(Keiichiro Ono) UC, San Diego Trey Ideker Lab Research Associate/ Software Engineer 2

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1 Google Summer of Code, Mentor Summit, and Open Source Software Development Keiichiro Ono UC, San Diego Department of Dec. 5,

2 (Keiichiro Ono) UC, San Diego Trey Ideker Lab Research Associate/ Software Engineer 2

3 My Main Project: Cytoscape 3

4 Google Google Summer of Code Mentor Summit 4

5 5

6 Open Source Initiative 6

7 NO 7

8 Open Source is Everywhere OS 8

9 Google 9

10 Google Google OSS Chromium Google Web Toolkit Android OSS Webkit Python Subversion Linux 10

11 Google Google Summer of Code (GSoC) 11

12 Google Summer of Code 12

13 Google Summer of Code Google $4,500 13

14 from 14

15 from 15

16 Google $4,500 16

17 Google Summer of Code

18 The Apache Software Foundation Eclipse Foundation The FreeBSD Project The Linux Foundation Mozilla Project 18

19 Boost C++ Libraries GCC Git Ruby on Rails haskell.org 19

20 Center for the Study of Complex Systems, University of Michigan GenMAPP OMII-UK R Foundation for Statistical Computing 20

21 Free Software Initiative of Japan (FSIJ) NPO Battle of Wesnoth Chromium / Native Client Google 21

22 GSoC Google 22

23 23

24 OMII-UK 24

25 GenMAPP 25

26 GenMAPP GenMAPP Cytoscape WikiPathways PathVisio 26

27 IDEA 5: Superpathways in Cytoscape Goal: Create a Cytoscape plugin that merges multiple pathways into a single Cytoscape network Biological pathways are highly interconnected. To find out how different processes influence each other, it can be useful to visualize the connectivity between pathways by merging them into a single superpathway. Cytoscape would be an ideal tool for such a visualization, since it has interactive layouts, making it possible to work with a large number of nodes. The goal of this project is to create a Cytoscape plugin that allows you to select multiple pathways from Wiki Pathways and load them in a single network. The plugin needs to merge nodes that represent the same biological entity (e.g. gene, protein or molecule). Existing code already provide some functionality that is needed to make this work: AdvancedNetworkMerge plugin, merges nodes and edges from different networks based on their attribute values GpmlPlugin for Cytoscape, load WikiPathways pathways as a Cytoscape network Synonym databases, connect genes, proteins and metabolites that are annotated to different database systems By reusing as much existing code as possible, it should be possible to create a user friendly tool that allows researchers to combine different pathways on the fly. Features you could think of to make this work are a dialog to search and select pathways, a custom layout that groups nodes from the same pathway and a visualization that indicates the origin pathway of each node (e.g. by color-coding it). Language and Skills: Java Idea by: Thomas Kelder Potential Mentors: Thomas Kelder, Martijn Van Iersel, Alexander Pico 27

28 28

29 Community Bonding Period 29

30 Skype 30

31 Google Summer of Code 31

32 Google Google Mentor Summit 32

33 Google Summer of Code Mentor Summit 33

34 Google Summer of Code Mentor Summit GSoC Google 34

35 Unconference? 35

36 ... OSS OSS... 36

37 37

38 UI Wii 38

39 SCM, Wiki, Issue Tracker, Build System, etc. GitHub SourceForge 39

40 OSS 40

41 41

42 42

43 43

44 OSS RMS 44

45 45

46 OSS 46

47 47

48 48

49 OSS - Subversion, Git, etc. - Wiki, CMS, Issue Tracker - 49

50 Google Code Source Forge GitHub 50

51 51

52 Google GSoC Mentor Summit 52

53 Thank You! 53

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