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What's New in Cytoscape

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Presentation slides for SDCSB Cytoscape Workshop on 5/19/2016. The presentation contains current status of Cytoscape project and overview of the Cytoscape ecosystem. It briefly mentions the Cytoscape Cyberinfrastructure.

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What's New in Cytoscape

  1. 1. What’s New In Cytoscape? Keiichiro Ono UCSD Trey Ideker Lab Cytoscape Core Team SDCSB Workshop 5/19/2016@Sanford
  2. 2. Keiichiro Ono Cytoscape Core Developer since 2005 @UCSD Trey Ideker Lab Area of Interest: Biological Data Integration & Visualization
  3. 3. Outline - Cytoscape Project Updates - Cytoscape Core - Cytoscape and the Web - Cytoscape Ecosystem and CI
  4. 4. Quick Introduction to Cytoscape
  5. 5. What is Cytoscape?
  6. 6. An Open Source Platform for Biological Network Data Integration, Analysis and Visualization Cytoscape
  7. 7. Cytoscape 3.4
  8. 8. Cytoscape - Open Source: LGPL - Free for both commercial and academic use - Developed and maintained by universities, companies, and research institutions - De-facto standard software in biological network research community - 13k downloads / month - Expandable by Apps - Platform, not a stand-alone desktop application
  9. 9. C. Elegans Interactome from BioGRID Database ?
  10. 10. Biological Networks - Tell us anything by themselves - Just a big hairball…
  11. 11. Module 1 Need a tool to extract meaningful biological modules
  12. 12. Basic Workflow
  13. 13. Networks Public Interaction Databases
  14. 14. List of Genes
  15. 15. Other Data
  16. 16. APPS.CYTOSCAPE.ORG
  17. 17. Real World Use Cases cytoscape-publications.tumblr.com
  18. 18. Cytoscape Ecosystem
  19. 19. Cytoscape For Desktop Cytoscape 3.4 Publish to the web For Building Web Applications Cytoscape.js Interaction Data Repository NDEx Cyberinfrastructure (CI) Sample Services Fast ID Mapping Network Image Generator Format converter Data Format CX Job Router ELSA Visualization Widgets Network Widget Table Widget Composite Widget NDEx Valet
  20. 20. For Desktop Cytoscape 3.4 For Building Web Applications Cytoscape Interaction Data Repository
  21. 21. Cytoscape 3.4
  22. 22. Cytoscape 3.4 • Latest version of Cytoscape Desktop application • New Features: • New Network View Manager • App Collections • Performance Improvements for browsing large number of networks (grid view) • Lots of bug fixes
  23. 23. New Network View Manager
  24. 24. Grid View
  25. 25. Grid View • Display all networks as tiles of network images • Can easily handle hundreds of networks without any performance penalty
  26. 26. Detached View
  27. 27. Detached View • Display networks in separate windows • Useful when you have large workspace (e.g. dual display)
  28. 28. App Collections
  29. 29. App Collections • Users can install multiple Apps at once • Organized for specific use cases • Mass Spec • Omics Analysis • Functional Enrichment • EmrichmentMap
  30. 30. Cytoscape 3.4.0 www.cytoscape.org/download.php Download Link:
  31. 31. Cytoscape For Desktop Cytoscape 3.4 Publish to the web For Building Web Applications Cytoscape.js Interaction Data Repository NDEx Cyberinfrastructure (CI) Sample Services Fast ID Mapping Network Image Generator Format converter Data Format CX Job Router ELSA Visualization Widgets Network Widget Table Widget Composite Widget NDEx Valet
  32. 32. 3.4 Publish to the web ons Cytoscape.js n Data ry NDEx
  33. 33. Cytoscape and The Web
  34. 34. 11 Years Ago…
  35. 35. 2005 - Cytoscape 2.2: a Java Desktop Application - Google released an application called Google Maps beta - “Re-discovery” of JavaScript, or Ajax - Virtually no smartphone market
  36. 36. Today
  37. 37. Today - JavaScript is a programming language for large-scale applications - Tablets and other touch-based devices are important platform for data visualization - Web is a competitive application platform
  38. 38. Our Approach to the Web - Cytoscape project should support use cases such as: - Sharing network data over the web - Visualizing network data on web browsers
  39. 39. cytoscape.js
  40. 40. - A JavaScript Library - NOT A WEB APPLICATION! - A building block for web apps - For web application programmers - But there are many web applications using Cytoscape.js cytoscape.js
  41. 41. http://bit.ly/1W4vBzk
  42. 42. bit.ly/22hkOlv
  43. 43. cytoscape.js - Fast enough for relatively large networks - Stable - Open source (MIT)
  44. 44. ScienceDirect App Publish your networks as interactive diagrams Interactive paper figures Collaboration Project with Elsevier
  45. 45. Network Diagrams in Papers - Problem: - OK for small networks/pathways - Does not helpful for large networks - Solution: - Make them interactive - Pan / Zoom
  46. 46. https://www.elsevier.com/books-and-journals/content-innovation/interactive-network-viewer
  47. 47. Example: Host cell interactome of PA protein of H5N1 influenza A virus in chicken cells – Journal of Proteomics http://www.sciencedirect.com/science/article/pii/S1874391916300215
  48. 48. How to Export your Networks for Interactive Viewers
  49. 49. Preview
  50. 50. Demo Load a Network Preview in Web Browser Export
  51. 51. cynetshare A web application using cytoscape.js
  52. 52. bit.ly/1DNmetV
  53. 53. bit.ly/1DNmetV - Location of Network File - Visual Style - Zoom Level - Viewable Area
  54. 54. Cytoscape For Desktop Cytoscape 3.4 Publish to the web For Building Web Applications Cytoscape.js Interaction Data Repository NDEx Cyberinfrastructure (CI) Sample Services Fast ID Mapping Network Image Generator Format converter Data Format CX Job Router ELSA Visualization Widgets Network Widget Table Widget Composite Widget NDEx Valet
  55. 55. P For Building Web Applications Cytoscape.js Interaction Data Repository NDEx Sample Services Fast ID Mapping Network Image Generator Format converter
  56. 56. e Interaction Data Repository NDEx Cyberinfrastructure (CI) Sample Services Fast ID Mapping Network Image Generator Format converter Data Format CX Job Router ELSA Visualization Widgets Network Widget Table Widget Composite Widget NDEx Valet
  57. 57. Cytoscape Cyberinfrastructure
  58. 58. Cyberinfrastructure?
  59. 59. –Wikipedia Cyberinfrastructure: Research environments that support advanced data acquisition, data storage, data management, data integration, data mining, data visualization and other computing and information processing services distributed over the Internet beyond the scope of a single institution
  60. 60. ?
  61. 61. Computing Infrastructure Community
  62. 62. Computing Infrastructure
  63. 63. Problems in Bioinformatics - No more free lunch - Even if you buy expensive machines, you cannot get free performance gain anymore. You have to design your code for massively distributed environment. (From Scale-up to Scale-out) - This is a problem especially when you analyze omics-scale data sets
  64. 64. Problems in Bioinformatics - Complex Data Analysis Pipeline - Need to build pipeline by connecting multiple resources, or services - Needs for complex, customized data visualization
  65. 65. Problems in Bioinformatics - Reproducibility ➡ Building, deploying, and maintaining reproducible data analysis / visualization pipeline is not straight- forward
  66. 66. Data Preparation Analysis Visualization
  67. 67. ALL tools should work nicely together with other popular software packages
  68. 68. REST
  69. 69. What is cyREST? - Platform-independent, RESTful API module for Cytoscape - Means you can access basic Cytoscape data objects programmatically - Now this is a Cytoscape Core feature! REST
  70. 70. Two sides of modern biology ✔
  71. 71. Use Cases - I have 200 networks in my session and I need to create one PDF per view. How can I do it with Cytoscape? - I need to use igraph for network analysis, but its visualization feature is limited. I want to use Cytoscape as an external visualization engine for R. - Usually I use IPython Notebook to record my work. How can I integrate Cytoscape into my workflow? - I want to generate Style for each time point and create small multiples of networks.
  72. 72. cyREST RESTful API for Cytoscape
  73. 73. https://github.com/idekerlab/cy-rest-R/blob/develop/ workflow1_structure_based_visualization.R
  74. 74. cyREST and other programming tools for Cytoscape will be covered in the Advanced Cytoscape Workshop from 3:15PM
  75. 75. Interactive Data Analysis Environments In-House Databases External Computing Resources - Graph Layout - Statistical Analysis - Data Pre-processing RStudio - NumPy - SciPy - Pandas - NetworkX IPython Notebook File / Code Hosting ServicesPublic Data Repository PSICQUIC Services EBI RDF Platform Other Bioinformatics Web Applications / Services - igraph - rCurl Command Line Tools > sed > awk > grep > curl Web Browsers Data Repository & Collaboration Service Data Bus (Internet) Your Workstation Cytoscape App Store Cytoscape Desktop Apps Core REST
  76. 76. Interactive Data Analysis Environments In-House Databases External Computing Resources - Graph Layout - Statistical Analysis - Data Pre-processing RStudio - NumPy - SciPy - Pandas - NetworkX IPython Notebook File / Code Hosting ServicesPublic Data Repository PSICQUIC Services EBI RDF Platform Other Bioinformatics Web Applications / Services - igraph - rCurl Command Line Tools > sed > awk > grep > curl Web Browsers Data Repository & Collaboration Service Data Bus (Internet) Your Workstation Cytoscape App Store Cytoscape Desktop Apps Core REST → Service Repository → Network Data Repository
  77. 77. Service - Service = ANY program wrapped with REST API - Examples: - ID Mapping - Format converter - BioPAX to GraphML - GO Enrichment Analysis
  78. 78. Writing CI Services 1. Write a command line tool 2. Wrap it with REST API 3. Register to job manager (provided by us)
  79. 79. Why this is important? In most cases, cutting-edge bioinformatics algorithms are published as (hard-to-use) command line tools written by researchers/graduate students Rewriting it as Cytoscape App is hard But wrapping it with REST API is not so difficult Once published as service, it can be called from any tools, including R/Bioconductor, Python, and Cytoscape
  80. 80. Cytoscape For Desktop Cytoscape 3.4 Publish to the web For Building Web Applications Cytoscape.js Interaction Data Repository NDEx Cyberinfrastructure (CI) Sample Services Fast ID Mapping Network Image Generator Format converter Data Format CX Job Router ELSA Visualization Widgets Network Widget Table Widget Composite Widget NDEx Valet
  81. 81. NDEx Sample Services Fast ID Mapping Network Image Generator Format converter Data Format CX Job Router ELSA
  82. 82. Computing Infrastructure Community
  83. 83. Community
  84. 84. - Large user and developer community - Lots of examples and documents - Workshops / Lectures
  85. 85. Community is equally important as technology for successful CI
  86. 86. How to Participate
  87. 87. 2016 Keiichiro Ono kono@ucsd.edu
  88. 88. • https://flic.kr/p/bFZpyg • https://flic.kr/p/bmXUz1 Photo Credits
  89. 89. • https://www.flickr.com/photos/23629083@N03/15409436041/in/photolist-ptFotK-9uS2gj-hypkSp-hypk9F-hypjha-99c472-9Xkuuc-huNmqB-7NMxMz-rg2Xh2-qYABcA-qjnGoB-rg2WVF- rdQYMf-qjaxy7-rg5Aoo-rg2Wre-qYAAt1-rg2Wev-qYAAaA-rg2W1V-rdQXT1-qjawtS-rg9ePH-rg5zb3-qjnEtV-qYHAvc-qYBA9d-rg2V7F-qYHAeF-qYAySA-rg5ys9-rg9dLF-rg2Utg-rg9drH-qYAyew- rg9dmc-rg5xP5-rg5xDA-qYAxV5-rg2TLe-rg5xp7-rg5xfQ-aq32tC-hba7em-hbafzE-gbeABq-gck7Dv-7PoYg1-fkisQL • https://www.flickr.com/photos/nebulux/10000066526/in/photolist-geEXo7-58r1VP-6GioJH-9juEda-53HFiR-4sq7n3-4gyg7e-8ag9VV-8uqK43-4E89Gc- iWDeiJ-9G47M4-9G71KC-9waYuP-5FWSrX-87Mhxi-9G71XY-7Ai8hs-48vd2B-7B7o6n-6D9uWd-6hffXv-gYExNx-7defC1-66ygvB-4LsWSN-6D5n5k-6hfg5z-eucXAh-8uyuuG- aAY6cH-76QCEX-7f6mdp-RntfW-eFuVBC-5nY8Vc-7utTA2-brdj8F-92k6n3-5KdCfh-83uVKy-8unxG8-3d3zxi-cdz8S7-4HT5qQ-99SwEn-7Akbcb-8y7ds9-fvo9zH-9zZky3 • https://www.flickr.com/photos/stratman2/8613731520/in/photolist-e8aChq-7LLUoQ-8s8eBL-6uGRmE-77wKJF- dqo6ar-6hffGK-7rykRT-6fG8WV-8unyFa-8AeF8A-93Xpo2-9XLXCj-7GVMym-5Tu3dJ-7v58RC-5K9nBF-2MbvpL-2M77nV-et54Ce-6hfgvr-6hffQa-67wNj5-9FDGTz-49NmoE-eFXB7u-76QB7H- brdbSP-brcYHT-22zYYv-6fFZoM-ckuXNC-a8UZ3D-dzGXYU-6nf4MN-4j7TzA-47fYur-2kutoV-56catX-apUJgr-cSJHkG-88w1ie-6Nbj1a-8MYxve-6xL3SF-6fL87j-4G6x71- dUL16b-7auq8Q-6hwbVB • https://www.flickr.com/photos/gcwest/281385801/in/photolist-5mFJtX-4o3Ria-hD9E92-qSbck-9abnoA-7hsWoU-ntEmgy-oSAQtv-nx5Chg-iuZJCa-j7eWKk-hD7JTZ-4iECHX-j8M2r7-bSrWHc- prpFcX-db7xd-jLmzoF-75mqRx-pnSzL-6gVcao-9F5bop-j77HEs-73Umq1-5kRyNp-hD9cR2-mTvNB8-gyXWaf-Lkro7-idQBY4-fRYu1-5eR2cn-3EK4k-nnxH8u-9uDMLx-4NY3Yi-kDQagt- ioGRSb-75qid1-82RzYt-5qQuwt-n8hvL6-ifemz5-3iYUQG-aJnNiX-mzirX2-23rDNy-qx3KEd-h5UnGW-hD7Jqz

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