1. August 2012 This work is licensed under the Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. BEL Editor 1

2. BEL Editor Overview BEL Editor is a text editor designed to support the creation and management of BEL Documents You can create and edit BEL Documents in any text editor – BEL Editor is not required © 2012, Open BEL Community2

3. Contents Getting started – Installation – Configuration Creating BEL Projects and Documents Features – Namespace value lookup – Help for BEL Functions – Cytoscape visualization 3

4. Getting Started Requirements: – BEL Framework 1.3 or higher (current version is 2.0.0) – Eclipse (Indigo) – Java Runtime Environment (JRE) Detailed Installation instructions on the BEL Editor GitHub page wiki – https://github.com/OpenBEL/bel-editor/wiki/Getting-Started https://github.com/OpenBEL/bel-editor/wiki/Getting-Started Install Eclipse (Indigo) – If in doubt, select Eclipse Classic package Open Eclipse – Go to Help -> Install New Software… – Add link to stable repository for BEL Editor 4

5. Install BEL Editor Stable repository location: https://raw.github.com/OpenBEL/eclipse/master/stable https://raw.github.com/OpenBEL/eclipse/master/stable 5

6. Configure BEL Editor Go to Window -> Preferences, then select BEL Editor from the left panel – For OS X Preferences are in the Eclipse menu Specify the path to your BEL Framework installation (required) – This is the folder which contains belc.cmd/belc.sh Specify the path to your Cytoscape installation (optional) 6

7. Configure Eclipse – Change Text File Encoding to UTF-8 Go to Window -> Preferences -> General -> Workspace Under Text file encoding select UTF-8 from the pull-down menu next to Other 7

8. Configure Eclipse Text Editor Options – Show Line Numbers Go to Window -> Preferences -> General -> Editors -> Text Editors Select Show line numbers – This will be helpful for resolving compilation errors 8

9. Open Perspective Go to Window -> Open Perspective…-> Other Select BEL Editor and click OK 9

10. Contents Getting started – Installation – Configuration Creating BEL Projects and Documents Features – Namespace value lookup – Help for BEL Functions – Cytoscape visualization 10

11. Create New BEL Project 11

12. Create New BEL Project Select BEL Editor-> BEL Project Click Next Give your project a name Click Finish Your new BEL project should appear in the Project Explorer in the upper left panel 12

13. BEL Document Overview Can be expressed in one of two formats: – BEL Script (.bel) – XML (.xbel) Header Section – Document name, description, version, authors, etc. – Definitions Namespace references Annotation definitions Body Section – BEL Statements 13 Document Header BEL Statements

14. Create New BEL Document 14

15. Create New BEL Document 15

16. Create New BEL Document Select a location for your document – Must be in a Documents folder Give your Document a name Click Finish 16

17. Create New BEL Document Your new document will be pre-populated with a BEL document header containing Namespace and Annotation definitions 17

18. Import Existing BEL Document Select File -> Import… Select BEL Editor -> BEL Script/XBEL Document Click Next 18

19. Import Existing BEL Document Browse your files to select a document Select an BEL Editor folder for your document – Must be a Documents folder Click Finish 19

20. Import Existing BEL Document Alternatively, you can move your document to the folder within your workspace – If you select the folder for the Project Explorer and click 'F5' the documents will be updated 20

21. Contents Getting started – Installation – Configuration Creating BEL Projects and Documents Features – Namespace value lookup – Help for BEL Functions – Cytoscape visualization 21

22. Look Up Namespace Value From Namespace panel (lower left hand corner) – Select namespace from pull-down – double-click value of interest 22

23. Look Up Namespace Value A new tab will open with a search for the selected namespace value 23

24. Mouse-over Help for BEL Functions and Relationships Information window appears with mouse- over for any BEL function (red) or relationship (dark red) The information for reaction is shown here 24

25. Visualize BEL Document in Cytoscape Requirements – Document must be valid BEL or xbel Must compile without validation errors – Cytoscape configuration set within BEL Editor – BEL Framework server not running (if local) Two options: – With Phase III compilation Phase III adds information from resource documents Gene scaffolding, protein family expansion – Without Phase III compilation 25

26. Visualize BEL Document in Cytoscape Right-click document name in Project Explorer panel Select Cytoscape from bottom of menu Select either: – Visualize in Cytoscape – Visualize in Cytoscape (no Phase III) Tip – close Cytoscape prior to launching visualization 26

27. Visualize BEL Document in Cytoscape Cytoscape will launch and open a view of your network 27