Kepler User Manual Version 2.4 March 2013 Table of Contents 1. INTRODUCTION TO KEPLER ........................................................................................................ 6 1.1 WHAT IS KEPLER? ............................................................................................................................................ 6 1.1.1 Features .................................................................................................................................................. 9 1.1.2 Architecture ........................................................................................................................................ 11 1.2 HISTORY OF THE KEPLER PROJECT ............................................................................................................. 13 1.3 KEPLER CODE CONTRIBUTORS .................................................................................................................... 15 1.4 FUTURE GOALS ............................................................................................................................................... 17 1.5 PARTICIPATING IN KEPLER DEVELOPMENT .............................................................................................. 19 1.5.1 Using Eclipse ...................................................................................................................................... 21 1.5.2 Contributing to Kepler ................................................................................................................... 22 1.6 REPORTING BUGS ........................................................................................................................................... 22 1.7 FURTHER READING ........................................................................................................................................ 22 2. INSTALLING AND RUNNING KEPLER ..................................................................................... 24 2.1 SYSTEM REQUIREMENTS .............................................................................................................................. 24 2.2 INSTALLING KEPLER ...................................................................................................................................... 24 2.2.1 Installing on Windows ................................................................................................................... 24 2.2.3 Installing on Macintosh ................................................................................................................. 25 2.2.4 Installing on Linux ........................................................................................................................... 26 2.3 STARTING KEPLER ......................................................................................................................................... 26 2.4 THE USER INTERFACE ................................................................................................................................... 28 2.4.1 Menu Bar ............................................................................................................................................. 29 2.4.2 Toolbar ................................................................................................................................................. 33 2.4.3 Components, Data Access, and Outline Areas ...................................................................... 35 2.4.4 Workflow Canvas ............................................................................................................................. 40 2.4.5 Navigation Area ................................................................................................................................ 42 3. SCIENTIFIC WORKFLOWS .......................................................................................................... 44 3.1 WHAT IS A SCIENTIFIC WORKFLOW? ......................................................................................................... 45 3.2 COMPONENTS OF A WORKFLOW ................................................................................................................. 46 3.2.1 Directors .............................................................................................................................................. 47 3.2.2 Actors .................................................................................................................................................... 48 3.2.3 Composite Actors ............................................................................................................................. 55 3.2.4 Ports ...................................................................................................................................................... 56 3.2.5 Channels and Tokens ...................................................................................................................... 60 3.2.6 Data Types .......................................................................................................................................... 61 3.2.7 Relations .............................................................................................................................................. 63 3.2.8 Parameters .......................................................................................................................................... 64 4. WORKING WITH EXISTING SCIENTIFIC WORKFLOWS .................................................... 68 4.1 OPENING WORKFLOWS ................................................................................................................................. 68 4.1.1 Opening Local Workflows ............................................................................................................ 68 4.2 RUNNING WORKFLOWS ................................................................................................................................ 70 4.2.1 Runtime Window ............................................................................................................................. 70 4.2.2 Run Button .......................................................................................................................................... 72 4.2.3 Running Workflows with Adjusted Parameters ................................................................. 74 4.3 MODIFYING WORKFLOWS ............................................................................................................................ 78 4.3.1 Substituting Data Sets .................................................................................................................... 79 4.3.2 Substituting Analytical Components ........................................................................................ 86 4.4 SAVING WORKFLOWS .................................................................................................................................... 89 4.5 SEARCHING FOR DATA AND COMPONENTS ................................................................................................ 89 4.5.1 Searching for Available Data ....................................................................................................... 89 4.5.2 Searching for Standard Components ....................................................................................... 93 4.5.3 Searching for Components in the Kepler Repository ........................................................ 94 5. BUILDING WORKFLOWS WITH EXISTING ACTORS .......................................................... 97 5.1 PROTOTYPING WORKFLOWS ....................................................................................................................... 98 5.2. CHOOSING A DIRECTOR ............................................................................................................................. 101 5.2.1 Synchronous Dataflow (SDF) ................................................................................................... 104 5.2.2 Process Networks (PN) ............................................................................................................... 109 5.2.3 Discrete Events (DE) .................................................................................................................... 110 5.2.4 Continuous Time ........................................................................................................................... 112 5.2.5 Dynamic Dataflow (DDF) ........................................................................................................... 115 5.3 USING EXISTING ACTORS ........................................................................................................................... 120 5.3.1 Using Actors from the Standard Component Library .................................................... 120 5.3.2 Instantiating Actors Not Included in the Standard Library ......................................... 121 5.3.3 Using the Kepler Analytical Component Repository ...................................................... 124 5.3.4 Saving Actors to Your Library .................................................................................................. 126 5.3.5 Importing Actors as KAR Files ................................................................................................. 128 5.3.6 Actor Icon Families ......................................................................................................................