1. UCSD / BIRN Coordinating Center NAMIC Group
Site PI: Mark H. Ellisman
Site Project Lead: Jeffrey S. Grethe

2. Who are we – people Faculty Grid Application Development
Mark Ellisman
Jeffrey Grethe
Grid Application Development
Integration of Slicer3 Execution model with Grid infrastructure
Marco Ruiz
Algorithm Development
N-Channel Automated Colocalization Analysis
Portal Development
Integration of Slicer / NA-MIC Toolkit components w/ User Portal
Ramil Manansala
Application Integration
Integration of NA-MIC Toolkit with BIRN environment
Vicky Rowley
Systems Support
Support for NA-MIC components of BIRN grid
Bao Nguyen

3. What do we contribute - Collaboration
Provide collaborative portal environment
Enable researchers to store and interact with large collections of federated data within a distributed data grid

4. What do we contribute - Algorithm Development
N-Channel Automated Colocalization Analysis
Quantitative tools to assess the co-distributions of molecular markers within individual cells and immuloabeled tissue slices.
Colocalization and spatial distribution analysis module within Slicer3

5. Incorporating Microscopy Processing and Analysis Into 3-D Slicer
Slice view
Surface view
File readers to deal with variety of image file formats generated at NCMIR
Developing Slicer interface for existing tools used by NCMIR researchers (eg. IMOD, TxBR, etc)
Create a single, user-friendly application to unify image processing, visualization, analysis and annotation

6. What do we contribute - Grid Computation
Provide researchers with customizable access to a computing environment that takes advantage of Grid-based infrastructures
Grid Execution Module
Heterogeneous collection of arge scale compute resources are available to NA-MIC researchers and users of the NA-MIC kit (e.g. BIRN, TeraGrid, local clusters)
Provide interface module (Grid Wizard Interface) for the NA-MIC kit to enable distributed execution of algorithms from Slicer and modules such as BatchMake

7. A Researcher’s “Grid”
A researcher’s high performance computing resource is usually a collection of resources (i.e. clusters)
To use this collection of resources, the “Client” is responsible to provide the logic to integrate the the disparate clusters within the logic of their specific applications
Most of the times this effort is non-trivial, non-reusable, non-extensible, lacks robustness and is far from giving the end user all the desired functionality

8. “Grid Wizard Enterprise” enabled Cluster
Tight integration with cluster internals and transparent access to them.
Granular level of execution control: submission, pause, resume, abort.
Real time monitoring and alerting capabilities.
Granular reporting of historic, diagnostics and statistics data.
Transparent environment translation for requests.
Programmatic control with rich and simple API.

9. Tool Integration - Generic: Slicer3

10. Grid Interface prototype
Immediate Goals
February 2008
June 2008
April 2008
Current
On-Going:
BatchMake Integration
Grid Interface prototype
Pre-release. Alpha version of complete infrastructure including automatic deployment
These are (my) immediate goals for the next 6 months or so.
Pre-release (Beta version) - Full Slicer 3 Integration
Production Release - Stable version with drivers for most popular cluster components (including full transparent SRB support), full monitoring, alert capabilities and API bundles.