Kepler: A System for Scientific Workflows

Version: 1.0.0alpha2


Welcome to the Kepler scientific workflow tool. You can select from one of the example workflows below or create your own by going to the file menu and selecting new/graph editor. Please send any questions/comments to our developer mailing list at kepler-dev@ecoinformatics.org.

Kepler is a collaboration between computer and domain scientists with the SEEK project (http://seek.ecoinformatics.org), the SDM Center (http://sdm.lbl.gov/sdmcenter), the Ptolemy II project (http://ptolemy.eecs.berkeley.edu), the GEON project (http://www.geongrid.org), the ROADNet project (http://roadnet.ucsd.edu). Kepler extends the underlying Ptolemy II system in the direction of scientific workflows. For more information on the Kepler collaboration, visit http://kepler-project.org.

Ready-to-run Workflows

Workflow Description
EML2 Simple Plot Example A workflow to test the EML 2.0 ingestion actor.
Promotor Identification Workflow A workflow that tests a number of the SciDAC actors including the genbank web service query actor and the BLAST actor.
GEON Map Workflow GEON geology map integration workflow using web services.
Discrete Logistic Single species Discrete Logistic model
Lotka-Volterra Predator Prey Model LV Predator Prey Model
Lotka-Volterra Predator Prey Model with logistic growth Logistic version of the LV Predator Prey Model
Elk/Wolf Predator Prey Model Elk/Wolf Predator Prey Model
Biodiversity Index Calculator Example of Calculations of Various Biodiversity Indices
Orb Image Viewer Workflow A workflow that displays image data coming from a remote camera via an Antelope ORB server.
Orb Workflow A workflow that shows a simple use of the Antelope ORB interface.
Orb Packet Objects to Record Conversion Workflow A workflow that extends the OrbPacketObjectDemo to demonstrate the use of several other actors, specificially ObjectToRecord.
Geological Data Creation and Registration A workflow to generate geoloical datasets on the fly and register them.

Configurable Workflows

Workflow Description (Please visit http://kepler.ecoinformatics.org/downloads.html for configuration instructions.)
GEON Mineral Classifier A workflow for modal classification of Igneous rocks.
Database Query (MS)
Database Query (DB2)
A workflow that tests a generic database query actor and shows the query result using a browser-based user interface.
Example Grid-based Workflow A workflow that tests and shows the use of ProxyInit, GlobusJob and GridFTP actors.
ARC -> GRASS import example A wokflow that imports an ARC file into the GRASS database.
GARP Native Species Prediction Demo Experimental implementation of the Genetic Algorithm for Ruleset Production (GARP). This may or may not work right now.
Neural network back propagation pipeline. Experimental implementation of a neural network back propagation pipeline. This will eventually be used in GARP.
Interactive R This is an example of interacting with an interactive subprocess ('R' in this case'). It requires R system to be installed on your system.
Composite R Data Reader Workflow This is an example of running an R script inside Kepler using the CommandLine actor. It requires R system to be installed on your system. Please look inside the file for the annotated configuration instructions.
Biodiversity Example This is an example of how to calculate biodiversity indices from a column.

Other workflows will be added here as they are created.

Additions to ptolemy by the Kepler team include many actors as well as additional dialog functionality within ptolemy. The actor additions include:

  • Generic Web Service Client and Harvesting Actors
  • Relational Database Management Systems access and query support actors
  • Ecological Metadata Language 2.0 ingestion actor
  • Globus proxy and job runner actors
  • File transfer actors suppoting SRB, GridFTP and scp
  • BIO-Web services including BLAST, GenBank, ClustalW, Transfac
  • Actors for implementation of GARP and GRASS ecological pilpelines
  • Configurable web browser and email actor for friendly user interface and notification
  • Command line actor shell command executions
  • Various file and record handling, and data transformation actors

Functionality has been added to create stub actors dynamically at runtime. To try out this functionality, open a new graph editor and choose view/new actor. Once you create the actor, it will be added to the actor library (the tree on the left of the screen) under actors/dynamic actor. The actor can then be drug out into the design screen but cannot be edited. This is useful for creating skeleton workflows which can then be implemented later.

To see the main Ptolemy intro screen click here.

Links

Science Environment for Ecological Knowlege
Scientific Data Management Center
Cyberinfrastructure for the Geosciences
Knowledge Network for Biocomplexity
San Diego Supercomputer Center
The National Center for Ecological Analysis and Synthesis

This software is protected by this license.