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Table of Contents
Table of Contents ....................................................................................................................... 2
Introduction to BiblioSphere PathwayEdition ........................................................................................ 4
Knowledge Database ...................................................................................................................... 5
What Data is BSPE Based on? ..................................................................................................... 5
Methods and Data Sources ......................................................................................................... 6
Network Generation and Analysis .................................................................................................... 8
Data Input, Network Calculation and Biological Ranking............................................................... 8
User Controlled Network Construction and Analysis ..................................................................... 9
Technical Requirements .................................................................................................................... 12
Operating Systems........................................................................................................................ 12
Java Runtime Environment............................................................................................................ 12
Connection to the Internet ............................................................................................................ 14
Installation of BSPE........................................................................................................................... 14
Download ..................................................................................................................................... 14
Get Login and Password................................................................................................................ 16
Registration .............................................................................................................................. 16
Change Password ..................................................................................................................... 18
Password Policy ........................................................................................................................ 19
Installation ................................................................................................................................... 20
Configuration of BSPE ................................................................................................................... 22
Proxy Configuration .................................................................................................................. 24
SSL Configuration ..................................................................................................................... 25
Server Configuration ................................................................................................................. 26
Check for Updates ........................................................................................................................ 27
Turning on Automatic Update Notification ................................................................................. 28
Updating your Application Manually........................................................................................... 29
How to Prepare your Input Data........................................................................................................ 31
Gene Identifiers ............................................................................................................................ 31
Gene List ...................................................................................................................................... 31
User Interface .......................................................................................................................... 31
Excel Files ................................................................................................................................ 32
Starting an Analysis........................................................................................................................... 32
Inputting your Data ...................................................................................................................... 32
Sign In ..................................................................................................................................... 32
Project Management................................................................................................................. 33
Create a New Project ................................................................................................................ 33
Edit an Existing Project ............................................................................................................. 34
Create a New Analysis .............................................................................................................. 34
Input Data................................................................................................................................ 35
Accessing your Analyses ........................................................................................................... 38
Running your Analysis................................................................................................................... 38
Ambiguities .............................................................................................................................. 38
Hit List ..................................................................................................................................... 39
Network View ................................................................................................................................... 41
Pathway View ............................................................................................................................... 41
Overview .................................................................................................................................. 41
Connection Modes .................................................................................................................... 43
Relation Info Panel ................................................................................................................... 43
Node Info Panel........................................................................................................................ 44
Docking and Undocking ............................................................................................................ 46
Zoom ....................................................................................................................................... 46
Shortest Path............................................................................................................................ 46
Layout Optimization.................................................................................................................. 46
Color Scheme Chooser .............................................................................................................. 46
Export Networks ....................................................................................................................... 47
Metabolic & Signal Transduction Pathways ................................................................................ 47
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