2010 5th Summer Institute

The National Biomedical Computation Resource (NBCR) will hold its fifth Summer Institute (SI) the week of August 2-6, 2010.

Summer Institute in the Newsroom (posted 25 August, 2010)

The Goal
of this fifth NBCR SI is to provide significant training opportunities for members of the biomedical research community in targeted areas of computational multiscale biomedical research: computer aided drug discovery; mesoscale modeling; and computational cardiac electrophysiology and mechanics.
will include hands-on use of key NBCR tools that are freely available to the academic community. For NBCR a positive outcome of the workshop will be the creation of new users of these tools. In particular, there will be opportunities for participants to work with their own data and analyses in extended sessions.
The Institute will be held in La Jolla California on the University of California San Diego and The Scripps Research Institute campuses.
OVERVIEW OF THE SUMMER INSTITUTE, Monday - Friday, 2-6 August, 2010

The workshop is aimed at graduate students, postdocs and researchers interested in learning how to use specific tools covered by this summer institute or who are interested in understanding specific examples of computational approaches to multiscale biomedical research and in learning how to address the Challenges in Multiscale Computational Modeling.

This years workshop will have three major activities:
  • In-depth, Hands-on Training sessions in key areas of multiscale biomedical research (see list of tracks below).
  • Plenary Talks on multiscale computational modeling
  • Special Sessions, including special short topics or additional time with instructors to work with student brought data.
In addition there will be a poster session by participants, to allow NBCR instructors and researchers to interact with the participants and to explore new opportunities for collaboration or user needs. Flyer: NBCR Summer Institute 2010

Each of the following topics represents a parallel track that will meet half days, for five days, August 2-6, 2010. Each participant may sign up for maximum of two tracks. Special topics labs to gain additional experience with specific tools or to work on students own problems; discussion based on participants interests.
* There will be no afternoon session on Aug 6, 2010, Friday.

Morning Session Afternoon Session
1 Computational Cardiac Electrophysiology and Mechanics
Tutorials on use of Continuity 6.3 by NBCR
4 Virtual Screening and Computer Aided Drug Discovery (CADD)
Tutorials on use of AutoDock and AutoDock Tools and a cloud computing based virtual screening CADD pipeline.
2 Molecular Electrostatics and Diffusion
Tutorials on use of Adaptive Poisson Boltzmann Solvers (APBS) and BrownDye
5 From Cluster to Cloud Computing
Tutorials on the Opal Toolkit, Rocks, along with virtualization and running inside Amazons EC2 platform.
3 Programming Scalable Scientific Workflows
Tutorials on Vision and application of the Vision Workflow environment
6 Special Topics on Emerging Technologies in Multiscale Modeling
Minitalks and/or Tutorials on emerging software and novel algorithms in multiscale modeling

PLENARY SESSION Computational Seminar Series: Challenges in Multiscale Computational Modeling with an emphasis in bridging scales and on the mesoscale.

POSTERS SESSION There will be a poster session offered for participants, to allow greater interaction with NBCR researchers and networking with other Summer Institute participants.


REGISTRATION Enrollment is limited. To ensure your place in the Summer Institute program and to help us accommodate you, we ask that you register as early as possible.


LOGIN INSTRUCTIONS for the tracks participants



NBCR Summer Institute 2010 Flyer

California Institute for Telecommunications
and Information Technology (Calit2)

Pacific Rim Application and
Grid Middleware Assembly

Center for Research In Biological Systems
San Diego Supercomputer Center

Whitaker Institute of Biomedical
Engineering, UCSD
NBCR is grateful and wishes to thank our partners whose contributions have helped to organize the 2010 Summer Institute. Our partners have offered time, assistance and training to enhance quality of Summer Institute's sessions and events.

National Center for Microscopy
Imaging and Research

Rocks Clusters


If you'd like to become a sponsor, Please contact This email address is being protected from spambots. You need JavaScript enabled to view it.

Group photo, August 2, 2010 NBCR is one of the National Centers funded by the National Center for Research Resouces (NCRR), NIH.