2011 6th Summer Institute

The sixth National Biomedical Computation Resource (NBCR) Summer Institute (SI)

Monday - Friday, 1-5 August, 2011

The Goal
is to provide significant training opportunities for the biomedical research community members in targeted areas of computational multiscale biomedical research:
  (1) computer aided drug discovery,
  (2) mesoscale modeling,
  (3) computational cardiac electrophysiology and mechanics.

includes hands-on sessions for key NBCR tools freely available to the academic community. Participants may bring their own data and analyses for an immediate impact to their research. User feedbacks are critical to the development and enhancement of software features. Participants are encouraged to discuss new collaborations with NBCR faculty and staff members.

SI 2011 will be held in San Diego, California on the campuses of University of California, San Diego (UCSD) and The Scripps Research Institute (TSRI). Students may choose to stay off campus or use UCSD Campus housing. Participants are required to bring their own laptops and install the necessary software where indicated by the instructors prior to their arrival.


NBCR is one of the National Centers funded by the National Center for Research Resouces (NCRR), NIH.

The workshop is aimed at graduate students, postdocs and researchers interested in 1) learning how to use specific tools covered by this summer institute, or 2) understanding specific examples of computational approaches to multiscale biomedical research, and 3) learning how to address the Challenges in Multiscale Computational Modeling.

This 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 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.


Each of the following topics represents a parallel track that will meet half days, for five days, Monday - Friday, 1-5 August, 20111. Each participant may sign up for maximum of two tracks. Special topics sessions may be included to allow students to gain additional experience with specific tools or to work on their own problems. Students are encouraged to contact the instructors prior to their arrival with their special topics of interest.
1There will be no afternoon session on Friday, Aug 5, 2011.

Morning Session Afternoon Session
1 Computational Cardiac Mechanics
Tutorials on use of Continuity 6.3 by NBCR
4 Virtual Screening using AutoDock Suite of Tools
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 Mesoscale Modeling of Cardiac Myocytes
Tutorials on meshing using FETK/Gamer and simulations using CSMOL through the Blender Interface
3 Computer Aided Drug Discovery (CADD) pipeline
Tutorials on using the Relaxed Complex Scheme and the CADD pipeline in drug discovery for infectious diseases
6 Scalable Scientific Applications and Workflows using Cloud Services
Tutorials on the deployment of user applications as Cloud based services and development of complex workflows.

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


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.





NBCR Summer Institute 2011 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 2011 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, Monday, August 1, 2011