Welcome Letter ytoscape
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1. 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 accordingly 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 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 y2. 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 still a work in progress and continues to mature 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 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 there are growing pains While we hope our users will learn to love v3 s new features users may also expect to relearn rationalized features and occasionally uncover a bug With version 3 0 we are rolled 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 We continue to improve these materials monthly 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
3. network Cytoprophet CytoSaddleSum CytoscapeRPC Finds enriched function based on sum of weight scores Allows user to query and modify networks through an XML RPC connection CytoSEED CytoSQL DisGeNET DomainGraph D3 js Exporterer dynamicXpr DynNetwork edgeLengthPlugin edgeLister Enhanced Graphics EnhancedSearch EnrichmentMap eXamine ExprEssence ExpressionCorrelation FERN FluxViz 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 Retrieves interactions associated with input IDs Detailed information associated with interactiong proteins can also be obtained Export Cytoscape network and table as Available in App D3 js style JSON Store Dynamically change colors of nodes like a movie according to their expression level across many conditions Visualize dynamic networks Available in App Store 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 char
4. May 27 2014 Welcome Summary e Cytoscape v3 1 1 is now available for immediate download e It addresses 46 issues relative to v3 1 o Several small issues with new filter facility including reverting topology filers to pre v3 1 behavior Improved network and attribute imports for Excel CSV and TXT files Occasional hangs during startup shutdown circular layout and session load Better user and App Developer documentation O O O O Feature improvements for exporting networks to web pages e 9 more Apps are available in the App Store as compared to the v3 1 release e Itis ready for use by all segments of the Cytoscape community e It continues v3 1 s core feature set specifically o It is upward compatible and can coexist with previous Cytoscape versions o The most popular plugins from previous versions are available with more to follow What to do next Release notes http www cytoscape org releasenotes html 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 v3 1 11 Apps were added to the App Store bringing the total to 53 The new ones include AllegroLayout Cyrface setsApp BridgeDB CytoCopteR Variation chemViz2 KDDN WormPlot clusterMaker2 Rene If you are a new or casual Cytoscape user welcome aboard Feel free to either read on or jump ahead
5. aving as expected Mapping Column for Existing Network tunable has unwieldy confusing name Command processing using S is broken All Users All Users All Users All Users All Users All Users All Users All Users All Users All Users Developers Power Users Developers Power Users
6. ctionality 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 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 o
7. ded 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 edited 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 PanGIA Performs integrated analysis and visualization of PPls and genetic interactions to infer functional modules and interactions that connect these modules PathExplorer Finds paths filters them based on node Available in App and edge attributes and saves them Store Pathintegrator Integrates pathways in which given proteins are associated Pathway Scoring Application Evaluates the biological activity of genes Available in App and processes in pathways Store PEPPER Find meaning
8. e of its functional dissimilarity GIANT Network analysis according to the Available in App Guimera Amaral cartography Store GoogleChartFunctions Creates image from attribute values URL using the Google Chart API GPML Plugin Enables import of GPML file via import menu GraphletCounter Calculates graphlet small connected non isomorphic subgraph degree distribution GraphMLReader Loads interactions or pathways in GraphML Available as part format of core GroovyEngine Provides scripting interface of Groovy GroovyScriptingEngine Provides scripting interface of Groovy GroupTool Enables user to defines groups of nodes For In Progress each group basic information such as number of nodes will be displayed on the panel HiderSlider Provides user sliders which can hide nodes whose continuous attribute is below threshold specied by sliders HyperEdgeEditor Enables one to create hyper edge by Cytoscape editor HyperModules Uses local graph search heuristics to detect Available in App closely connected gene network regionsin Store which gene mutations correlate with clinical features IgraphPlugin Brings some functionality of Igraph such as layouts into Cytoscape Mac only IntActWSClient Retrieves interactions associated with Replaced by input IDs PSICQUIC Interference iRefScape jActiveModules JavaScriptEngine JEPETTO KEGGscape KeyPathwayMiner KGMLReader MetaNetter MetanodePlugin2 MetDisease MetScape MiMl
9. educe delays when merging large networks Large network handling Improved layout interactive and load performance Java 8 Support Allow Cytoscape to run with JVM 8 Faster startup times Reduce delay to get to initial Welcome screen Nodes displayed as charts Enable users to visualize nodes as value sensitive complex graphics Movies Clear and interactive engagement Beneficiary Power users New Casual users All users All users Power users All users All users Power users New Casual users Timeframe Fall 2014 Fall 2014 Fall 2014 Fall 2014 Fall 2014 Fall 2014 Fall 2014 Fall 2014 TBD Additional Visualizations TBD Additional Analytics TBD Wallpaper Collection Publicize good results associated with Cytoscape Case Studies Streamlined productivity Cytoscape Clinics Chat rooms give instant New Casual User response based on Power User community availability App Developer All users potential users general public New Casual Users All users 11 Issues Addressed The following issues were addressed in v3 1 1 Details for each issue can be found at Cytoscape s RedMine issue repository Issue 521 1541 1841 1875 1979 2041 2050 2055 2066 2185 2334 2429 2438 2465 2470 2475 2497 2501 2504 2510 2511 2512 2514 2516 2520 2537 2548 2556 2559 2560 2563 2564 http code cytoscape org redmine Description Port KGMLReader Cytoscape 3
10. escribed 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 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 1 beta version please uninstall it before proceeding The Cytoscape v3 0 and v3 1x versions can coexist with v3 1 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 cons
11. f 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 7 P 3 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 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 Fea
12. ful 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 into the network PhyloTree Reads a file in phylogenetic tree format Phylip or phyloXML and visualizes it as a network PINA4MS 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 PsicQuiCUniversalClient 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 Reactome FI Plugin 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 ReConn Communicates with reacto
13. in App on various resources Store 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 single node CentiScaPe Calculates topological characteristic values Available in App ex Centralities for each node Store ClojureEngine Provides Clojure API 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 clusterExplorerPlugin Explores a given similarity graph a 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 CommFinder 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 Cy3 Performance Rep
14. iplugin 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 Performs biological gene sets enrichment analysis based on interaction network and topological properties In Progress Available in App Store Available as part of core Available in App Store aa tl Constructs KEGG pathway on Cytoscape3 Detects highly connected sub networks where most genes show similar expression behavior 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 weighting by local neighborhood density and outward traversal from a locally dense seed protein to isolate the dense regions Infers of metabolic networks based on high resolution metabolomic data Enables user to define meta node a group of nodes Meta nodes can have hierarchy Annotates metabolic networks with MeSH disease terms and links to references Loads human or mouse metabolic network Sophisticated GUI is provided which allows user to perform various tasks inc
15. luding gene expression analysis along the pathways Retrieves interactions associated with input IDs User can add own annotations to genes which can be viewed by different users Available in App Store Available in App Store Available in App Store Available as part of core Available in App Store Available in App Store In progress Clusters a given 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 Mosaic 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 loa
16. me 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 SemScape Visualizes Semantic Data Landscapes Available in App Store SessionForWeb Saves Cytoscape session in Web format leg es ml SFLDLoader Represents structural protein families and their homologs by graph on Cytoscape ShortestPath Finds shortest pathway between two selected nodes SimTrek Assesses similarity of gene ontologies for given genes and their neighbours All files must be installed in plugin folder StringWSClient Retrieves interactions associated with input protein name structureViz Enables user to traverse from biological In Progress networks to detailed view of their structures Superpathways Plugin Downloads and integrates multiple pathways from Wikipathways TransClust Clusters a given similarity graph a cence al Venn and Euler Diagrams Provides a diagram view and a details view Available in App for comparing two or more Cytoscape Store groups at a time VistaClaraPlugin WikiPathways WordCloud WormPlot Provides effective visualization and analysis platform to a
17. nalyse 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 Available in App Store 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 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 googlegroups 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 10 Future Plans Table Feature Purpose R Mathlab Python Enable model access integration analysis and visualization from popular tools Fast preset network loads Improve load times leading to quicker analysis Publish layouts to web Enable web users to view and interact with networks via browser Fast network merge R
18. o create Store interaction network based on the search result m ell 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 performs various analyses including protein motif GO hub identification etc through the original GUI Equipped with impressing rainbow coloring of nodes 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 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 BridgeDB Performs identifier mapping services based Available
19. orter CyAnimator CyClus3D CyGoose CyKEGGParser Cyni Toolbox Retrieves interaction evidences for given pair of genes or proteins Collects information about Cytoscape 3 Available in App performance Store 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 Available in App specificity of KEGG pathways Store Network Inference Toolbox for inferences Available in App from bio data Store CyOog CyPath2 CyTargetLinker CyThesaurus ID Mapping CytoCluster cytoHubba CytoKegg CytoNCA GUI client app for Pathway Commons 2 Available in App BioPAX L3 pathway data web service Store a Extends biological networks with Available in App regulatory interactions Store Performs ID mapping using BridgeDb and other public or custom database sources Analyze and visualize clusters from Available in App network Store Predicts and explores important nodes and subnetworks in a given network by several topological algorithms Identify Kegg pathways associated to Available in App specific expression profiles Store Providing calculation evaluation and Available in App visualization analysis for several Store centralities of weighted and unweighted
20. ou 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 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 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 v3 0 2 or 3 1 you can install v3 1 1 without uninstalling your previous version How to Download and Install v3 x e Su
21. rf 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 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 d
22. tions 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 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 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 fun
23. 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 as a feature release including greatly improved visual styles node filtering and web publishing While all version 3 releases
24. ts and Available in App gradients Store Performs keyword search Wildcards Available as part logical operators etc are allowed of core Visualizes enrichment of specific functions GO terms by interactions between functions Set oriented visual analysis approach for Available in App annotated modules that displays set Store membership as contours on top of a node 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 FunNetViz Integrates and visualizes co expression network with biological role of transcripts e g GO terms Centrality measures are equipped Gasoline Multiple local alignment of protein protein Available in App interaction PPI networks Store GeneMANIA Generates interaction networks from Available in App public databases based on user s list of Store genes Also provides annotation and putative function for those genes GenomeSpace Enables communication with Available in App GenomeSpace Store GFD Net Analyze a gene network based on Gene Available in App Ontology GO and calculate a quantitative Store measur
25. ture Table Feature Beneficiary WET ELIS Y rad oda 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 Power 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 Group annotations Users with highly annotated networks 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 t
26. ult 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 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 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 op
27. urrentModificationException When Recreating CyNetworkViews Enable CytoscapeConfiguration to exist in a settable location Collapsed groups are not properly restored from sessions Edge weighted Spring Embedded spring strength setting not having any effect Topology filter changed behavior in v3 1 relative to v3 0 Can t search based on Integer column values Beneficiary All Users All Users All Users All Users All Users All Users Power 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 All Users All Users All Users All Users All Users All Users Power Users Power Users All Users All Users All Users 2565 2575 2576 2579 2586 2587 2593 2609 2613 2617 2637 2639 2642 2653 Legacy Node Attributes Format Should Support Lists of Strings Nested filters can t be deserialized Initial state of column filter has null criterion Filters no longer support boolean columns Ding deadlock in 3 1 1 Network import file command does not work for txt and csv files Table importing attribute mapping dialog malformed and fails for certain networks Cytoscape js JSON reader does not read network table Node x y positions are ignored in 3 1 0 Slider interval should always be visible editable Mapping Column for New Network sourceColumnList Tunable exists in GUI but is never used Cytoscape group not beh
28. x lt gt Cytoscape js integration import export and app deployment to web Implement a JSON I O bundle Design formats for JSON I O Module Edge handles recreated Tasks returned by createTasklterator File in TaskFactories abort with NPE Can save a big network but cannot reload it JVM SIGSEGV appears on Cytoscape startup shutdown on Ubuntu 13 04 Oracle Java 7 Import network from MS Excel Enable Compiling Without An Internet Connection CyNetworkViewDesktopMgr setBounds Fails for Maximized Internal Frames Can t import List columns from exported table Import Ontology Annotation table preview doesn t use column colors shown in legend JDialogTaskManager CyTablelmpl threw column already exists layoutAlgorithm Circular Layout Progress Stalled Event chain can be disrupted by a listener that throws an exception Undo Cut Nodes Edges does not restore bypass values Redo Cut throws NullPointerException and does not work Edge attributes don t apply to subsequently imported sif files containing same edge IDs Cytoscape freezes on Mac Java 7 when importing multiple networks using keyboard shortcuts Mappings sometimes not applied when restoring session KEGG XML Session saved with equation return type not matching column type results in instability when reloaded Filters not cleared when starting loading new session Filters not restored properly when opening saved session with modified default filter Merge networks hangs Conc
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