-
Notifications
You must be signed in to change notification settings - Fork 16
/
roadmap.html
1358 lines (1280 loc) · 81.4 KB
/
roadmap.html
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
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>Cytoscape Product Roadmap</title>
<meta name="description" content="Cytoscape Product Roadmap">
<meta name="author" content="Barry Demchak">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<script src="https://code.jquery.com/jquery-2.1.1.min.js"></script>
<link rel="stylesheet" href="https://netdna.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css">
<script src="https://netdna.bootstrapcdn.com/bootstrap/3.2.0/js/bootstrap.min.js"></script>
<link href="css/main.bootstrap.css" rel="stylesheet">
</head>
<body>
<div class="narrow white">
<div class="container centering">
<h1>Cytoscape Product Roadmap</h1>
<div class="row">
<img src="images/logo/cy3logoOrange.svg">
</div>
</div>
</div>
<div class="belt white">
<div class="container">
<div class="row">
<div class="col-xs-12 col-md-5">
<h2>Introduction</h2>
<p class="narrow">Cytoscape was initially released in 2002, and has undergone numerous development sprints. The most recent major sprint ended in 2014 with the release of Cytoscape v3, which refactored major internal data models and greatly improved
support for third party plugin applications (via the App Store, semantic versioning disciplines, published APIs, and code management via OSGi).</p>
<p>Since v3, we have focused on addressing outstanding bugs and upgrading a number of user-facing features, including visual styles (VizMapper), fast node filtering, network capacity, and overall speed and UI consistency. The Cytoscape
app developer community has upgraded a number of v2 plugins into v3 apps, and has contributed a steady stream of new apps (apps.cytoscape.org).
</p>
<p>As of late 2023, our efforts have been rewarded, as Cytoscape has become more popular than ever –
<a href="stat.html">20,000 downloads per month
worldwide</a>.</p>
<p>This page explains our roadmap for future deliveries and activities. Feel free to contribute to this discussion our
<a href="https://cytoscape.org/community.html">community</a> and
<a href="https://cytoscape.org/documentation_users.html">user documentation</a> pages.
</p>
<p class="narrow">Cytoscape is going down a number of roads simultaneously:
</p>
<ul>
<li>Cytoscape Desktop</li>
<li>Cytoscape Expansion to the Cloud</li>
<li>Cytoscape Community Outreach</li>
</ul>
<p>This page describes the Cytoscape Desktop roadmap and inroads into the wider Cloud Ecosystem.</p>
</div>
<div class="col-xs-12 col-md-7">
<h2>Vision: Cytoscape Automation</h2>
<p class="narrow">Cytoscape has traditionally relied on the Cytoscape Apps mechanism for defining and delivering novel calculations and workflows, and the <a href="http://apps.cytoscape.org">Cytoscape App Store</a> has proven successful at collecting
and disseminating them. We are developing Cytoscape Automation features to enable the Cytoscape community to economically create novel workflows using state of the art tools such as Python/Jupyter, R/RStudio and GenomeSpace while
leveraging their feature rich libraries and web presence. </p>
<p class="narrow">Cytoscape Automation will enable users to create workflows executed entirely within Cytoscape or by external tools, and whose results are reproducible. This will enable Cytoscape to scale to large collections of datasets and to larger
more complex workflows than is practical via keyboard and mouse.</p>
<p class="narrow">Cytoscape Automation will exist in two skins – the Commands interface and the Functions interface. Both will accomplish similar results, but will be focused on different usage styles. Commands will reprise user-initiated interactions
(e.g., open session, import data, export image), whereas the Functions interface will enable programmers to manipulate and operate on networks as internal Cytoscape data. Commands and Functions will both available via a REST interface.</p>
<p class="narrow">Under the Cytoscape Automation vision, all new and many existing apps will be upgraded to respond to REST calls. Additionally, most Cytoscape core functions will be exposed via REST calls. In the ideal, all Cytoscape functionality
will become controlable from outside workflow systems.
</p>
<p class="narrow">For more information on Cytoscape Automation, consult the <a href="https://github.com/cytoscape/cytoscape-automation/wiki">Cytoscape Automation wiki.</a></p>
</div>
</div>
<div class="row">
<div class="col-xs-12 col-md-5">
<h2>Vision: Cytoscape Core and Core Apps</h2>
<p class="narrow">Before v3.3, we viewed Cytoscape as consisting of the Cytoscape Core as augmented by the Cytoscape Apps. As of v3.3, we have created a middle ground: the Cytoscape Core Apps. The Core is the code that organizes, displays, reads, and
writes networks but is agnostic as to network meaning or use – the Core does not contain biology-related functionality. Cytoscape Core Apps are installable modules that perform non-Core functions but are still integral to most
Cytoscape usage (e.g., network biology).</p>
<div class="centering">
<img src="images/roadmap/core-picture.png">
<h4>Fig. 1: Cytoscape Desktop</h4>
</div>
<p class="narrow">To date, a Cytoscape release has consisted of the Core + Core Apps (Fig. 1). Beginning in v3.3, the Core Apps are available individually in the App Store, though they are all installed with the Core when Cytoscape is installed. However,
unlike previous Cytoscape versions, Core Apps are upgradable without releasing all of Cytoscape. (For example, bugs can be fixed or features can be added to the Network Merge at any time.) This enables the Cytoscape team to upgrade
specific features much more quickly than in the past.</p>
<p class="narrow">A close cousin to Core Apps is the App Store concept of Collections, which are bundles of apps that apply to a particular workflow. Installing a Collection causes the installation of all apps in the Collection. From time to time, we
will add new Collections or add to existing Collections.</p>
<p class="narrow">As Cytoscape use cases evolve, we expect to add Core Apps to the Cytoscape release, thereby packaging advanced functionality useful in common workflows. The criteria for promoting an app to a Core App is ultimately decided by the Cytoscape
Core developers, but includes:</p>
<ul>
<li>Availability in the App Store and intensive evaluation of requirements, proper targeting and other feedback over a period of at least six months
</li>
<li>Assessment and agreement by Cytoscape Core developers</li>
<li>Realistically maintainable by multiple developers</li>
<li>Minimal (or no) biological domain-specific semantics</li>
</ul>
<p class="narrow">Additional criteria include:</p>
<ul>
<li>How much other apps or workflows depend on it</li>
<li>Value in driving user behavior to achieve higher productivity</li>
<li>Incremental size contributed to Cytoscape installer</li>
<li>Specific maintenance plan (including maintainability by core developers)</li>
<li>Open source and in Cytoscape github repository</li>
<li>Expected size of interested user community</li>
<li>Appeal as compared to existing alternatives</li>
<li>Evaluation of usability and stability</li>
<li>Existence of high quality documentation and tutorials</li>
</ul>
</div>
<div class="col-xs-12 col-md-7">
<h2>Vision: Key Workflows</h2>
<p class="narrow">A top priority for Cytoscape development is to enable efficient execution of new and existing key workflows, including:
</p>
<ul>
<li>Cytoscape Main (core network analysis)</li>
<li>Functional enrichment analysis</li>
<li>Network analysis of proteomics data</li>
<li>Pathway analysis of gene expression data</li>
</ul>
<p class="narrow">Functionality that implements the Core Apps feature is used to enable the user to customize Cytoscape quickly and easily to implement various workflows. Using a Collection (i.e., an app that represents multiple apps), the user can
install all apps needed to execute the Functional Enrichment workflow.</p>
</div>
<div class="col-xs-12 col-md-7">
<h2>Vision: Themes and Features</h2>
<table class="table table-striped">
<tr class="info">
<td><b>Release</b></td>
<td><b>Date</b></td>
<td><b>Themes</b></td>
<td><b>Features</b></td>
</tr>
<tr>
<td>
<h3>3.11</h3>
</td>
<td>TBD 2025
</td>
<td>
<ul>
<li>Web and notebook interoperability</li>
<li>Performance improvements and ...</li>
</ul>
</td>
<td>
<ul>
<li>Java 21 support</li>
<li>and...</li>
</ul>
</td>
</tr>
</table>
</div>
</div>
<div class="row">
<div class="col-xs-12">
<h2>Policies and Practices</h2>
<p>Consequently, we have the following policies, subject to periodic change:</p>
<p style='margin-left:.5in'><b><u>P1:</u></b> Past releases of Cytoscape Desktop have been made roughly every 12 months, with minor releases for bug fixes and minor features occurring every 3-6 months. Beginning with v3.3, a new version of Cytoscape Desktop is
released every six months (~April 15 and ~November 15), with updates of Core Apps to the App Store on an as-needed basis. </p>
<p style='margin-left:.5in'><b><u>P2:</u></b> A high risk Core feature (which could substantially affect overall usability or which are impossible to definitively verify) must be built into the Core eight weeks before the Core is released, or the feature will
be carried over to the next Core release. </p>
<p style='margin-left:.5in'><b><u>P3:</u></b> Other features must be built into the Core five weeks before Core release. </p>
<p style='margin-left:.5in'><b><u>P4:</u></b> Bug fixes may be performed (with proper review) up to ten days before Core release. </p>
<p style='margin-left:.5in'><b><u>P5:</u></b> An external API must be frozen, documented, and with preliminary implementations eight weeks before the Core is released, or the API will be carried over to the next Core release. This includes CyREST functions, parameters
and return results. A developer release will be created and made accessible on cytoscape.org. </p>
<p style='margin-left:.5in'><b><u>P6:</u></b> Milestone builds are created and made available to the user and app developer community eight weeks, five weeks, and ten days before a Core release. If bugs need to be fixed, features need to be withdrawn before the
release, or developers see a good reason, additional milestone builds are created.
</p>
<p style='margin-left:.5in'><b><u>P7:</u></b> Milestone builds (including nightly builds) are made available via a developer Download page on the Cytoscape web site.</p>
<p style='margin-left:.5in'><b><u>P8:</u></b> Emerging API definitions (or references to definitions) are posted on the developer Download page, too.</p>
<p style='margin-left:.5in'><b><u>P9:</u></b> A preliminary feature list is published five months prior to a Core release, and is updated periodically until ten days before a Core release, at which time it is frozen.</p>
<p style='margin-left:.5in'><b><u>P10:</u></b> Notably, Cytoscape has expanded beyond its role as a desktop application by also exposing Cytoscape functionality to external control via automation features (also known as Cytoscape Automation). Feature and workflow
testing is performed to a large degree through external scripting (e.g., PyUnit tests driven by Python). </p>
<p style='margin-left:.5in'><b><u>P11:</u></b> Nominations for new Core Apps will be taken until eight weeks before Core release. Core developers can accept prospective Core Apps until five weeks before Core release. Core App nominations not accepted by the this
time will be eligible for consideration for the next release.
</p>
<p>Note that Core Apps are considered to be part of the Cytoscape core, and are subject to the same Q/A process as core code. Particularly, the interaction of <b><u>P4</u></b> with Core Apps means that changes to Core Apps intended for
immediate deployment must undergo review as if they were last minute changes to the core itself. Core Apps will be deployed to the App Store by core developers.</p>
</div>
</div>
<div class="row belt">
<div class="col-xs-12">
<h2>Vision: Integration with Cytoscape Cyberinfrastructure</h2>
<p class="narrow">As a member of the Cytoscape Cyberinfrastructure (CI), Cytoscape exchanges networks with a number of CI services, including NDEx and viewers based on cytoscape.js.</p>
<p>One long term vision is to tightly integrate Cytoscape and NDEx so that users naturally load and store their networks using the NDEx service. This enables seamless sharing of networks between Cytoscape and other CI services (e.g.,
Network Based Stratification), and with other users and publishers. Upon startup, Cytoscape will enumerate the NDEx networks best suited for the user’s use, including networks previously saved by the user and/or the user’s NDEx-based
groups, networks pertinent to the user’s interest (e.g., by species, curation properties, etc), or other networks proposed by a recommendation engine. Cytoscape and NDEx will cooperate to make sampling of networks nearly costless
so as to encourage exploration (e.g., by caching and displaying network layouts and statistics). Finally, once selected, Cytoscape and NDEx will cooperate to make network loads fast enough that users can remain on task. This vision
will initially be realized by a new Core App that replaces the Welcome screen with a panel (a sibling of Network and Select panels) that presents NDEx networks and serves as a jumping off point for workflow execution.</p>
<p>Cytoscape currently exports a network as a file that can be used as supplemental material for a journal article. A journal publisher’s online article viewer is free to display the network in an interactive viewer, which allows the
user to zoom into the network and move nodes. In our vision, advanced viewers may perform lookups on selected nodes and show the results in windows, perform new layouts and network analysis/clustering, and export the network to
NDEx for integration with Cytoscape and other services – the network would be furnished to the publisher via NDEx directly from Cytoscape instead as a file in supplementary data. Currently, Elsevier offers a <a href="https://www.elsevier.com/connect/new-tool-lets-you-view-and-visualize-complex-data-networks">simple
viewer</a> that accepts a network file and allows zooming and node movement:</p>
<ul>
<li><a href="http://www.sciencedirect.com/science/article/pii/S2405471216300333">http://www.sciencedirect.com/science/article/pii/S2405471216300333</a>
</li>
<li><a href="http://www.sciencedirect.com/science/article/pii/S1874391916300215">http://www.sciencedirect.com/science/article/pii/S1874391916300215</a>
</li>
<li><a href="http://www.sciencedirect.com/science/article/pii/S1874391916300112">http://www.sciencedirect.com/science/article/pii/S1874391916300112</a>
</li>
<li><a href="http://www.sciencedirect.com/science/article/pii/S1874391916301944">http://www.sciencedirect.com/science/article/pii/S1874391916301944</a>
</li>
<li><a href="http://www.sciencedirect.com/science/article/pii/S2352340915000724">http://www.sciencedirect.com/science/article/pii/S2352340915000724</a>
</li>
<li><a href="http://www.sciencedirect.com/science/article/pii/S2352340915000840">http://www.sciencedirect.com/science/article/pii/S2352340915000840</a>
</li>
</ul>
<p>The ScienceDirect app makes it very easy for a Cytoscape user to generate supplemental material containing a Cytoscape network, as shown in this movie:
</p>
<ul>
<li>
<a href="http://www.screencast.com/users/bdemchak/folders/Jing/media/1c1e23e9-02ed-495c-8767-baed14a24ac6">http://www.screencast.com/users/bdemchak/folders/Jing/media/1c1e23e9-02ed-495c-8767-baed14a24ac6</a>
</li>
</ul>
<div class="col-xs-12 col-md-12">
<h2>Release History</h2>
<table class="table table-condensed table-striped table-responsive">
<tr class="info">
<td><b>Version</b></td>
<td><b>Release Date</b></td>
<td><b>Features</b></td>
</tr>
<tr>
<td>
<h3>U24 Award</h3>
</td>
</tr>
<tr>
<td>3.10.3</td>
<td>10/24/2024</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">Other</td>
<td>
<ul>
<li>Improved Style Panel labels</li>
<li>Require naming of root network</li>
<li>Fix test failure</li>
<li>Enforce column naming across networks</li>
<li>Fix to Equation Builder dialog</li>
<li>Make group collapse/expand more robust</li>
<li>Fix LayoutSettingsDialog NPE (Linux)</li>
<li>Update to latest version of JavaFX</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.10.2</td>
<td>3/26/2024</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">Other</td>
<td>
<ul>
<li>Layout tools exposed in CyREST: rotate and scale</li>
<li>SVG export with Japanese locale</li>
<li>Lucene wildcard query enabled in search bar</li>
<li>Minor bug fixes</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.10.1</td>
<td>8/31/2023</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">Other</td>
<td>
<ul>
<li>Better support for all versions Java 17</li>
<li>Minor bug fixes</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.10.0</td>
<td>5/11/2023</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">Visualization</td>
<td>
<ul>
<li>Edge label rotation allows edge labels to be aligned with the edge slope</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Architecture</td>
<td>
<ul>
<li>String tunables have a "password" property that masks the text field</li>
<li>New LEN() equation function returns the length of a list</li>
<li>JavaFX version upgraded to 18.0.2</li>
<li>The OpenCL app has been moved into core. OpenCL support is now part of the Cytoscape API as the ‘cycl-api’ bundle</li>
<li>The TableVisualMappingManager has new API methods for working with table styles</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">UI</td>
<td>
<ul>
<li>New selection lasso tool</li>
<li>Table styles are now part of the Network Style and are applied to nodes and edge tables</li>
<li>New App Store panel has replaced old "App Manager"</li>
<li>Search bar is faster, more reliable, and includes new types of search queries</li>
<li></li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Other</td>
<td>
<ul>
<li>Java 17 support</li>
<li>Automation: network view can now be exported using new commands</li>
<li>The framework-cytoscape.log file no longer grows forever (entries > 30 days removed)</li>
<li>Native build for Apple silicon processors (M1+)</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>
<h3>R01 Award (Renewal)</h3>
</td>
</tr>
<tr>
<td>3.9.1</td>
<td>1/24/2022</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">UI</td>
<td>
<ul>
<li>Minor fixes to table equations</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Other</td>
<td>
<ul>
<li>Updated log4j dependencies</li>
<li>Automation: updates to annotation and app-related commands</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.9.0</td>
<td>10/21/2021</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">Visualization</td>
<td>
<ul>
<li>Support for native 4k Ultra-HD and Retina display</li>
<li>Improved network rendering performance</li>
<li>Haystack edge rendering improved</li>
<li>New ability to rotate node labels and annotations</li>
<li>Fit content now takes node labels into account</li>
<li>New visual property for z-order</li>
<li>Network view now supports SVG graphics for node and annotation images</li>
<li>New features for Table Panel: cell styles, charts, and copy/paste</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">UI</td>
<td>
<ul>
<li>Equation builder has been redesigned with free form editing field</li>
<li>Color palettes are now universally available in the color picker</li>
<li>Improved hotkey mapping</li>
<li>Filters can now select or highlight nodes and edges</li>
<li>New auto page size option for network view PDF export</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Other</td>
<td>
<ul>
<li>Support for Jupyter Notebooks</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.8.2</td>
<td>10/29/2020</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">I/O</td>
<td>
<ul>
<li>Fixed memory issues when opening large sessions</li>
<li>Fixed memory issues when exporting large networks</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Other</td>
<td>
<ul>
<li>Fixed bug with CyBrowser installation of yFiles and other Apps</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.8.1</td>
<td>9/24/2020</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">UI</td>
<td>
<ul>
<li>Bug fixes for the renderer:
<ul>
<li>Edge tooltip not rendering</li>
<li>Edge bend editing causing all edges to bend</li>
<li>Network view double click not working</li>
</ul>
</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Other</td>
<td>
<ul>
<li>Bug fixes to address memory leaks and race conditions in automation scripts</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.8.0</td>
<td>4/17/2020</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">Analysis</td>
<td>
<ul>
<li>Network Analyzer updated with improved interface and Automation support</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">UI</td>
<td>
<ul>
<li>Updated user interface</li>
<li>Toolbar customizations improved</li>
<li>Panels can now be minimized, set to float, or docked to workspace</li>
<li>Improved rendering performance with interactive experience for networks with 10,000 nodes and 3,000,000 edges</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Other</td>
<td>
<ul>
<li>Java 11 support</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.7.2</td>
<td>9/5/2019</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">Other</td>
<td>
<ul>
<li>Fixed CyNDEx-2 bug where JXBrowser component could not be downloaded</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.7.1</td>
<td>1/10/2019</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">I/O</td>
<td>
<ul>
<li>Fixed freezing bug when exporting Annotations</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">UI</td>
<td>
<ul>
<li>About dialog updates</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.7.0</td>
<td>10/22/2018</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">Installation</td>
<td>
<ul>
<li>Greatly decreased installer size</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">UI</td>
<td>
<ul>
<li>Annotations</li>
<li>Animated Tooltips</li>
<li>Element selector toggles</li>
<li>Splash Screen</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Visualization</td>
<td>
<ul>
<li>BrewerColor palettes in styles</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Other</td>
<td>
<ul>
<li>Updated NDEx Integration</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.6.1</td>
<td>3/26/2018</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">Installation</td>
<td>
<ul>
<li>Automatic Java Installation</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Other</td>
<td>
<ul>
<li>Support for loading/saving NDEx networks</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.6</td>
<td>11/15/2017</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">Workflow</td>
<td>
<ul>
<li>Cytoscape Automation</li>
<li>CyBrowser Integration</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Visualization</td>
<td>
<ul>
<li>yFiles Update</li>
<li>Copycat Layout</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Analysis</td>
<td>
<ul>
<li>Diffusion</li>
<li>New Starter Networks</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">UI</td>
<td>
<ul>
<li>Network Search Bar</li>
<li>Starter Panel</li>
<li>Drag & Drop sessions, networks & tables</li>
<li>Customizable Toolbar</li>
<li>Improved Selection Performance</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Other</td>
<td>
<ul>
<li>Unattended Installation</li>
<li>Mac High Sierra Support</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.5.1</td>
<td>4/26/2017</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">Bug fixes</td>
<td>
<ul>
<li>Malfunctioning slider control</li>
<li>Misdirected link in toolbar help icon</li>
<li>Search bar missed common words</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.5</td>
<td>3/24/2017</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">Workflow</td>
<td>
<ul>
<li>Symbol translation using BridgeDB</li>
<li>Drag/drop for network and table files</li>
<li>Restored BioMart functionality</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Sharing</td>
<td>
<ul>
<li>Integration with NDEx network sharing database</li>
<li>Added web.cytoscape.org for network sharing</li>
<li>Improved/optimized Export dialogs</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Visualization</td>
<td>
<ul>
<li>CoSE Layout (for compound nodes)</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.4</td>
<td>05/13/2016</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">UI</td>
<td>
<ul>
<li>Modern window manager enables use of multiple monitors</li>
<li>Web-based user manual with improved formatting</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Architecture</td>
<td>
<ul>
<li>Support for app collections</li>
<li>Long running task API</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Sharing</td>
<td>
<ul>
<li>Support for interactive networks in Elsevier journals</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.3</td>
<td>11/25/2015</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">Workflow</td>
<td>
<ul>
<li>Network Analyzer is more than 1000x faster</li>
<li>Filtering based on properties of adjacent nodes</li>
<li>Improved/optimized network and table file importer</li>
<li>GPU support for Prefuse layouts (100x faster)</li>
<li>New GPU-based graph render (100K nodes in 1/40 second)</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Visualization</td>
<td>
<ul>
<li>Improvements in Group settings & visualization</li>
<li>Default network layout is now force directed</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">UI</td>
<td>
<ul>
<li>Aesthetic and consistency improvements in many dialogs</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Architecture</td>
<td>
<ul>
<li>Core functions repackaged as apps for frequent improvement</li>
<li>Automatic new version alerts for installed apps</li>
<li>cyREST as core app delivered with Cytoscape</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.2.1</td>
<td>02/11/2015</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">Other</td>
<td>
<ul>
<li>Java 8 support</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.2</td>
<td>11/07/2014</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">Workflow</td>
<td>
<ul>
<li>Refactored/optimized visual attribute mapper interface</li>
<li>Faster startup, session load, and network merge</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Virtualization</td>
<td>
<ul>
<li>Ability to show nodes as dynamic charts</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Automation</td>
<td>
<ul>
<li>RESTful interface enables “Cytoscape as a Service”</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Other</td>
<td>
<ul>
<li>Higher capacity for large graphs (both memory and draw speed)</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Sharing</td>
<td>
<ul>
<li>Export graph as a fully packaged web site ready for a web server
</li>
<li>CyNetShare web-based network viewer</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.1.1</td>
<td>05/27/2014</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">Workflow</td>
<td>
<ul>
<li>Improved network and attribute imports for Excel, CSV, and TXT files
</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.1</td>
<td>02/13/2014</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">I/O</td>
<td>
<ul>
<li>Fast PSICQUIC download and merging</li>
</ul>
</td>
</tr>
<tr>
<td style="width: 100px; vertical-align: text-top">Workflow</td>
<td>
<ul>
<li>Fast filter execution - O(n) instead of O(kn)</li>
<li>Welcome screen improvements w/<i>D. rerio</i> and <i>E. coli</i> presets
</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>3.0.2</td>
<td>07/30/2013</td>
<td>
<table>
<tr>
<td style="width: 100px; vertical-align: text-top">UI</td>
<td>
<ul>
<li>Reorganized user interface</li>
</ul>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td>
<h3>R01 Award (Initial)</h3>
</td>
</tr>
<tr>
<td>3.0.1</td>
<td>04/22/2013</td>
<td>
<table>
<tr>