BEL Editor

Report
BEL Editor
August 2012
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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 Community
2
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
– 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
Install BEL Editor
• Stable repository location:
https://raw.github.com/OpenBEL/eclipse/master/stable
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
Document Header
• Can be expressed in one of
two formats:
– BEL Script (.bel)
– XML (.xbel)
• Header Section
BEL Statements
– Document name, description,
version, authors, etc.
– Definitions
• Namespace references
• Annotation definitions
• Body Section
– BEL Statements
13
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 mouseover 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

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