1. biology.sdsc.edu CIPRes in Kepler: An integrative workflow package for streamlining phylogenetic data analyses Zhijie Guan 1, Alex Borchers 1, Timothy McPhillips 2, Shirley Cohen 3, Mark A. Miller 1, Ilkay Altintas 1 1 San Diego Supercomputer Center, UCSD 2 University of California, Davis 3 University of Pennsylvania

2. biology.sdsc.edu What is a Scientific Workflow?  Combination of  data integration, analysis, and visualization steps  larger, automated "scientific process"  Mission of scientific workflow systems  Promote “scientific discovery” by providing tools and methods to generate scientific workflows  Create an extensible and customizable graphical user interface for scientists from different scientific domains  Support computational experiment creation, execution, sharing, reuse and provenance  Design frameworks which define efficient ways to connect to the existing data and integrate heterogeneous data from multiple resources  Make technology useful through user’s monitor!!!

3. biology.sdsc.edu Promoter Identification Workflow Source: Matt Coleman (LLNL)

4. biology.sdsc.edu A Workflow for Phylogeny Analysis

5. biology.sdsc.edu Kepler is a Scientific Workflow System  … and a cross-project collaboration  June 2, 2006 Beta release www.kepler-project.org Ptolemy II: A software system used for prototyping engineering system KEPLER: A platform to design and execute Scientific Workflows KEPLER = “Ptolemy II + X” for Scientific Workflows  Builds upon the open-source Ptolemy II framework

6. biology.sdsc.edu Some Kepler Contributors Ptolemy II Resurgence Griddles SRB LOOKING SKIDL NLADR Contributor names and funding info are at the Kepler website!! Other contributors: - Chesire (UK Text Mining Center) - DART (Great Barrier Reef, Australia) - National Digital Archives + UCSD-TV (US) - …

7. biology.sdsc.edu A co-development in KEPLER: GEON Dataset Generation & Registration SQL database access (JDBC) % Makefile $> ant run % Makefile $> ant run

8. biology.sdsc.edu Phylogeny Analysis Workflows Local Disk Multiple Sequence Alignment Phylogeny Analysis Tree Visualization

9. biology.sdsc.edu Kepler Workflow: Actors  Actor  Encapsulation of parameterized actions  Interface defined by ports and parameters  Port  Communication between input and output data  The place where data get in/out  Model of computation  Flow of control  Sequential / parallel execution  Implementation is a framework Actor-Oriented Design

10. biology.sdsc.edu CIPRes Workflow: Actors Input Port: Nexus File Content Data Matrix Tree Taxa Info Output Ports:

11. biology.sdsc.edu Some actors in place for… Generic Web Service Client and Web Service Harvester Customizable RDBMS query and update Command Line wrapper tools (local, ssh, scp, ftp, etc.) Some Grid actors- Globus Job Runner, GridFTP-based file access, Proxy Certificate Generator SRB support Native R and Matlab support Interaction with Nimrod and APST Communication with ORBs through actors and services Imaging, Gridding, Vis Support Textual and Graphical Output …more generic and domain-oriented actors…

12. biology.sdsc.edu CIPRes Workflow Run ClustalW Choose the input file Get the subset of the aligned sequences Read the tree Parse the tree Display the tree Run PAUP for Tree Inference Channel: Convey the data GUIGen: Parameter Setting Actor: Results:

13. biology.sdsc.edu CIPRes Workflows: Demo  Read Sequences  Multiple Sequence Alignment  Display the Alignment  Matrix Alignment  Tree Inference  Consensus Tree  Tree Visualization

14. biology.sdsc.edu Summary  Kepler is good at:  Integrating data, programs, and computing resources  Capturing your ideas and realizing them  Supporting computational experiment creation, execution, sharing, and reuse  Quickly prototyping scientific workflows  Building streamlining applications  Visual programming language  Don’t write your application, “draw”/compose it  Cipres-Kepler package can be used to build scientific workflows for phylogenetic data analyses

15. biology.sdsc.edu Future Work  Cipres-Kepler can help you  There is (always) a lot more to work on:  More actors for phylogeny analyses  Automatically generating actors based on CORBA services  Database (TreeBase) support to store large amounts of data  More computing power for large dataset processing  Need your collaboration:  Sharing experiences  Teaching each other the domain knowledge  Locating a specific problem and solving it

16. biology.sdsc.edu Questions? Zhijie Guan guan@sdsc.edu 1-858-822-3620 www.sdsc.edu Cipres-Kepler Release: ftp://ftp.sdsc.edu/outgoing/borchers/cipresReleases/20060621/cipresKepler_Dist.tgz