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

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

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

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 – 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

Install BEL Editor Stable repository location: 5

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

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

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

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

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

Create New BEL Project 11

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

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

Create New BEL Document 14

Create New BEL Document 15

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

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

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

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

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

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

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

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

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

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

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

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