1. Pipeline Execution Environment
Laboratory of NeuroImaging
UCLA

2. Motivation You have the algorithms You have the data
Possibly located on different platforms, different machines
You have the data
Possibly located on different machines, have different format
How do you get your work done?

3. What is the Pipeline? It is a data flow execution environment
It is useful for…
Any task where you can draw the steps in a flowchart
Any task where you need to write instructions for someone
We use it for neuroimaging analysis
To be extended in the near future to bioinformatics and other computational biology subdomains

4. Why you might find it useful…
Integrate your program as part of an analytic process
Send a collaborator an analytic process
Parallel batch processing with error handling

5. Sample useful pipeline…
Download all ITK/VTK/Slicer sources
Run CMake for configuration
Execute makefile
Downloaded all examples
Compiled and test all examples
Available on the NAMIC Wiki page

6. LONI/NAMIC collaboration
Pipeline’s modular architecture make is easy to integrate external tools
Users want to see the data as it is being processed
Visualization component
Users want to make use of new algorithms implemented
Wrap command line executables as pipeline modules
ITK Filter integration (vs. command line executables)
Users want to utilize Pipeline resources
Open specification for communications with Pipeline server

7. Pipeline features Platform independent
Modular, extensible architecture
Components
Events
Modules- user defined
High grade encrypted communications
Automatic & transparent resource management
Shell script output
Feature rich GUI

8. Pipeline features (cont.)
Distributed computing
Cluster computing
Local clusters (e.g PVM)
Intranet grid computing
Grid engine
Internet/overlay grid computing
In development

9. A live example
(bear with me while I try this)

10. Integrating additional functionality into the Pipeline
As modules
Typically programs that do some sort of processing
Rigidly structured
User oriented
As components
Typically programs that support the processing and/or improve the usability (e.g. visualization)
More flexibility
Developer oriented

11. Developing a component
Extend AbstractComponent class
Override processEvent(Event) method
Place into extensions directory to be loaded at startup
Visualization component is <200 lines

12. Roadmap 6/2005 12/2005 Beta to be released Data-centric GUI
Fault tolerance
Overlay grid implementation

13. Roadmap (cont.) 6/2006 Ongoing ITK/VTK integration SCIRun integration
Provenance
Data validation
Information recovery
Ongoing
Ontologies
Self learning system
Automated analysis
Natural language interface

14. LONI Resources
CVS
Mantis
Wiki
Compute grid
Data grid

15. For more information… Michael Pan mjpan@loni.ucla.edu

16. Software license
Permission is granted to use this software without charge for non-commercial research purposes only.

17. NIH software terms This is compliance with NIH requirements, i.e.
The software should be freely available to biomedical researchers and educators in the non-profit sector, such as institutions of education, research institutes, and government laboratories.
The terms of software availability should permit the commercialization of enhanced or customized versions of the software, or incorporation of the software or pieces of it into other software packages.