Computational technologies provide much needed microscopic views of cellular processes, coming in the form of genetic, structural, and dynamic information. Translating this ever growing amount of information into health relevant strategies requires not only the proper tools, but also the proper training. Scientists new to the notion of a "computational microscope" need training in the use of molecular modeling and visualization software tools, while those from a computational background need training in the application of the tools to biological problems. To this end, we propose five-day computational biophysics workshops introducing the widely used software of the Center for Macromolecular Modeling and Bioinformatics (CMMB). The proposed effort will take advantage of the CMMB's experience in the training of biomedical scientists, starting from over 720 pages of written training material an a past series of popular hands-on workshops. The program of the workshops will provide training in the CMMB's software programs, VMD (visual molecular dynamics;204,000 registered users) and NAMD (nanoscale molecular dynamics;49,400 registered users), and their application to scientific inquiries. Workshop participants (typically experimental and computational graduate students and postdoctoral associates in the life sciences) will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. 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. Updated learning materials used in the workshops and evaluation data will be subsequently disseminated to the biomedical community. The CMMB seeks to host three hands-on workshops per year, one local workshop at its home institution, and two extramural workshops in large metropolitan areas.
Computational tools for visualization, simulation, and analysis of molecular processes (for example, the Center's software, VMD and NAMD) provide biomedical researchers today with a new perspective into the dynamics of cellular processes hitherto inaccessible to observation. However, use of such tools requires training and currently few to no opportunities exist. The Center for Macromolecular Modeling and Bioinformatics (CMMB) will fill this need through three annual workshops that over a five-day period provide scientists with conceptual understanding and hands-on experience in the use of the Center's VMD and NAMD, and their application to biomedicine.