1. For New Cytoscape Users
Contents
1. 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 x marks a major reorganization of Cytoscape program code it enables 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 are particularly excited about the new Cytoscape App Store described below which affords 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 While version 3 x is upwardly compatible with previous Cytoscape versions i e it can load analyze and display networks and attributes stored using previous versions including v2 x it can coexist with previous versions on the same workstation It is not necessary to uninstall previ2. link layout Searches for differentially altered links in a given network using multiple set of expression data Makes a similarity network where nodes are genes and edges denote highly correlated genes Performs stochastic simulation of chemical reaction networks Visualizes fluxes as visual effect to edges on Cytoscape network Performs one of the fastest multilevel force directed Layouts called FM3 Layout introduced by Hachul S et al 2005 Integrates and visualizes co expression network with biological role of transcripts e g GO terms Centrality measures are equipped Multiple local alignment of protein protein interaction PPI networks Generates interaction networks from public databases based on user s list of genes Also provides annotation and putative function for those genes Enables communication with GenomeSpace Available in App Store Available in App Store Available as part of core Available in App Store Available in App Store Available in App Store Available in App Store Genoscape GFD Net Analyze a gene network based on Gene Ontology GO and calculate a quantitative measure of its functional dissimilarity Network analysis according to the Guimera Amaral cartography Creates image from attribute values URL using the Google Chart API Enables import of GPML file via import menu Calculates graphlet small connected non isomorphic subgraph degree distribution Goog
3. 1802 cannot save All Users 1844 New table Merge Tool Power Users 1846 IOException resetting to invalid mark when trying to find a Developers CyNetworkReader for a FilelnputStream 1867 App Manager does not retry accessing App Store if first connection All Users failed 1869 Unloading a bundle that registers a layout doesn t unregister Developers layouts 1872 Layout settings dialog does not respond to newly loaded layouts All Users 1873 Export gt Network Menus are disabled if network view does not All Users exist 1895 Cancel does not work for Session Loader All Users 1898 Prompt to continue opening session appears after expanding cys All Users file 1906 Update sample POM files to reflect release API Developers 1908 Tunable dialog lost title if the params ForceSetDirectly true is set All Users 1909 NetworkAnalyzer UI doesn t fit in Results CytoPanel All Users 1918 Samples are useless until we rename those New Users 1919 Launching Cytoscape via scripts on Mac doesn t initialize menu All Users properly 1928 Create new filter API and UI Developers 1930 unable to scale nodes All Users 1935 Filtering unusably slow with large networks 500K nodes edges Power Users 1944 Select gt Nodes gt File ID list File does not work Power Users 1957 importing scientific notation values All Users 1968 Mac Pan Add edge handle All Users 1969 Feature revamp the vizmapper GUI All Users 1970 Pointless menu item All Users 1977 Tool
4. Developers 2405 Fit Label Width feature does not work in 3 1 All Users 2407 Reader manager returns wrong reader for URL import All Users 2408 Tools menu order different from Cytoscape 3 0 x All Users 2414 Ontology and Annotations not working again Seems to be related All Users to table import 2423 CSV replaces commas with newlines All Users 2424 File exported to incorrect location and incorrect name All Users 2430 Update documentation for annotation api to reflect correct Developers package 2433 Need to replace fragile getExtension methods Developers 2435 Cannot read PSIMI XML v2 5 4 All Users 2441 tableimport failed to create a tmp file All Users 2442 Loading large network from cys file results in deadlock Power Users 2444 BioPAX ID_UNIPROT column displays not a primary ID All Users 2445 File gt Export gt Table is always disabled All Users 2450 Network Merge throws NPE when user specify List column as merge Power Users key 2455 Some of the Link Out URLs are broken Developers 2461 Cancel takes forever in Network Merge All Users 2463 Reinstating modal task manager Developers 2466 Clearing visual properties in DGraphView s setViewDefault degrades All Users performance 2467 Need NCBI Gene Column for BioGRID Data Import All Users 2469 Edge Color unselected All Users 2471 Copy Style feature does only a shallow copy All Users 2476 VisualStyle apply CyRow View is broken Developers 2481 Undo Delete Nodes Edge
5. a User Manual link and follow the instructions in the Launching Cytoscape section 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 provided you use the apps formerly known as plugins available for v3 x apps are available from the new Cytoscape App Store which you can browse directly Section 6 Note that some v2 x apps have been incorporated directly into Cytoscape and need not be downloaded or installed Consult the Apps Status table Section 8 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 converting 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 9 including the Cytoscape App Store Section 6 The General Background section Section 5 describes the rationale advantages and issues with v3 x Will Support
6. 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 1 beta version please uninstall it before proceeding The Cytoscape v3 0 x versions can coexist with v3 1 and do not need to be uninstalled 2 Consult the Apps Status table Section 8 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 described in Section 6 3 Browse the New Features table Section 7 to see what we have added since v2 x 4 Browse the Future Plans table Section 10 and Support Offering table Section 9 to see where the Cytoscape community is going 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 4 For Cytoscape App Developers Cyt
7. panel blocks Vizmapper All Users 1984 Panning de selects nodes All Users 1986 Installing apps via command line arguments b or p doesn t Power Users work 1998 Icon suggestion Table settings All Users 2008 Loading network from file All Users 2009 MapTableToNetworkTablesTask should provide a way to map to Developers columns other than SHARED_NAME 2011 Importing files All Users 2016 getJMenu in CySwingApplication blindly appends gravity value to Developers menu string creates new menus if they don t exist 2022 cannot be saved All Users 2026 Backport 2002 All Users 2027 Cannot load network in 3 0 1 All Users 2029 VizMapper ClassCastException when editing Discrete Mapping for All Users visual property Node Label 2030 Edge label font size All Users 2032 h option doesn t properly display help screen All Users 2034 Search should have an option to not be case sensitive All Users 2036 Bugs in Group Ungroup collapse expand hide unhide All Users 2041 2044 2047 2051 2052 2054 2060 2063 2068 2072 2079 2080 2087 2088 2089 2090 2091 2092 2093 2095 2096 2098 2099 2102 2109 2112 2114 2119 2121 2126 2137 2140 2141 Tasks returned by createTaskiterator File in LoadTableFileTaskFactory abort with NPE edge font size NPE when setting Continuous Mapping to Node Edge Label if current Network View is null Add a column when a local column already exists throws an exception but ge
8. the Core refer to http wiki cytoscape org Cytoscape _3 CoreDevelopment Are there App Samples Yes See http opentutorials cgl ucsf edu index php Tutorial Creating a Simple Cytoscape 3 A 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 working 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 elem
9. 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 file 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 9 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 1 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 or v3 0 2 you can install v3 1 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
10. February 13 2014 Welcome Summary e Cytoscape v3 1 is now available for immediate download e Relative to v3 0 2 it addresses 236 issues e Itis ready for use by all segments of the Cytoscape community e It continues v3 0 s core feature set specifically o Itcontains improvements for all segments of the Cytoscape community o Itis upward compatible and can coexist with previous Cytoscape versions o The most popular plugins from previous versions are available with more to follow o Support offerings have been updated and broadened e t includes 10 major feature updates e 18 more Apps are available in the App Store as compared to the v3 0 2 release e What to do next Dear Cytoscape User We are proud and pleased to release Cytoscape v3 1 This new release contains both new features and improvements to functionality and documentation all of which are described in Section 11 Additionally the App Store contains 28 more Apps than were available when v3 0 0 was released bringing the total to 41 Since v3 0 2 18 Apps were added including bayelviraApp eXamine MetDisease CoNet Gasoline MetScape CyKEGGParser GenomeSpace Pathway Scoring Application CyTargetLinker GIANT PEPPER CytoNCA HyperModules Reactome FI Plugin Enhanced Graphics KEGGScape WikiPathways If you are a new or casual Cytoscape user welcome aboard Feel free to either read on or jump ahead to What to Do Next for a quick start For clarity references to
11. e node CentiScaPe Calculates topological characteristic values Available in App ex Centralities for each node Store ChemViz Visualizes chemical structure of each compound in chemical network with original interface Creates and visualizes a functionally Available in App organized GO term network or pathway Store from given interaction network CluePedia Pathway insights using integrated Available in App experimental and in silico data Store clusterMaker Clusters densely connected nodes and node In Progress attributes i e expression data in a given network Results of these two types of clustering can be analysed in the integrated interface ClusterONE Finds overlapping protein complexes in a Available in App protein interaction network Clusters are Store visualized by original interface with their p values ClusterViz Clustering based on FAG EC EAGLE or Available in App MCODE Found cluster can be subjected to Store GO enrichment analysis commandTool Provides simple command line interface to Cytoscape Comm Finder Clustering based on QCUT HQCUT MCL MCODE Commonattributes Find attributes shared between selected nodes Clustering based on FAG EC EAGLE or Available in App MCODE Found cluster can be subjected to Store GO enrichment analysis ConsensusPathDBplugin Retrieves interaction evidences for given pair of genes or proteins Cy3 Performance Reporter CyAnimator CyClus3D CyGoose Cyni Toolbox Collects
12. ent 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 from 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 As a result we incurred a number of current and future costs Cost Reason Time frame for addressing Slower startup time OSGi module inventorying near to medium term Loss of plugins Lag in upgrading less popular as needed plugins 1 A www osgi org als
13. er 11 Issues Addressed The following issues were addressed in v3 1 Details for each issue can be found at Cytoscape s RedMine issue repository http code cytoscape org redmine Issue Description Beneficiary 766 Need to think about Tools menu item Likely confusion between All Users Tools and Apps 1087 New edge drawn incorrectly if you zoom while placing edge All Users 1251 Checking to save session before closing and opening another All Users session 1383 Need more realistic tests for Session Integration Test All Users 1419 Visual Style is not refreshing All Users 1448 Toggling Show All under VizMapper gt Visual Mapping Browser All Users causes z order to change 1516 Newly installed version of Cytoscape using old cached bundles All Users 1524 Nested Network renderer doesn t compute bounds properly Power Users 1540 Node disappears after adding its own network as a nested one Power Users 1644 Handling of app dependencies in the App Manager Developers 1645 Need way to specify order for Tunables Developers 1700 Exported cytable files can t be imported into a different session All Users due to use of SUID as primary key 1707 Annotation selection not working right All Users 1767 Need API to allow apps to clean up after being uninstalled Developers 1795 VizMapper does not refresh after visual styles are applied All Users 1796 Visual mappings not applied to view as attributes are specified in All Users table view
14. er users wanting to present 23 Cytoscape js and networks on web pages Cytoscape Merge columns Users of attributes in multiple tables 17 2 Merging Tables Command line interface Power users creating repeatable 24 Scripting workflows REST interface Power users using other applications to communicate with Cytoscape New filter facility All users 12 Finding and Filtering Nodes and Edges Automatic citations Users publishing Cytoscape analyses 5 3 8 Help Improved PSICQUIC All users needing to download access protein databases 8 App Status Table For the most up to date list of apps see the App Store described in Section 6 A URL for our development list is shown below as a list of apps and their status at the time this letter was authored https docs google com spreadsheet ccc key OArzUWDuvdBn dDIOROkwOERjN1ZhcDZseCOOdVZNNIE amp authkey CMGe99EM gid 0 App Capability Status addParentNeighbors For a selected node in child network adds neighboring nodes from a parent network AdvancednetworkMerge Merges multiple networks AgilentLiteratureSearch Mines scientific literatures to find ones Available in App related to search term and to create Store interaction network based on the search result AllegroMCODE Very fast clustering based on MCODE algorithm APCluster Uses affinity propagation described in Frey BJ and Duec D 2007 to perform clustering APID2NET Downloads PPI data from http bioinfow dep usal es apid and p
15. erforms various analyses including protein motif GO hub identification etc through the original GUI Equipped with impressing rainbow coloring of nodes BiLayout Finds a bipartite network for two sets of user selected nodes and performs layout Calculates overrepresented GO terms in Available in App the network and display them as anetwork Store of significant GO terms bioCycPlugin Loads any pathway in bioCyc database In Progress Original panel provides useful information for each node BiomartClient Retrieves attributes associated with given gene or protein BioNetBuilder Through the wizard user can easily construct networks from public databases User can also create interologs BioQualiPlugin Performs consistency check of regulatory network and expression data Bisogenet Retrieves interactions associated with input IDs Sophisticated UI gives links to GO KEGG etc BLAST2similarityGraph Visualizes BLAST similarity as graph bayelviraApp Builds Bayesian networks using a file of Available in App patterns as input data using Naive Bayes Store Semi Naive Bayes Selective Naive Bayes TAN KDB and Class Tree Naive algorithms Integrates interaction datasets from different resources to explore the integrated network and to perform confidence analysis for interactions User can give weight to each interaction set which will be used for the level of confidence CalculatenodeDegree Simply calculates degree for selected singl
16. ganic network interface Changes to one edge bend apply to all in network with edge bend visual mapping PSICQUIC Expand Node feature should use new importer not the MiCluster one Legend labels are not alphabetically ordered Table Browser Selecting rows through the keyboard do not change node edge selection Update Preset Visual Style for 3 1 Table Browser Control click deselects other selected rows on Mac VizMapper should treat NAN as empty value Cannot Unlock Node Width Height Layout gt Clear Edge Bends doesn t do anything Missing test cases for Cytoscpae js exporter Provide more useful message for cancellation in PSICQUIC Client Keep data source selection as a part of core property for PSICQUIC Race condition when columns deleted while BrowserTable is updating NetworkAnalyzer Help Does Not Point to Valid URLs New task monitor displays last task s message indefinitely Importing a Table from File Should Act LoadTableFileTaskFactory no longer merges table in 3 1 Merge data access rest service to rest impl Importing a broken BioPAX does not provide correct user feedback Map Uniprot ID or NCBI Gene ID as String Column for PSICQUIC Equations are not saved in the session Power Users Power Users All Users All Users All Users All Users All Users All Users All Users All Users Power Users All Users All Users All Users All Users All Users All Users All Users Power Users Power Users Develo
17. hen All Users Default Has Bends 2318 After Clearing Edge Bends Network Is No Longer Responsive to All Users Changes to the Default 2319 Changes to the default edge bend do not have an effect after All Users Layout gt Bundle Edges gt All Edges and Nodes is called 2320 UI still refers to Visual Style instead of just Style All Users 2324 Decrease number of iterations for Edge Bundling Power Users 2327 Size Visual Property does not work for Continuous Mapping All Users 2329 Need to rework the View menu All Users 2330 Update VizMapper GUI whenever new Bypass is created or when All Users the default is cleared 2331 When all edges are cleared the default displayed inthe VizMapper All Users ought to display properly 2335 JSON is the default format for Style export Power Users 2336 When node width and height are locked mappings does not work All Users 2337 Add user developer document for JSON exporter Power Users 2338 Network Table should be exported as a part of JSON file Power Users 2339 The clear all edge bends menu item does not eliminate mappings All Users 2340 Clear All Edges From This Bend No Longer Working All Users 2342 Create View menu item appears twice on Edit menu since All Users Commands implementation 2343 News section of Welcome screen has light background on Linux All Users 2344 export fails All Users 2350 Remove D3 js JSON exporter code and create external App Power Users 2353 Network View as Gra
18. ianti for news on welcome screen All Users 2186 Need to be able to quit Cytoscape without asking the user if they All Users want to save the session 2190 Visual Style Discrete Edge Mappings Using EDGE_PAINT Don t Work All Users 2191 Malfunctioning Edge paint All Users 2195 Fix bug reporting on Mac All Users 2197 Grid Layout task monitor is passed to a reader Developers 2199 Right click Ctrl click brings up context menu when zooming All Users 2202 Vizmapper Color scheme reverts back to the default if NaN values All Users 2206 Exception when changing layout parameters and executing the All Users layout from settings dialog 2216 PSICQUIC Client creates less edges than actual number of records All Users 2218 Need an event to notify when all apps successfully started Developers 2221 2222 2223 2224 2226 2227 2235 2236 2245 2247 2250 2251 2257 2259 2261 2262 2267 2268 2269 2271 2272 2273 2274 2279 2280 2281 2282 2283 2285 2286 Fix small PSICQUIC GUI Problems Optimize PSICQUIC get interactome query Fix Cancel function for PSICQUIC Client Table Browser ArrayIndexOutOfBoundsException after clicking the Function Builder button with no selected rows Fix cancel function for PSICQUIC Search File gt Import gt Ontology and Annotation does nothing Cy3 hangs during Indexing Network Data task Table Browser Popup menu shown when Change Table Mode button is disabled Improve or
19. information about Cytoscape 3 performance Creates animation based on added frames of network views Clusters a given network based on three node motifs Accepts multiple types of interactions Cluster ID is given to edge attributes EdgeCluster Provides Gaggle Boss which routes data from one application to another Parses and increases accuracy and specificity of KEGG pathways Network Inference Toolbox for inferences from bio data Available in App Store Available in App Store Available in App Store CyOog CyPath2 CyThesaurus ID Mapping CytoCluster cytoHubba CytoKegg GUI client app for Pathway Commons 2 BioPAX L3 pathway data web service Extends biological networks with regulatory interactions Performs ID mapping using BridgeDb and other public or custom database sources Analyze and visualize clusters from network Predicts and explores important nodes and subnetworks in a given network by several topological algorithms Identify Kegg pathways associated to specific expression profiles Providing calculation evaluation and visualization analysis for several centralities of weighted and unweighted network Available in App Store Available in App Store Available in App Store Available in App Store Available in App Store Cytoprophet CytoSaddleSum CytoscapeRPC CytoSEED CytoSQL DisGeNET DomainGraph Finds enriched function based on sum of weight scores Allows use
20. ited using original GUI NetworkAnalyzer Computes basic properties of whole Available as part network degree distribution clustering of core coefficients centrality etc NetworkEvolution Allows interactive comparative analysis of networks across different species nodeCharts Paints bar line or pie graphs onto nodes OmicsAnalyzer Integrates omics data such as expression data proteome data etc onto the network to visualize such data by graph on the network OrthoNets Enables simultaneous comparison of interaction network of two species Protein domain information can be visualized PathExplorer Finds paths filters them based on node Available in App and edge attributes and saves them Store Performs integrated analysis and visualization of PPIs and genetic interactions to infer functional modules and interactions that connect these modules Pathintegrator Integrates pathways in which given proteins are associated Evaluates the biological activity of genes Available in App and processes in pathways Store Find meaningful pathways complexes Available in App connecting a protein set members withina Store PPI network using multi objective optimization PerturbationAnalyzer Evaluates how perturbation of selected nodes affect other nodes in a given network based on level of each node ex protein abundances and law of mass action PhosphositePlus Web Service Integrates phosphorylation related Client Module information in
21. leChartFunctions GPML Plugin GraphletCounter GraphMLReader format Available in App Store Available in App Store Loads interactions or pathways in GraphML Available as part of core GroovyEngine Provides scripting interface of Groovy GroovyScriptingEngine Provides scripting interface of Groovy GroupTool each group basic information such as number of nodes will be displayed on the panel Provides user sliders which can hide nodes whose continuous attribute is below threshold specied by sliders Enables one to create hyper edge by Cytoscape editor Uses local graph search heuristics to detect closely connected gene network regions in which gene mutations correlate with clinical features Brings some functionality of Igraph such as layouts into Cytoscape Mac only Retrieves interactions associated with input IDs Evaluates the topological effects of single or multiple nodes removal from a network using the effect to Radiality Closeness Betweenness Centroid Value and Eccentricity Retrieves interactions associated with input IDs Detailed information for each interaction as well as link to iReflndex is provided Finds clusters where member nodes show significant changes in expression levels Provides Java Script API HiderSlider HyperEdgeEditor IgraphPlugin IntActWSClient Interference iRefScape jActiveModules JavaScriptEngine JEPETTO Performs biological gene sets enrichment analysis ba
22. llation Streamlined productivity Enable casual learning Commonly used App development code Beneficiary All users All users New Casual users All users All users App Developers URL mailto cytoscape helpdesk googlegroups com mailto cytoscape discuss googlegroups com http wiki cytoscape or UserManual Section 3 of http wiki cytoscape or UserManual http opentutorials cgl ucsf edu inde x php Portal Cytoscape3 https speakerdeck com cytoscape Cytoscape 3 Cytoscape 3 http wiki cytoscape org Cytoscape_3 AppDeveloper Cytoscape_3 App Co okbook 10 Future Plans Table Feature Purpose Beneficiary Timeframe Movies Clear and interactive New Casual users TBD engagement Additional Visualizations TBD Additional Analytics TBD Wallpaper Collection Publicize good results All users potential associated with users general public Cytoscape Searchable Web Site Fast access to manuals All users tutorials group transcripts clinic transcripts Case Studies Streamlined New Casual Users productivity Cytoscape Clinics Chat rooms give instant All users New Casual User response based on Power User community availability App Developer Cytoscape v3 1 is the first feature intensive release after the major refactoring represented by v3 0 We expect minor features and bug fixes to be released in v3 1 1 and we are planning another major feature release in v3 2 Though there is no time table yet for eith
23. mScape Visualizes Semantic Data Landscapes Available in App Store SFLDLoader Represents structural protein families and their homologs by graph on Cytoscape ShortestPath Finds shortest pathway between two selected nodes SimTrek StringWSClient structureViz Superpathways Plugin TransClust Venn and Euler Diagrams VistaClaraPlugin WordCloud Assesses similarity of gene ontologies for given genes and their neighbours All files must be installed in plugin folder Retrieves interactions associated with input protein name Enables user to traverse from biological In Progress networks to detailed view of their structures Downloads and integrates multiple pathways from Wikipathways Clusters a given similarity graph Provides a diagram view and a details view Available in App for comparing two or more Cytoscape Store groups at a time Provides effective visualization and analysis platform to analyse expression data on a given network WikiPathways web service client and GPML Available in App file format importer Store Summarizes functions of interacting clusters as logos where sizes of logo represents frequencies of these functions Feature Cytoscape Google Groups Helpdesk Discuss User Manual Installation Guide Tutorials Presentation Slides on Web Site Code Snippets 9 Support Offering Table Purpose Community response on best effort basis Comprehensive manual Cytoscape insta
24. o 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 Plugin 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 Section 8 contains a list of apps available for v3 x To access the App Store access Cytoscape s new Apps menu and choose the App Manager menu item or use your browser to surf directly http apps cytoscape or 7 New Feature Table Feature Beneficiary Manual Section Welcome screen New users for solicitousness casual 5 1 Welcome Screen and power users for convenience New Style replaces All users 14 Styles VizMapper Export to cytoscape js Pow
25. oscape 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 8 The porting exercise is substantial 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 To convert a v2 0 plugin to a v3 x app refer to http wiki cytoscape org Cytoscape_3 AppDeveloper PluginPortingGuide For a broader view of the Cytoscape system including
26. ous versions before installing version 3 x and you can choose to use both on the same workstation Version 3 x is still a work in progress and continues to evolve due to the outstanding efforts of its vibrant worldwide development community Notably while the Cytoscape team has ported the most popular plugins as apps from previous versions porting less popular plugins was deferred so as to deliver version 3 x sooner and with features that support cutting edge investigation A table of apps and their status is presented in Section 8 Finally we recognize that with all new software including version 3 x there are growing pains While we hope our users will learn to love v3 x s new features users may also expect to relearn rationalized features and occasionally uncover a bug With version 3 x we are rolling out new manuals tutorials web pages and support channels that we hope can create and maintain highly productive experiences for all types of Cytoscape users A table describing Cytoscape support is presented in Section 9 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 yo
27. pers All Users All Users All Users All Users Power Users Developers All Users Power Users Power Users 2287 Trying to bend an individual edge results in all edges being bent All Users 2292 Change Table Mode button does not make sense for Network Table All Users 2293 GenericReaderManager getReader Developers CopylnputStream copyKBytes IOException amp Incorrect Reader Returned 2294 Race condition ends in deadlock when deleting network All Users 2296 CyActions TaskFactories without specified gravity appear on menu All Users in indeterminate order 2298 Use scientific species name for buttons on Welcome Screen All Users 2300 Import Table from URL examples aren t valid table files New Users 2303 Equation cannot be restored from session file if it belongs to a Power Users shared table but references a local table s column 2309 Splash screen overlays Windows Security Alert dialog All Users 2310 JSON Exporter does not export edge color Power Users 2311 JSON Exporter does not export edge arrow shape and color Power Users 2312 Replace spaces in column name when exporting to Cytoscape js Power Users Visual Style 2313 Locked Visual Properties are not properly handled in Cytoscape js Power Users exporter 2314 filter api needs to be locked down Developers 2315 filter api needs Javadoc Developers 2316 Filters chapter in manual needs to be rewritten All Users 2317 Clear Edge Bends Menu Sets Everything to Default Even W
28. phics It is difficult to put dots in filenames All Users 2358 Filters Deactivating then reactivating Apply automatically All Users checkbox prevents filter from being applied 2359 Deprecate some vizmap gui api interfaces and methods Developers 2362 Command command run commands is unnecessarily redundant Power Users 2363 File gt Run doesn t work properly All Users 2365 Deadlock in CyApplicationManager All Users 2367 Remove unnecessary PSICQUIC columns Power Users 2369 Edge bend editor overwrites current mappings if canceled All Users 2370 Nightly builds failing regularly due to Sonar failure Developers 2371 Bugs with task status bar clearing All Users 2376 Custom value editor broken Power Users 2379 Welcome Screen s news section should not use JLabel use Editor All Users Pane 2384 BioPAX reader is not detected when importing a biopax network All Users from URL 2386 Some options in Merge Tables shouldn t be available in some cases Power Users 2387 BasicCyFileFilter extensionsMatch uri and getExtension name All Users bugs 2392 network import file command only imports networks from tables Power Users 2395 REST server should return 4xx series status code for errors Power Users 2397 Cannot get list of edges from REST Power Users 2401 CSV table network import doesn t parse quotes All Users 2402 rest impl doesn t load due to missing package Developers org cytoscape rest RESTResource 2403 AnnotationManager was never exposed
29. r to query and modify networks through an XML RPC connection Enables users to view manipulate and analyze metabolic models created by the Model SEED The reactions are organized into a set of maps based on each reaction s membership in KEGG pathways Retrieves attributes from SQL databases by invoking query command Queries and analyzes networks of diseases and their associated genes Visualizes domain domain interactions which connect pairs of interacting proteins dynamicXpr DynNetwork edgeLengthPlugin edgeLister EnhancedSearch EnrichmentMap ExprEssence ExpressionCorrelation FERN FluxViz FunNetViz GeneMANIA Retrieves interactions associated with input IDs Detailed information associated with interactiong proteins can also be obtained Dynamically change colors of nodes like a movie according to their expression level across many conditions Visualize dynamic networks Calculate edge length in the main network view window and stores them as edge attributes length Records selected edges and provides some functionality for them ex hiding recorded edges Passthrough mapper for charts and gradients Performs keyword search Wildcards logical operators etc are allowed Visualizes enrichment of specific functions GO terms by interactions between functions Set oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node
30. s does not restore bypass values All Users 2484 Key column drop down list does not update when changing table Power Users import type 2485 Sample attribute data files should be renamed with proper New Users extension 2486 Hang on MacOS 10 8 5 when opening a network All Users 2491 Selected network not set properly when sessions reload All Users 2495 Add JSON format version number to exported JSON files for Power Users cytoscape js 2509 Off by one error during filter serialization Power Users 2511 Mappings sometimes not applied when restoring session All Users
31. sed on interaction network and topological properties Enables user to defines groups of nodes For In Progress Available in App Store Replaced by PSICQUIC In Progress Available in App Store Available as part of core Available in App Store Available in App Store KeyPathwayMiner Detects highly connected sub networks Available in App where most genes show similar expression Store behavior KGMLReader Enables import of KEGG XML file via import menu Clusters given network Subnetwork is indicated by set of nodes and they are shown by selecting subnetwork number Clusters a given network based on vertex Available in App weighting by local neighborhood density Store and outward traversal from a locally dense seed protein to isolate the dense regions MetaNetter Infers of metabolic networks based on high resolution metabolomic data MetanodePlugin2 Enables user to define meta node a Available as part group of nodes Meta nodes can have of core hierarchy Annotates metabolic networks with MeSH Available in App disease terms and links to references Store Loads human or mouse metabolic network Available in App Sophisticated GUI is provided which allows Store user to perform various tasks including gene expression analysis along the pathways MiMIplugin Retrieves interactions associated with input In progress IDs User can add own annotations to genes which can be viewed by different users Clusters a gi
32. sers All Users Developers All Users All Users All Users Developers All Users All Users All Users All Users All Users All Users All Users All Users All Users All Users All Users Developers Developers All Users 2142 Acceptable values for ServiceProperties PREFERRED_ACTION not Developers documented 2144 Virtual columns are firing incorrect set events All Users 2145 When new attributes are loaded VizMapper does not refresh All Users 2150 Visual Styles are completely lost when opening 2 x session All Users 2155 inaccessible buttons All Users 2157 Enhancement Request API Access to Java Network View Area amp Developers JInternalFrames 2158 Enhancement Request Add API For Choosing Control Panel Tab Developers 2162 CyApplicationConfiguration getAppConfigurationDirectoryLocation Developers Doesn t Work for Simple Apps 2165 Destroyed network view not removed immediately by Developers NetworkViewManager 2166 The v and version command line options cause invoke Karaf and Power Users cause Cytoscape to be run unnecessarily 2169 bug in searching node name All Users 2172 Need Cy3 Repalcement for DingNetworkView setGraphLOD Developers 2175 Need a way to enable REST from GUI Power Users 2176 Need a way to select nodes based on selected rows Power Users 2178 Node sorting by numbers All Users 2180 cytoscape sh syntax error All Users 2182 Table browser context menu needs to be changed All Users 2184 Ping Ch
33. tColumn does not see the local column VizMapper Discrete Mapping values set to wrong attribute Edge Label Transparency and Size VizMapper Typing error in LinkOut class Command line error loading table Default node edge labels do not work Update Karaf to 2 2 11 VizMapper Ugly descriptions on discrete mapping s font chooser and editor is slow to open extend network error Edit gt Remove Duplicated Edges doesn t trigger screen update Gradient editor min max change automatically App bundles that fail to load still show as installed Saving Continuous Mapping Values Installation problem Open Save dialog boxes in Cytoscape lag on Mac Java 7 Tunable ListMultipleSelection causes NPE if empty Network Merge Tunable changes have broken Layout Settings Font Face icons incorrectly aligned on Continuous to Discrete Mapping Editor Undo Hide Selected Nodes does not work Vizmapper refresh ExportNetworkViewTaskFactory always uses SIF format when called with File regardless of file extension Bad image export settings Bad csv table import settings installation warning XGMML Wrong type on attribute BioPAX reader features fixes Add SessionAboutToBeLoadedEvent as a CyEvent Update SynchronousTaskManager Javadoc to clarify function Race condition at DestroyNetworkTask Developers All Users All Users Developers All Users All Users Developers Power Users All Users Developers All Users All Users All U
34. to the network PhyloTree Reads a file in phylogenetic tree format Phylip or phyloXML and visualizes it as a network PICRClient A visualization and analysis tool to study Available in App interactions between multiple sets of Store proteins Finds candidate genes in a network that are associated with user defined target GO terms PinnacleZ Searches for subnetworks which can discriminate givein conditions according to PPI network and gene expression data obtained in given conditions PSiICQUICUniversalClient Retrieves interactions associated with Available as part input IDs from databases having PSICQUIC of core implementation Randomnetworks Generates random network or randomizes already loaded network RDFScsape Allows to query visualize and reason on ontologies represented in OWL or RDF within Cytoscape Accesses to Reactome Functional Available in App interaction Fl network to perform Store pathway analyses such as identification of pathways enriched with proteins in given network Communicates with reactome server to load pathway data onto Cytoscape Additional features such as integration of expression data are supported RemainingDegreeDistribution Calculates remaining degree excess degree distribution ReOrientPlugin Layouts node positions according to reference Cytoscape session file ScriptEngineManager Manages scripting engines for Cytoscape Available as part Supports Ruby JavaScript Groovy and of core Python Se
35. u 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 accordingly Type of Cytoscape User New Casual Power App Developers General Interest Where to Read Next For New Users Section 1 For Casual Users Section 2 For Power Users Section 3 For App Developers Section 4 Try getting oriented by reading General Background Section 5 Cytoscape App Store Section 6 Then try browsing New Features Section 7 App Status Section 8 Support Offering Section 9 Future Plans Section 10 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
36. ven network based on agglomerative clustering algorithm very similar to MCODE but it uses a modified vertex weighting strategy and can factor ina measure of network modularity Adjustment of only few parameters are necessary MiSink Provides network interface to MiSink enabled Web sites including DIP Predicts gene regulatory network from biological annotations and expression data Systematically partition the given graph and layout and color nodes based on GO terms NamedSelection Assign name to selected nodes and after unselection enables user to re select the nodes according to the name NCBlEntrezgeneUserInterface Imports various data from NCBI database Available as part of core NeighborHighlight Highlights the current node and all its neighboring nodes and edges when the user hovers the mouse over it Identifies densely connected and biopartite network modules based on combination of a unique neighbour sharing score with hierarchical agglomerative clustering NetAtlas Integrates gene expression data of multiple tissues ex from Symatlas into pre loaded network genes showing characteristic expression in specified tissues can be filtered and colored NetCirChro Visualizes interaction network on circular genome Original GUI with some network analysis functions shortest path degree distribution etc are equipped NetMatch Finds user defined network motifs in a given network network motif can be created and ed
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