TCBG Workshops

Current Workshops

"Hands-On" Workshop on Computational Biophysics in Urbana, February 11-15, 2012. The workshop will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. The course will be based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers and steered molecular dynamics simulations.

Prior Workshops

Computational Biophysics

     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 over 500 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:

Cluster Building

     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.

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.

Online Workshops

    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.

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