Workshops
The Center has presented more than 60 "hands-on" workshops covering topics on Computational Biophysics since 2003. Workshops are designed to provide beginning to intermediate level training for students and researchers in the application of NAMD, VMD, and other scientific software toward the study of biomolecular systems. Both theoreticians and experimentalists are welcome! Workshop formats typically consist of 4-5 days, with lecture material in the mornings and hands-on, guided tutorials in the afternoons. For descriptions on the various types of workshops the Center has offered, see Types of Workshops. Send general questions regarding workshops here.
Upcoming Workshops
2024
- #62. Auburn, Alabama (December 16-20, 2024): Hands-On Workshop on Computational Biophysics
- #61. Auburn, Alabama (June 24-28, 2024): Hands-On Workshop on Computational Biophysics
Prior Workshops
2023
- #60. Auburn, Alabama (July 17-21, 2023): Hands-On Workshop on Computational Biophysics
- Seattle, Washington (July 13-14, 2023): Allen Institute Modeling Software Workshop
2022
- Chicago, Illinois (August 10-11, 2022): NAMD Developer Workshop
- Seattle, Washington (July 25-26, 2022): Allen Institute Modeling Software Workshop
- #59. Online based on Pittsburgh, Pennsylvania (July 5 - 8, 2022): Virtual Hands-On Workshop on Computational Biophysics
2021
- #58. Online based on Urbana, Illinois (October 18-22, 2021): Online Hands-on Workshop on Computational Biophysics
- Online based on Urbana, Illinois (September 22-23, 2021): NAMD Developer Workshop
- #57. Online based on Pittsburgh, Pennsylvania (June 28 - July 1, 2021): Virtual Hands-On Workshop on Computational Biophysics
2020
- CoMET: Computational Materials Education and Training, PennState University (October 20): Modeling Quantum Chemistry with VMD
- #56. Pittsburgh, Pennsylvania (October 12-15): Virtual Hands-On Workshop on Computational Biophysics
2019
- Urbana, Illinois (August 19-20): NAMD Developer Workshop
- Stockholm, Sweden (June 10-13): PRACE Spring School - HPC for Life Sciences
- #55. Pittsburgh, Pennsylvania (May 13-17): Hands-On Workshop on Computational Biophysics
2018
- #54. Urbana, Illinois (September 24-26): Hands-On Workshop on Structural DNA Nanotechnology
- #53. Urbana, Illinois (September 10-14): Hands-On Workshop on Enhanced Sampling and Free-Energy Calculation
- Urbana, Illinois (September 10-14): NCSA GPU Hackathon 2018 - All GPU programming paradigms are welcome
- #52. Urbana, Illinois (July 18-20): Hands-On Workshop on Cell Scale simulations
- Dalian, China (July 9-13): Biomolecular Dynamics Simulation Workshop
- Urbana, Illinois (June 11-12): NAMD Developer Workshop
- #51. Pittsburgh, Pennsylvania (May 21-25): Hands-On Workshop on Computational Biophysics
- #50. Urbana, Illinois (April 5-7): Hands-On Workshop on QM/MM Simulations
- Tokyo, Japan (March 5): Hands-on Workshop on Enhanced Sampling and Free-Energy Calculations.
2017
- Santiago, Chile (December 11-13): Beyond Kds: New computational and experimental methods to address challenges in drug discovery.
- #49. Urbana, IL USA (September 25-29): Hands-On Workshop on Enhanced Sampling and Free-Energy Calculations
- Upton, New York (June 5-9): GPU Hackathon 2017 - All GPU programming paradigms are welcome
- #48. Pittsburgh, PA USA (May 30 - June 2): Hands-on Workshop on Computational Biophysics
- Chicago, IL USA (May 22-23): NAMD Developer Workshop
- #47. Urbana, IL USA (April 17-21): Hands-on Workshop on Computational Biophysics
- Stockholm, Sweden (April 10-13): PRACE Spring School - HPC for Life Sciences
2016
- #46. San Francisco, CA USA (December 12-16): Hands-On Workshop on Integrative Modeling and Simulations
- #45. Atlanta, GA USA (November 14-18): Hands-On Workshop on Computational Biophysics
- #44. Urbana, IL USA (October 17-21): Hands-On Workshop on Computational Biophysics
- #43. Juelich, Germany (August 15-19): Hands-On Workshop on Cryo-EM Guided Modeling and Simulation
- #42. Pittsburgh, PA USA (June 6-10): Hands-On Workshop on Computational Biophysics
- Chicago, IL USA (May 26-27): NAMD Developer Workshop
2015
- #41. Odense, Denmark (October 12-16): Hands-On Workshop on Computational Biophysics
- #40. San Diego, CA USA (September 21-25): Hands-On Workshop on Simulation-Based Drug Discovery
- #39. Okazaki, Japan (September 9-11): Three-Day Workshop on Computational Biophysics
- #38. Berkeley, CA USA (August 3-7): Hands-On Workshop on Computational Biophysics
- #37. Pittsburgh, PA USA (June 1-5): Hands-On Workshop on Computational Biophysics
- #36. Urbana, IL USA (April 6-10): Hands-On Workshop on Computational Biophysics
- #35. Santiago, Chile (January 26-29): Hands-On Workshop on Combining Cryo-Electron Microscopy & Biomolecular Simulations
2014
- #34. Atlanta, GA USA (November 3-7): Hands-On Workshop on Computational Biophysics
- #33. Bremen, Germany (June 16-20): Hands-On Workshop on Computational Biophysics
- #32. Pittsburgh, PA USA (May 19-23): Hands-On Workshop on Computational Biophysics
- #31. Munich, Germany (March 25-28): Hands-On Workshop on Computational Biophysics
- #30. Urbana, IL USA (January 8-10): Three-Day Workshop on Cryo-EM Modeling Based on X-ray Crystallography
2013
- #29. Urbana, IL USA (November 18-22): Hands-On Workshop on Computational Biophysics
- #28. Beijing, China (October 14-17): Hands-On Workshop on Computational Biophysics
- Urbana, IL USA (August 2-4): Workshop on GPU Programming for Molecular Modeling
- #27. Pittsburgh, PA USA (June 10-14): Hands-On Workshop on Computational Biophysics
2012
- #26. Urbana, IL USA (October 22-26): Hands-On Workshop on Computational Biophysics
- Urbana, IL USA (July 16-27): Two-Week In-Residence Training Workshop
- #25. Urbana, IL USA (February 11-15): Hands-On Workshop on Computational Biophysics
2011
- Broadcast from Urbana, IL USA (November 28-December 1): Online Workshop on Simulating Membrane Channels
- #24. Bremen, Germany (October 17-21): Hands-On Workshop on Computational Biophysics
- Broadcast from Urbana, IL USA (August 1-4): Online Workshop on Simulating Membrane Channels
- Urbana, IL USA (July 25-August 5): Two-Week In-Residence Training Workshop
- #23. Pittsburgh, PA USA (May 16-20): Hands-On Workshop on Computational Biophysics
- #22. Atlanta, GA USA (March 21-25): Hands-On Workshop on Computational Biophysics
2010
- #21. Urbana, IL USA (November 29-December 3): Hands-On Workshop on Computational Biophysics
- #20. Urbana, IL USA (November 1-5): Hands-On Workshop on Computational Biophysics
- Urbana, IL USA (August 6-8): Workshop on GPU Programming for Molecular Modeling
- #19. San Diego, CA USA (July 12-16): Hands-On Workshop on Computational Biophysics
- #18. Pittsburgh, PA USA (May 10-14): Hands-On Workshop on Computational Biophysics
- #17. Houston, TX USA (January 14-17): Hands-On Workshop on Modeling Cryo-EM Maps
2009
- #16. Talca, Chile (November 23-26): Hands-On Workshop on Computational Biophysics
- #15. Champaign, IL USA (August 10-14): Hands-On Workshop on Computational Biophysics
- #14. Champaign, IL USA (July 6-10): Hands-On Workshop on Computational Biophysics
2007
- #13. Bangalore, India (November 6-16): School on Biomolecular Simulations
- #12. Bethesda, MD USA (Novemer 5-7): Three-Day Workshop on Computational Biophysics
- Broadcast from Urbana, IL USA (February 22-27): Online Workshop on Simulating Membrane Channels
2006
- Urbana, IL USA (November 30-December 1): Hands-On Workshop on Cluster Building
- #11 Talca, Chile (November 14-16): Three-Day Workshop on Computational Biophysics
- #10 Pittsburgh, PA USA (November 6-9): Hands-On Workshop on Computational Biophysics
- Urbana, IL USA (April 20-21): Hands-On Workshop on Cluster Building
- #9 Frankfurt, Germany (March 20-23): Hands-On Workshop on Computational Biophysics
- Urbana, IL USA (March 16-17): Hands-On Workshop on Cluster Building
2005
- #8 Pittsburgh, PA USA (November 28-December 1): Hands-On Workshop on Computational Biophysics
- Urbana, IL USA (November 10-11): Hands-On Workshop on Cluster Building
- Urbana, IL USA (September 22-23): Hands-On Workshop on Cluster Building
- #7 San Francisco, CA USA (June 26-30): Hands-On Workshop on Computational Biophysics
- #6 Chicago, IL USA (June 9-13): Hands-On Workshop on Computational Biophysics
- #5 Lake Tahoe, CA USA (May 23-27): Hands-On Workshop on Computational Biophysics
2004
- #4 Boston, MA USA (December 5-9): Hands-On Workshop on Computational Biophysics
- #3 Urbana, IL USA (November 8-12): Hands-On Workshop on Computational Biophysics
- #2 Perth, Australia (June 7-18): Two-Week Workshop on Computational Biophysics
2003
- #1 Urbana, IL USA (June 2-13): Summer School on Computational Biophysics
Types of Workshops
Modeling the molecular processes of biological cells is a craft and an art. Techniques like theoretical and computational skills can be learnt by training, but meaningful applications are achieved only with experience and sensitivity. The Theoretical and Computational Biophysics Group has produced a series of workshops, attempting to teach both the craft and art of modeling through learning by doing. Participants learn how to stretch proteins, pull water through molecular channels, mine genomic data, and study their favorite biomolecules. After lectures and discussions in the morning, afternoons are devoted to hands-on computer laboratories where participants delved into hundreds of pages of tutorials, on laptops humming with computational biology software, e.g., VMD and NAMD.
GPU Programming for Molecular Modeling
A workshop of about two days in length designed for researchers in computational and/or biophysical fields who seek to extend their GPU programming skills to include molecular modeling. The workshop extends GPU programming techniques to the field of molecular modeling, including subjects such as particle-grid algorithms (electrostatics and molecular orbitals), particle-particle algorithms with an emphasis on non-bonded force calculations, radial distribution functions in GPU histogramming, single-node multi-GPU algorithms, and GPU clusters.
In online workshops, participants are provided with a recorded, streaming video of a workshop lecture provided by TCBG faculty, along with the opportunity to complete tutorials with assistance from teaching assistants. Also provided is a conference call with the faculty member who provided the lecture, on the fourth and final date of the workshop.
The in-residence workshop program invites 5-7 scientists to the home of TCBG for advanced training and consultation on their ongoing individual molecular dynamics studies. In-residence training provides an opportunity for experimentalists and theorists who are not experts in modeling to initiate a project that requires advanced modeling. During their two-week stay, participants are provided with office space, use of computing facilities, and access to the expertise of TCBG group members. The goal of the in-residence workshop program is to facilitate the launch and refinement of participant modeling projects.
These day and a half workshops help users and system administrators explore how to specify, design, build, and deploy PC Clusters running Linux, and even determine if a cluster is right for a specific application. Following a discussion of clustering basics, participants actually build their own PC clusters and experiment with running their own applications. These workshops are aimed at systems administrators who desire a greater understanding of cluster technologies, as well as end-users who want to better understand the systems that they run on for their day-to-day work. All cluster building workshops are held in Urbana, Illinois, at the Beckman Institute.