LEARN VMD! LEARN NAMD! LEARN GPU PROGRAMMING! SIMULATE LARGE SYSTEMS! Pittsburgh • Bremen • Urbana • Lake Tahoe • Urbana
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. Learn more about each workshop by following the links below:
- Munich Workshop (March 25-28, 2014)
- Urbana Workshop (November 18-22, 2013)
- Beijing Workshop (October 14-17, 2013)
- Pittsburgh Workshop (June 10-14, 2013)
- Urbana Workshop (October 22-26, 2012)
- Urbana Workshop (February 11-15, 2012)
- Bremen Workshop (October 17-21, 2011)
- Pittsburgh Workshop (May 16-20, 2011)
- Atlanta Workshop (March 21-25, 2011)
- Urbana Workshop (November 29 - December 3, 2010)
- Urbana Workshop (November 1-5, 2010)
- San Diego Workshop (July 12-16, 2010)
- Pittsburgh Workshop (May 10-14, 2010)
- Houston Workshop (January 14-17, 2010)
- Talca Workshop (November 23-26, 2009)
- Champaign Workshop (August 10-14, 2009)
- Champaign Workshop (July 26 - August 1, 2009)
- Champaign Workshop (July 6-10, 2009)
- Bangalore Workshop (November 6-16, 2007)
- Bethesda Workshop (November 5-7, 2007)
- Talca Workshop (November 14-16, 2006)
- Pittsburgh Workshop (November 6-9, 2006)
- Frankfurt Workshop (March 20-23, 2006)
- Pittsburgh Workshop (November 28-December 1, 2005)
- San Francisco Workshop (June 26-30, 2005)
- Chicago Workshop (June 9-13, 2005)
- Lake Tahoe Workshop (May 23-27, 2005)
- Boston Workshop (December 5-9, 2004)
- Urbana Workshop (November 8-12, 2004)
- Perth Workshop (June 7-18, 2004)
- Urbana Summer School (June 2-13, 2003)
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.
- February 22-27, 2007 - Computer Simulation of Biological and Artificial Membrane Channels
- August 1-4, 2011 - Simulating Membrane Channels
- November 28-December 1, 2011 - Simulating Membrane Channels
In this three-day workshop, participants learned relevant physical concepts, mathematical algorithms, and computational methods, including molecular dynamics simulation, de novo structure determination based on cryo-EM maps, deformable elastic networks, stereochemical validation of proteins and nucleic acids, and quality checks of fitted structures.
The in-residence workshop program invites 5-7 scientists to the home of the TCBG for advanced training and consultation with an ongoing molecular dynamics study carried out by the participants. The in-residence training program 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 at the TCBG, and access to the expertise of TCBG group members. The goal of the in-residence workshop is to facilitate 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 built their own PC cluster and got to test out their own applications. The workshops were aimed at systems administrators wanting a greater understanding of cluster technologies, as well as those end-users that want to better understand the systems that they work on for their day-to-day work. All cluster building workshops were held in Urbana, Illinois, at the Beckman Institute.