "name": "File Browser window",
"entries": [
{ "type": "added", "description": "Opening of a file by pressing <code>Enter</code> on (Mac) <a href=\"https://en.wikipedia.org/wiki/OS_X\">OS X</a>." }
]
},
{ "type": "subCategory", "name": "File Organiser window",
"entries": [
{ "type": "added", "description": "Opening of a file by pressing <code>Enter</code> on (Mac) <a href=\"https://en.wikipedia.org/wiki/OS_X\">OS X</a>." },
{ "type": "fixed", "description": "Retrieval of the contents of the file organiser." }
]
}
]
},
{ "name": "Simulation",
"entries": [
{ "type": "subCategory", "name": "Single Cell view",
"entries": [
{ "type": "improved", "description": "Rendering of the <a href=\"https://en.wikipedia.org/wiki/Graphical_user_interface\">GUI</a>." },
{ "type": "improved", "description": "Delay between two data points." },
{ "type": "improved", "description": "Information regarding a <a href=\"https://cellml.org/\">CellML</a> file." },
{ "type": "improved", "description": "Export to <a href=\"https://en.wikipedia.org/wiki/Comma-separated_values\">CSV</a>." },
{ "type": "fixed", "description": "Removal of a graph panel that is selected by another <a href=\"https://cellml.org/\">CellML</a> file." },
{ "type": "fixed", "description": "Property settings of a <a href=\"https://cellml.org/\">CellML</a> file that requires a non-linear algebraic solver." }
]
}
]
},
{ "name": "Solver",
"entries": [
{ "type": "subCategory", "name": "<a href=\"https://computation.llnl.gov/projects/sundials/cvode\">CVODE</a> solver",
"entries": [
{ "type": "added", "description": "Choice to interpolate the solution." }
]
},
{ "type": "subCategory", "name": "<a href=\"https://computation.llnl.gov/projects/sundials/ida\">IDA</a> solver",
"entries": [
{ "type": "added", "description": "Choice to interpolate the solution." }
]
}
]
}
]
},
{ "anchor": "0.2", "description": "Version 0.2", "day": 19, "month": 11, "year": 2013,
"categories": [
{ "name": "General",
"entries": [
{ "type": "added", "description": "<a href=\"licensing.html\">Open source license</a>." },
{ "type": "added", "description": "Showing/hiding of all the recent/current docked widgets at once." },
{ "type": "added", "description": "<a href=\"https://ncbi.nlm.nih.gov/pmc/articles/PMC1359535\">Noble 1962</a> as one of the <a href=\"https://cellml.org/\">CellML</a> file examples." },
{ "type": "added", "description": "Reloading of a file." },
{ "type": "improved", "description": "Keyboard navigation in tree views." },
{ "type": "improved", "description": "Handling of files." },
{ "type": "improved", "description": "Plugins dialog." }
]
},
{ "name": "Editing",
"entries": [
{ "type": "subCategory", "name": "CellML Annotation view",
"entries": [
{ "type": "added", "description": "Opening of an imported <a href=\"https://cellml.org/\">CellML</a> file." }
]
}
]
},
{ "name": "Miscellaneous",
"entries": [
{ "type": "added", "description": "<a href=\"user/plugins/tools/cellmlTools.html\">CellML tools</a>." }
]
},
{ "name": "Organisation",
"entries": [
{ "type": "subCategory", "name": "CellML Model Repository window",
"entries": [
{ "type": "improved", "description": "Retrieval of <a href=\"https://cellml.org/\">CellML</a> files." }
]
}
]
},
{ "name": "Simulation",
"entries": [
{ "type": "subCategory", "name": "Single Cell view",
"entries": [
{ "type": "added", "description": "Ability to have several graph panels." },
{ "type": "added", "description": "Plotting of any model parameter against any other." },
{ "type": "added", "description": "Plotting of simulation data from another simulation." },
{ "type": "improved", "description": "Various listings." },
{ "type": "improved", "description": "Simulation speed." },
{ "type": "improved", "description": "Graph panel features." },
{ "type": "improved", "description": "Support for <a href=\"https://en.wikipedia.org/wiki/Retina_Display\">Retina displays</a>." },
{ "type": "improved", "description": "Support for a wider range of <a href=\"https://cellml.org/\">CellML</a> files." }
]
}
]
},
{ "name": "Solver",
"entries": [
{ "type": "added", "description": "<a href=\"https://en.wikipedia.org/wiki/Heun%27s_method\">Heun</a> solver." },
{ "type": "added", "description": "Second-order <a href=\"https://en.wikipedia.org/wiki/Runge–Kutta_methods\">Runge-Kutta</a> solver." },
{ "type": "added", "description": "Fourth-order <a href=\"https://en.wikipedia.org/wiki/Runge–Kutta_methods\">Runge-Kutta</a> solver." }
]
}
]
},
{ "anchor": "0.1.2", "description": "Version 0.1.2", "day": 29, "month": 5, "year": 2013,
"categories": [
{ "name": "Simulation",
"entries": [
{ "type": "subCategory", "name": "Single Cell view",
"entries": [
{ "type": "fixed", "description": "Generation of the runtime of some <a href=\"https://cellml.org/\">CellML</a> files." }
]
}
]
}
]
},
{ "anchor": "0.1.1", "description": "Version 0.1.1", "day": 17, "month": 4, "year": 2013,
"categories": [
{ "name": "General",
"entries": [
{ "type": "improved", "description": "Plugin framework." }
]
},
{ "name": "Simulation",
"entries": [
{ "type": "subCategory", "name": "Single Cell view",
"entries": [
{ "type": "improved", "description": "Editing of property values." },
{ "type": "fixed", "description": "Plotting of property values." }
]
}
]
}
]
},
{ "anchor": "0.1", "description": "Version 0.1", "day": 1, "month": 4, "year": 2013,
"categories": [
{ "name": "Original version of OpenCOR" }
]
}
]
};