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1. and once a plugin is converted to an app it will continue to work at least until v4 0 is released there is no v4 0 planned at this time For more on this topic see http wiki cytoscape org Cytoscape 3 CoreDevelopment Motivation Should I Convert My v2 x Plugin to a v3 x App Yes Cytoscape v2 x will be supported by the Cytoscape community for now but with fewer upgrades and support options over time How Do I Get Started With App Development To get started with app development http wiki cytoscape org Cytoscape 3 AppDeveloper Cytoscape A Ladder To convert a v2 x plugin to a v3 x app refer to http wiki cytoscape org Cytoscape 3 AppDeveloper PluginPortingGuide or http f1000research com articles 3 150 v1 For a broader view of the Cytoscape system including the Core refer to http wiki cytoscape org Cytoscape 3 CoreDevelopment Are there App Samples Yes See Also note the App Cookbook http wiki cytoscape org Cytoscape 3 AppDeveloper Cytoscape 3 A Cookbook 5 General Background The overall mission of Cytoscape is to be a freely available worldwide asset supporting network analysis and visualization for systems biology science The major focus of v3 x is the modularization and rationalization of code to solve stability issues in v2 x encountered as multiple developers pursued multiple agendas Under v2 x internal programmatic interfaces evolved from one release to the next leading to the failure of wo2. the network Diffrent representation of group edges when using None vs Show Group Node Save session with groups on session restore groups are gone Need some way to change the shape for compound nodes Need some way to set the amount of padding for a compound node Group aggregation preferences added options Custom Graphics Manager and Charts Editor are hard to find InstallAppsPanel updated outside Swing thread causing occasional exceptions Change CyStatusBar icon if error warning occurs Move X axis line in bar chart to x 0 Layout with empty context causes warning dialog to appear at startup Command network import file doesn t provide a way to indicate column type Command line versions of network import file and network import url are broken Function Builder UI has some issues Missing Negate operator on filters Table merge shouldn t allow non Integer String columns to be selected as keys Import Network from Table ignores node identifier mapping column always uses name shared name Save layout settings Unable to retrieve the value of the Edge Target Arrow Shape property if set by style default Table preview does not reflect data used for import Table import doesn t display errors for values that are incompatible with selected column type Control font size on cychart domain and range labels When hiding nodes or edges they should be unselected Error warning icon persists after pop up dialog Filters pane is missing Topology Filt
3. 3 x e Surf to http www cytoscape org click on the Download Cytoscape button and follow the prompts e Be sure to consult with the Release Notes viewable via the Release Notes button for issues and solutions pertaining to your installation e Surf to http www cytoscape org click on the Release Notes button click on a User Manual link and follow the instructions in the Launching Cytoscape section How to Troubleshoot Cytoscape Installation Cytoscape v3 3 requires Java 8 preferably with 64 bit support You can learn whether your environment is sufficient to execute Cytoscape by following the Troubleshooting instructions at http www cytoscape org troubleshooting html 4 For Cytoscape App Developers Cytoscape manages graph storage and display and contains a number of common analytic and visualization functions App Developers may write apps formerly known as plugins to perform problem specific analytics graph layouts or other visualizations Before starting app development you should be familiar with overall Cytoscape usage and functionality see the Power Users section Section 3 to start working with v3 x if you have not already done so Note that v2 x plugins do not work with v3 x In order get the benefits of improved stability the Cytoscape team found it necessary to change the relationship between plugins apps and the Cytoscape core Many plugins have been ported to v3 x see Section 6 The porting exercise is substantial
4. November 15 2015 Welcome Summary e Cytoscape v3 3 is now available for immediate download e Major new features Network Analyzer is more than 1000 times faster Filters can select based on properties of adjacent nodes and can edit selections Improved network and table file importer GPU support for Prefuse layouts Improvements in Group settings amp visualization Default network layout is now force directed Aesthetic and consistency improvements in many dialogs Cytoscape core functions are repackaged as apps that can be improved often Cytoscape now detects when new versions of your installed apps are available cyREST is now delivered with Cytoscape Java 7 is no longer supported e Addresses 193 issues relative to v3 2 1 see Section 10 O O O OO Or 3O 2 3O O Numerous UI consistency amp operational issues Improvements in Group settings amp visualization New DOT file reader Updated BioGrid files Marching ant animation for edges Removing duplicate edges much faster More and better arrows on directed edges e 26 more Apps are available in the App Store as compared to the v3 2 1 release O O 0O 3 20 20 20 e Ready for use by all segments of the Cytoscape community e Continues v3 2 s core feature set specifically Oo Upward compatible and can coexist with previous Cytoscape versions Oo Most popular plugins from v2 x versions are available as apps with more to follow e What to do next Rele
5. and web publishing This new release is v3 3 While all version 3 releases are upwardly compatible with previous Cytoscape versions i e they can load analyze and display networks and attributes stored using previous versions including v2 x they can coexist with previous versions on the same workstation It is not necessary to uninstall previous versions before installing a version 3 release and you can choose to use both on the same workstation Version 3 is rapidly maturing and has achieved a reputation for speed reliability and support that makes it a superior choice compared to v2 x for most uses If you are using v2 x now may be a good time to switch to v3 x and enjoy the new Apps available in the App Store http apps cytoscape org A table describing Cytoscape support is presented in Section 8 We are very excited to make this release and hope you find it an indispensable tool in your research To get you started we have provided additional introductory material to get you started on the right foot and we have also provided background material for general interest Please let us know how we re doing and how we can better advance your research The Cytoscape Team What to Do Next We hope to help you use Cytoscape in the most productive way Your next steps depend on how experienced you are with Cytoscape and what you would like to do In the table below please find the category that best describes you and proceed acc
6. ase notes http www cytoscape org releasenotes html Dear Cytoscape User We are proud and pleased to release Cytoscape v3 3 This new release contains both new features and improvements to functionality and documentation as described in Sections 7 and 10 This release marks our most extensive testing efforts to date including 42 different combinations of operating systems and Java Virtual Machines across Windows Linux and Mac OS platforms Check out your system s configuration here http bit ly 1MBbQIJ Note that v3 3 retains support for 32 bit JVMs and Windows XP as they are a significant portion of Cytoscape installations Note too that v3 3 fully supports Java 8 but not Java 7 Finally in v3 3 26 Apps were added to the App Store http apps cytoscape org bringing the total to 102 not including 13 apps that are now part of Cytoscape Core The apps new for v3 3 include cyNeo4j SCODE AdjExplorer RenoDol CytoGEDEVO iCTNet2 ModuLand 2 0 StrongestPath PhosphoPath nciNetView Cy3sbml dot app SLiMScape CySpanningTree Bisogenet General SPARQL Pesca3 0 TieDIE AnatApp PSFC Obfuscator CyAnimator SocialNetwork cyTransFinder ExpressionCorrelation PTMOracle We expect to make a v3 4 release in mid Q2 2016 As our plans firm up we ll publish them to the Cytoscape community http www cytoscape org roadmap html For more on our roadmap see Section 9 If you are a new or casual Cytoscape user welcome aboard Feel free to either rea
7. d on or jump ahead to What to Do Next for a quick start For clarity references to Cytoscape 3 x apply to all Cytoscape versions 3 0 0 and later For Cytoscape v2 x Users Previous Cytoscape releases through v2 8 3 focused on adding numerous annotation import layout analysis and visualization features all of which have combined to deliver critical insights into biological processes of interest to Cytoscape s broad and loyal user community In fact many of these features were created and contributed by Cytoscape users themselves using Cytoscape s plugin architecture Version 3 0 marked a major reorganization of Cytoscape program code it enabled us to deliver additional features more quickly and reliably than before including improvements that benefit new users Casual users power users and app developers Along the way some features were changed to allow them to better interoperate with other features some little used features were dropped and user interface was improved We were particularly excited about the new Cytoscape App Store described below which afforded users access to the growing collection of apps formerly called plugins produced by fellow Cytoscape users A table of new features is presented in Section 7 Since v3 0 we released updates v3 0 1 and v3 0 2 as maintenance releases and then v3 1 and v3 2 as feature releases including greatly improved visual styles node filtering soeed network capacity
8. e formats including text and Excel Cytoscape can also load pre configured networks e g from BioGRID so you can leverage them without having to enter them yourself Can Cytoscape Help Me Get Started Yes The Cytoscape team had provided many resources tailored for all kinds of users see Section 8 To start there is an Installation Guide and numerous tutorials Once you load your graph you may find additional useful analytics and visualizations at the App Store see Section 6 Which Cytoscape Version Should I Use Generally you should use v3 3 the newest version v2 x has been in the field for several years and will be supported into the future but over time v3 x and successors will be better supported Note that if you have already installed v3 0 0 v3 0 1 v3 0 2 v3 1 v3 1 1 v3 2 or v3 2 1 you can install v3 3 without uninstalling your previous version How to Download and Install v3 x e Surf to http www cytoscape org click on the Download Cytoscape button and follow the prompts e Be sure to consult with the Release Notes viewable via the Release Notes button for issues and solutions pertaining to your installation e Surf to http www cytoscape org click on the Release Notes button click on a User Manual link and follow the instructions in the Launching Cytoscape section How to Troubleshoot Cytoscape Installation Normally the main requirement for installing Cytoscape is a Java Virtual Machine JVM appropriate fo
9. er available in v2 x Warning displayed on load when reloading any session saved with 3 3 0 SNAPSHOT The value attributed to a Visual Property may not be the right type JSON reader should accept output from Cytoscape js cy json method Improved arrow selection and control Show selected hide unselected elements Don t reset size on Show text file import options App dependencies not resolved for updates causing some not to load properly 3225 3227 3231 3236 3237 3239 3240 3245 3246 3254 3255 3258 3260 3261 3264 3266 3268 3278 3279 3280 3282 3286 3289 3290 3291 3296 3297 3300 3301 3302 3305 3306 3311 3312 3314 3315 3316 3317 3318 3319 3320 3321 3322 3323 Add extra option for JSON export Network JSON files Style JSON in one zipped file Impossible to assign custom VisualStyle within NetworkReader Calling TaskMonitor setTitle has different effect on second call Default layout for new network view Confirm dialog for creating view with new large network Missing all group edges on collapse groups in cytoscape 3 3 snapshot cytoscape 3 3 0 20150806 205609 608 If node attribute file is not UTF 8 encoded it is hard to determine why file is not loaded properly Creating a copy of a VisualStyle VisualPropertyDependencies not copied CyServiceRegistrar always uses service api BundleContext allowing registered services to outlive bundle Edge weighted layouts alway use Heuristic for weight
10. file loading issue 2960 Import Network from Web Service UI is not consistent with Cytoscape s LAF 2964 Focus issues with modal dialogs on Mac OS X with Java 7 2977 Removing custom graphics in visual mapper 2990 Feature Request Label Width property for edges 3001 Support Bypass in Web Session Exporter 3030 Bypass does not work for Label Width property 3033 Improve support for multiple renerers 3034 API changes for multiple renderers 3035 3036 3037 3038 3039 3043 3044 3045 3048 3051 3052 3053 3055 3058 3059 3060 3061 3065 3069 3071 3073 3075 3078 3079 3080 3082 3083 3084 3088 3089 3092 3094 3095 3096 3113 3115 3117 3118 3120 3121 3122 3123 3125 3126 Update layout API to support Z coordinates Add support for 3D to BioLayoutFRAlgorighmTask Allow a VisualLexicon to hide visual properties New network from selection button always creates a DNetworkView Import network dialog should allow you to choose the renderer The Style GUI shows Dependencies that are not supported by the current renderer The Style GUI shows discrete visual property values that are not supported by the current renderer New Empty Network dialog should allow you to choose the renderer CyApplicationManager should have a method that returns all the registered NetworkViewRenderers VizMapper does not properly support multiple visual lexicons Dialogs lack default ENTER ESC key mappings Deleted nodes and edges still show
11. groups com http wiki cytoscape or UserManual Section 3 of http wiki cytoscape org Cytoscape 3 UserManual http opentutorials cgl ucsf edu inde x php Portal Cytoscape3 https speakerdeck com cytoscape Cytoscape 3 http wiki cytoscape org Cytoscape_3 AppDeveloper Cytoscape_3 App Co okbook 9 Future Plans Table Feature Core workflow Distributed computing Additional Visualizations Additional Analytics Wallpaper Collection Cytoscape Clinics New Casual User Power User App Developer Purpose Enable symbol translation as networks tables are imported Link to NDEx and other external storage and compute services Publicize good results associated with Cytoscape Chat rooms give instant response based on community availability Timeframe Apr 2016 Beneficiary Power users All users Apr 2016 All users potential users general public All users 10 Issues Addressed The following issues were addressed in v3 3 Details for each issue can be found at Cytoscape s RedMine issue repository http code cytoscape org redmine Issue Description 1866 Design and implement Text Encoding Decoding Policy 2360 Adjusting an edge handle also moves selected nodes 2388 Inport Network From File or URL a bug that allows an app developer to make it unusable 2480 Rows of deleted nodes edges are displayed in the Table Panel 2498 Cut option not available from menubar Edit menu for edges 2518 Cytoscape com
12. he App Store http apps cytoscape org contains a list of apps available for v3 x To access the App Store from Cytoscape access Cytoscape s new Apps menu and choose the App Manager menu item 7 New Feature Table Feature Beneficiary Manual Section Fast Network Analyzer All users 18 NetworkAnalyzer Filtering on adjacent nodes values Power users 12 2 Filters New network table importer All users 6 Creating Networks Prefuse layout w GPU support Power users 13 Navigation and Layout New group settings visualization Power users 6 4 3 Grouping nodes Better default network layout All users 13 Navigation and Layout Consistency improvements New users Modular Cytoscape via core apps All users 3 Launching Cytoscape App update detection All users 15 App Manager Cytoscape as a service via cyREST Power users 25 Programmatic Access Java 8 now required All users 3 Launching Cytoscape Feature Cytoscape Google Groups Helpdesk Discuss User Manual Installation Guide Tutorials Presentation Slides on Web Site Code Snippets 8 Support Offering Table Purpose Community response on best effort basis Comprehensive manual Cytoscape installation Streamlined productivity Enable casual learning Commonly used App development code Beneficiary All users All users New Casual users All users All users App Developers mailto cytoscape helpdesk googlegroups com mailto cytoscape discuss google
13. ing v2 x plugins to v3 x apps you might occasionally revisit the App Store to see if an app you need becomes available What s New in v3 x As described in the Welcome letter above v3 x incorporates a number of new features Section 7 and productivity enhancing support offerings Section 8 including the Cytoscape App Store Section 6 The General Background section Section 5 describes the rationale advantages and issues with v3 x Will Support for v2 x Continue Cytoscape v2 x will be supported by the Cytoscape community for now but with fewer upgrades and support options over time Can I use v2 x and v3 x at the Same Time You can experiment with v3 x by installing it on your workstation you can use both v2 x and v3 x on the same workstation How to Prepare for v3 x 1 If you have already installed a v3 3 beta version please uninstall it before proceeding The Cytoscape v3 0 v3 1 and v3 2 versions can coexist with v3 3 and do not need to be uninstalled 2 Consult the App Store Section 6 to verify that the apps you need are available Some apps have become part of the Cytoscape core and you won t need to download them Other apps are available in the Cytoscape App store 3 Browse the New Features table Section 7 to see what we have added since v2 x 4 Browse the Future Plans table Section 9 and Support Offering table Section 8 to see where the Cytoscape community is going How to Download and Install v
14. m the v3 x by e experiencing fewer core and app bugs from one release to the next e the availability of more and richer apps due to developers spending less time tracking and fixing bugs e more core features with higher biological and logistical value due to improved flexibility provided by interface driven development During the creation of v3 x a number of features were added as listed in the New Feature Table below 1 n www osgi org also used as the basic framework for Eclipse and numerous commercial products 6 The Cytoscape App Store The Cytoscape App Store is new in v3 x and targets broad demographics through specific features Cytoscape User Benefit New or Casual Find Cytoscape functionality easier via familiar paradigms of search and tag navigation Power or Frequent Find and install apps easier and provide crowdsourced rating and reviews App Developers Have a dedicated presence for their work including a direct line to their users and critical statistics to justify their development on the Cytoscape platform Furthermore the App Store supports contests and social incentives that encourage critical technical and community development including porting analytics rating reviewing and so on Note that the App Store supports only Cytoscape v3 x and does not contain plugins compatible with earlier Cytoscape versions Likewise plugins that work with earlier versions are not compatible with v3 x t
15. mands use attribute for node edge network but column for table 2521 Error not displayed when app fails to install in App Manager 2541 Cytoscape Specific Functions 2567 Need way to export only certain visual styles 2573 Incorrect custom graphics width 2591 Create families of styles that can seed a style library 2658 Cytoscape does not import empty columns from an xml file 2754 Support the use of Java core libraries not included in default Karaf environment 2756 Style selector UI is too long 2787 Remove Duplicate Edges appears unresponsive extremely slow on large networks 2821 Some uses of Java Stream libraries do not explicitly specify UTF 8 2833 Subsequent import from excel files does not clear the import table preview does not show all sheets 2865 Custom Graphics Size Visual Property has no effect to charts 2867 SVG Export function is not fully functional 2907 Enable GraphML Writer 2908 Provide support for compound node visualization using groups 2910 AggressiveHeap not allocating sufficient memory on Java 8 2931 CollapsiblePanel does not look good on Nimbus LAF 2932 Advanced Network Merge dialog does not have consistent UI 2934 Tunables Group Labels panel titles should not be colored 2936 Table Merge dialog looks unprofessional 2937 Set Preferred Layout UI is more complicated than it should be 2938 The toolbar search field should have the Mac OS X style 2939 Cytoscape UI has some inconsistencies 2957 attribute
16. nted home directory Adding new CyNetwork with no name to CyNetworkManager does nothing Installable Upgradable Core Apps make NetworkAnalyzer an external app Startup check for installed apps Core wide logging mechanism for non fatal errors Report app failures to users Improve table loader UI Implement compound node visualization toward multiscale networks Reference implementation for alternate renderers incl docs recipes samples 3128 3130 3131 3134 3136 3137 3138 3139 3140 3141 3142 3143 3144 3145 3147 3148 3150 3154 3157 3159 3170 3179 3180 3181 3182 3186 3187 3191 3193 3197 3199 3202 3204 3205 3207 3208 3209 3211 3213 3215 3217 3218 3223 Update documentation tutorials for 3 3 Marching ant animations on edges Merge cyREST REST commands into single REST implementation Case sensitive checkbox for table import doesn t work XGMML Writer creates real type for Long column data Unable to specify key column for network when importing a table to to selected network only If you chose Edit gt Preferences gt Group Preferences gt Visualization for gorup Show group node you loose style on expanded group Unable to get rid of group single node representation once a group has been drawn that way Group edges missing names Group attribute aggregation not working Group Node does not disappear after collapse and expand Cloned network with groups adds all the group nodes to
17. or Network Analyzer core app Create description in App Store App Manager for Network Merge core app Create description in App Store App Manager for PSI MI core app Create description in App Store App Manager for SBML core app Create description in App Store App Manager for BioMart core app Create description in App Store App Manager for PSIQUIC core app 3324 3326 3327 3328 3330 3332 3333 3337 3340 3345 3348 3351 3352 3354 3356 3364 3365 3366 3369 3371 3374 3377 3384 3385 Create description in App Store App Manager for Welcome core app Topology filter bad performance Arrange edge interaction default to be interacts with instead of pp Can t load 3 2 topology filter in 3 3 Performance issues with nested topology filters MITAB files in new version of BioGRID not parsed correctly Filter Chain tab is not cancellable HTML not parsed in task status dialog Submit 3 3 0 core app versions to App Store create arrow annotation throws NPE External Links context menu throw exception when used on group node Views appear zoomed in after importing network Network windows have large border on OS X 10 11 El Capitan basic installing compiling not working Cannot disable menu items in network view context menu Color based continuous mapping uses incorrect min max values OpenCL Prefuse layout intermittently hangs on retina MacBook Pro Update default and custom node styles for galFiltered Create description in App St
18. ordingly Type of Cytoscape User Where to Read Next New For New Users Section 1 Casual For Casual Users Section 2 Power For Power Users Section 3 App Developers For App Developers Section 4 General Interest Try getting oriented by reading General Background Section 5 Cytoscape App Store Section 6 Then try browsing New Features Section 7 Support Offering Section 8 Future Plans Section 9 To get your feet wet try For New Users Section 1 1 For New Cytoscape Users What is Cytoscape Cytoscape is software that can help you visualize complex networks as graphs representing relationships between genes proteins or other entities Cytoscape tracks and displays these entities as graph nodes and relationships between them as graph edges Cytoscape per se does not assign meaning to either nodes or edges you can assign your own meanings to them and you can add your own node or edge attributes e g name measurements states etc that customize your graph to represent semantics important to you While Cytoscape provides simple analytics and visualizations others are available as apps from the Cytoscape App store see Section 6 What Do I Need Before I Can Use Cytoscape At the very least you must provide Cytoscape with a list of nodes You can also provide a list of edges and attributes You can enter your graph manually or import it from your own files Cytoscape supports a wide variety of fil
19. ore App Manager for CyCL core apps FitContent is not properly applied to dummy view in Edge Bend Editor Species images are mislabeled Invisible vertical slider Remove duplicated edges gt doesn t delete duplicated self edges By default the delimiters for importing a network or table from TXT files are TAB and SPACE
20. r your workstation For Windows users the JVM commonly installed is a 32 bit version even if the Windows itself is 64 bits For Cytoscape use the 64 bit version is recommended For all workstations Java 8 is required Regardless of your workstation operating system you can learn whether your environment is sufficient to execute Cytoscape by following the Troubleshooting instructions at http www cytoscape org troubleshooting html 2 For Casual Cytoscape Users If you re confident of your Cytoscape skills please read the Power Users information Section 3 If you re Cytoscape skills are rusty please continue with the New Users information Section 1 3 For Cytoscape Power Users Is v3 x for Me The answer is most likely yes Most modern v2 x plugins have been converted to v3 x apps and new v3 x apps are arriving in Cytoscape s App Store far more quickly than v2 x plugins app is the v3 x name for the installable features known as a plugin in v2 x To take stock you can browse the App Store directly Section 6 Note that some v2 x plugins have been incorporated directly into Cytoscape and need not be downloaded or installed Consult the App Store to see a list of these apps Note that v2 x plugins are not compatible with v3 x apps and vice versa If you rely on v2 x plugins that are not yet available for v3 x you may need to remain with v2 x instead of upgrading to v3 x Note also that the Cytoscape community is convert
21. rking plugins over time and negative interactions between otherwise working plugins Ultimately this resulted in loss of programmer and user productivity and undermined community confidence in Cytoscape v3 x addresses these issues by adopting modular coding practices promoted by the OSGi architectural framework This enables both the Cytoscape core and externally developed apps formerly called plugins to evolve independently without compromising unrelated functionality At the logical level Cytoscape leverages OSGi precepts to produce v3 x APIs having cleaner and clearer demarcations between functional areas At the deployment level OSGi enables on the fly substitution of one processing element for another e g apps in order to tailor Cytoscape to meet user requirements at runtime without reinstalling or reconfiguring Cytoscape Creating v3 x occupied an international team of engineers for over a year and represents a strong investment toward reducing future development and support costs and increasing reliability and evolvability With the completion of v3 x we expect to leverage v3 x as a platform to satisfy the evolving needs of multiple stakeholder groups and as a platform enabling research on leading edge analysis and visualization techniques v3 x is the intended successor to v2 x with development and support of v2 x expected to diminish and disappear over time in favor of v3 x We believe that users will benefit most directly fro
22. type Exception thrown when hiding certain nodes Add group column aggregation option for lists Update Cytoscape js library in the template to the latest version Error message displayed at bottom of TaskDialog File gt Recent Session doesn t report errors to user Layout Settings should be restored on startup Numeric equations have nonsense requirements Equations chained in integer columns cause bogus error Loading a table bug NullPointerException when creating a CyNetworkReader Column filter does not update properly when switching column type Column filter slider has erratic behaviour Create a Cytoscape Palette New transformers for Chain tab Unable to right click in mapping area Exception on loading cys file Recent session list should have some reliable order Filters Ul cleanup Remove pre java 5 dependencies org jdesktop layout Opening recent session in Welcome Screen does not show confirmation dialog Install from File doesn t test for app compatibility Console window has lots of cyREST warnings during startup Core apps should have description on App Store App Manager Core apps should have more concise titles Create description in App Store App Manager for BioPax core app Create description in App Store App Manager for Command core app Create description in App Store App Manager for cyREST core app Create description in App Store App Manager for BioGrid core app Create description in App Store App Manager f
23. up in table browser Error loading GML with edge amp quot directed amp quot attribute Sometimes collapse expand of CompoundNode doesn t result in CompoundNode visualization CyGroupSettings needs an API Group settings need to be serialized deserialized with sessions When doing compound nodes should automatically do implicit collapse expand on creation Field labels sometimes end in a colon sometimes don t Degree filter not functioning CSV file fails to import with loading network from table input length 1 error Open File Problem Add an edge after creating a group deletes edge when group is collapsed Make galFiltered easier to find Read and write GraphViz dot files Cannot import CytoscapeJS JSON file Error saving session with CyProperty that has SESSION_FILE_ AND_CONFIG_DIR save policy Compound nodes not getting visualized properly when the session is loaded Moving a node within a compound node that is within a compound node leads to some strange movement of first level compound node integration tests need to set GroupView property to work correctly Paths with backslashes don t work properly with N option and perhaps others Batch Analysis fails if input directory has invalid network file Tunables GUI is not consistent Groups nodes inside compound nodes are missing labels Groups strange rendering of compound node Need to fix Preferred Layout settings Copying Biogrid files on initial startup extremely slow with network mou
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