2006 Summer Institute Program

Program Overview
2006 Summer Institute Mini-Symposium
Date Period Track # Tracks Location Session Chairs

Aug 7, 2006


7:30 am Open to all Registration/Poster Setup Atkinson Hall Lobby Teri Simas
8:45 am-12:15 pm Mini-symposium Morning Session Atkinson Hall Auditorium Peter Arzberger
12:15 pm Lunch Canyon Vista /Price Center  
1:00 pm-1:45 pm Poster Session Atkinson Hall Lobby Teri Simas
2 pm-5 pm Mini-symposium Afternoon Session Atkinson Hall Auditorium Wilfred Li
5:15 pm Dinner Canyon Vista /Price Center  
6:45 pm -8:30 pm Opening Reception/Poster Session Atkinson Hall Lobby Peter Arzberger

2006 Summer Institute Training Sessions

Aug 8 - 11, 2006


9 am-12 pm


1 Cluster & Grid Computing (CGC) BCL (PFBH 161) Wilfred Li
Nadya Williams
2 Web Services & Ontology (WSO) CPL2 (Atkinson 2006)

Sriram Krishnan
Amarnath Gupta

3 Molecular Visualization & Virtual Screening (MVS) CTL (Scripps 350, T,Th,F), CPL1 (Atkinson, 6004, W). Michel Sanner
Garrett Morris

2 pm-5 pm


4 Computational Cardiac Electrophysiology and Mechanics (CEM) BCL (PFBH 161) Andrew McCulloch
Fred Lionetti
5 Molecular Electrostatics and Diffusion (MED) CTL (Scripps 350, W,F), CPL1 (Atkinson, 6004, T, Th) Nathan Baker
Yuhui Cheng
6 GridSphere Portals (GSP) CPL2 (Atkinson 2006) Jason Novotny
Abel Lin

Aug 11, 2006

6 pm 1-6 Closing Dinner Institute of the Americas Plaza (IOA) Teri Simas
Detailed Program
2006 Summer InstituteMini-Symposium and Training Sessions


Aug 7, 2006

Day 1
8:30 am Welcome

NBCR Summer Institute 2006

Peter W. Arzberger, Ph.D., University of California, San Diego

Atkinson Hall Auditorium Peter W. Arzberger
8:45 am  

Opening Remarks

Michael Marron, Ph.D., NCRR, NIH

9 am Mini-symposium

Cyberinfrastructure & Multiscale Modeling

Mark Ellisman, University of California, San Diego

9:45 am  

Building Cyberinfrastructure for Biomedical Informatics Research Network (BIRN)

Philip Papadopoulos, Unverisity of California, San Diego

10:30 am   coffee break
10:45 am  

CAMERA: Community Cyberinfrastructure for Advanced Microbial Ecology Research & Analysis

Paul Gilna, Unverisity of California, San Diego

11:30 am  

Open Science Grid

Frank Wuerthwein, UCSD, Fermilab

12:15 pm   Lunch Canyon Vista /Price Center  
1:00 pm - 1:45 pm   Poster Session Auditorium Lobby Teri Simas
2 pm  

Cardiac Systems Biology & Multiscale Modeling

Andrew McCulloch, Unverisity of California, San Diego

Atkinson Hall Auditorium Wilfred W. Li
2:45 pm  

Molecular Electrostatics & Diffusion

J. Andrew McCammon, Unverisity of California, San Diego

3:30 pm   coffee break
3:45 pm  

Static and Time Dependent Meshing for Multi-scale Modeling

Chandrajit Bajaj, University of Texas

4:30 pm  

Molecular Visualization

Michel Sanner, The Scripps Research Institute

5:15 pm  

Closing Remarks

John Wooley, Ph.D., UCSD

5:30 pm   Dinner Canyon Vista/Price Center
6:45 pm 8:30 pm Opening Night Reception/Poster Session Atkinson Hall Lobby
End of Mini-Symposium Events


Aug 8, 2006

Day 2 (actual course content may vary as deemed appopriate by the instructors, see course wiki for materials) Teri Simas
9 am-12 pm 1 CGC

Cluster and Grid Computing: What can I do now?

How to use cluster environment efficiently? How can I use grid computing today? Basic tutorials on use local batch schedulers in a cluster, and metaschedulers on the grid. Case studies using MEME, AutoDock, the Globus toolkit, Condor, as well as GAMA Certificate Management system through My WorkSphere.

Nadya Williams, Abel Lin & Damian Randal

PFBH 161

Web Services Based Access to Scientific Applications

How to use web services to deploy scientific applications? How to leverage the Globus toolkit and wrap applications as web services quickly? Introduction and tutorials on the key concepts in web services, AXIS, and the NBCR Opal web service wrapper toolkit.

Sriram Krishnan, Brent Stearn

Atkinson 2006

Python Molecular Viewer and Visualization Techniques

How to use the PMV for molecular visualization to study molecules and create publication quality images? Tutorials on key features of PMV such as calculations of molecular surfaces, and development of automated session/task scripts. Use of PMV to access distributed computing resources will also be included..

Michel Sanner & Sargis Dallakyan

Scripps 350 (shuttle service)
2 pm-5 pm 4 CEM

Systems modeling of cell biophysics and biochemistry

Common pool models of cardiac myocyte excitation-contraction coupling and its regulation
Introduction to reaction-diffusion models of cells with Continuity

Anushka Michailova, Andrew McCulloch & Stuart Campbell

PFBH 161

Principles and practices in protein electrostatics calculations

Background theory on electrostatics, and tutorial work with PDB2PQR to generate the input files for use with the Adaptive Poisson-Boltzman Solver (APBS).

Nathan Baker, Yuhui Cheng

Atkinson 6004

Telescience Portal: comprehensive environment to transparent cluster and grid computing

Telescience Portal is built over the GridSphere framework and customized for the use with Electron microscopy and tomographic reconstruction. A new ATOMIC layer is built to allow legacy applications to access compute and storage resources transparently. Other features such as session management, and data management will be illustrated.

Abel Lin

Atkinson 2006


Aug 9, 2006

Day 3
9 am-12 pm 1 CGC

Cluster and Grid Computing: Case Studies

How to run Embarassingly Parallel jobs? Which technology is suitable for my problem? Basic tutorials on Condor, MPI environment and Rocks roll development. Additional introduction to visualization on the grid using visualization cluster software such as SAGE will be demonstrated. Additional examples will be provided on using the PRAGMA Gfarm grid testbed.

Nadya Williams, Osamu Tatebe & Cindy Zheng.

PFBH 161

Gemstone: transparent access to web services based applications

How to leverage the Gemstone framework to build intuitive interfaces to your applications? Gemstone allows the development of application specific interfaces familiar to scientific application users. Examples will be provided on how to develop interfaces to your applications using the Gemstone framework, and the Opal web service wrapper toolkit.

Brent Stearn, Jerry Greenberg & Sriram Krishnan

Atkinson 2006

The Vision Visual Programming Environment

Vision framework may be used to develop applications and workflows using objected-oriented approach. Case studies and tutorials in AutoDock Tools, distributed computing and workflow composition will be provided.

Gillaume Vareille

Atkinson 6004
2 pm-5 pm 4 CEM

Continuum modeling of tissue mechanics and electrophysiology

Finite element discretization, meshes, and anatomic fitting with Continuity

Andrew McCulloch & Fred Lionetti

PFBH 161

Applications of APBS and analysis of results

Quantitative and visualization with standard examples. Introductory talk on practical aspects of diffusion and diffusion-controlled reactions.  Tutorial on SMOL, a new application based on the Finite Element Toolkit (FEtk)..

Nathan Baker , David Cerutti

Scripps 350 (shuttle service)


GAMA: Grid Account Management Architecture

How to provide users with grid credentials transparently within the GridSphere framework, and how the same technology may be used by other applications? GAMA allows a user to obtain grid credentials seamlessly from a GridSphere portal interface, or a standalone client such as PMV, Gemstone, or workflow composition environment such as Kepler. Users may use the proxies or credentials to perform many data and computing tasks transparently. New features and tutorials on using GAMA services will be provided.

Kurt Mueller & Sandeep Chandra

Atkinson 2006


Aug 10, 2006

Day 4
9 am-12 pm 1 CGC

Cluster and Grid Computing: How to Program?

MyMPI, cluster and grid programming using Ninf-G. How to benchmark and debug parallel applications in the cluster and grid environment. Case studies using Continuity and MEME will be used to illustrate the key points and in the tutorials.

Tim Kaiser, Yoshio Tanaka

PFBH 161

Data Integration and Ontology Tools

Approaches in data integration and effcient querying of distributed data sources. New tools such as OntoQuest in automated knowledge inference and discovery. Semantic annotation technology and its application in Pathsys based web services.

Amarnath Gupta, Michael Batailuc

Atkinson 2006

Using AutoDock with AutoDock Tools

How to use AutoDock Tools (ADT) to set up AutoDock docking experiments in a visual environment? ADT is an application based on PMV with specific modules for preparation and postanalysis of AutoDock experiments. Basic theories on docking and tutorials will be provided.

Ruth Huey, Garrett Morris

Scripps 350 (shuttle service)
2 pm-5 pm 4 CEM

Monodomain modeling in cardiac electrophysiology

Finite element methods for modeling action potential propagation with Continuity.

Andrew McCulloch, Fred Lionetti & Sarah Healy

PFBH 161

Applications of SMOL and analysis of results

Case study: Continuum Diffusion Rate of Tetrameric Acetylcholinesterase by Solving the Smoluchowski Equation.
Start individual projects with student-selected or other systems.

Yuhui Cheng & David Cerutti

Atkinson 6004

GridSphere Framework: portlet design and inteoperability considerations

How to design good portlets that interoperate and how to bridge existing applications and interfaces to the GridSphere framework? Basic introduction to portlet development and standard compliance using the examples from GridSphere, and a walk-through of portlet development and deployment. Specific examples of GridSphere integration with the Grid Computing environment and bridging with other web technology will be provided.

Jason Novotny

Atkinson 2006


Aug 11, 2006

Day 5
9 am-12 pm 1 CGC

Cluster and Grid Computing: Transparent Access and workflow management

Transparent access through portals, desktop clients and web browsers through workflow engines based on the Kepler environment. Use of Kepler as a stand alone workflow execution engine, and coupling of Opal based web services examples using MEME and MAST. Additional workflow examples will be provided in working with metaschedulers.

Ilkay Altintas, Zhaohui Ding, Yuan Luo

PFBH 161

Cell Centered Database and Semantic Integration

How to support large scale cell centered studies and develop database layers for web services based access with support for semantic integration? CCDB currently focuses of 3D microscopic image data collection, semantic annotation, and integration using ontology mapping and automated reasoning tools. It is fully accessible as GridSphere portlets, or as web services. Specific case studies and software components will be provided and demonstrated.

Mary Ann Martone & Amarnath Gupta

Atkinson 2006

Using AutoDock for Virtual Screening

How to set up AutoDock experiments for large scale virtual screening? Case studies and result analysis. The ability to screen a large number of natural or artificial compound libraries is becoming routine as the grid computing power increases. Specific examples and guidelines on parameter refinement and postanalysis will be provided and demonstrated in hands on tutorials.

Garrett Morris

Scripps 350 (shuttle service)
2 pm-5 pm 4 CEM

Finite deformation modeling in soft tissue biomechanics

Finite element modeling of cardiac mechanics and ventricular vascular coupling with Continuity
Project work

Andrew McCulloch, Fred Lionetti & Roy Kerckhoffs

PFBH 161

Individual projects and advanced tutoring

Advanced topics in applications of the FEtk. Advanced molecular dynamics simulations of subcellular systems. Integration with Charmm, Amber using iAPBS will also be demonstrated.

Yuhui Cheng & David Cerutti

Scripps 350 (shuttle service)

The BIRN portal framework

The BIRN portal is the largest production network with GridSphere as the main user interface. Examples and demonstrations of portal development for this complex environment will be provided. Reusable components are being made available in many other projects using portlet technolgy.

Jason Novotny, Ramil Manansala

Atkinson 2006
6 pm   2006 Summer Institute Closing Dinner IOA