Computational Biophysics Workshop - Urbana, July 18-20, 2018
Program
(subject to changes)Location: Beckman Institute, Room 5602
Wednesday, July 18:
09:00-09:30 Welcome09:30-10:30 Introduction to Metabolic and Genetic Information Processing Cellular Networks, Zan Luthey-Schulten
10:30-11:00 Coffee Break
11:00-12:00 Methods for Stochastic, Spatially-Resolved Whole Cell Simulations, Zan Luthey-Schulten
12:00-12:30 Q & A
12:30-13:30 Lunch Break
13:30-14:30 Lattice Microbes in the Cloud: Easy Simulation Execution using Amazon Web Services, Mike Hallock
14:30-15:00 Coffee Break
15:00-16:30 Introduction to Scientific Python with Jupyter Notebooks (jupyter notebook), Tyler Earnest and Marcelo Melo
16:30-18:00 Python Tutorials
18:00 Social Dinner
Thursday, July 19:
09:00-10:00 Overview of Lattice Microbes and pyLM, Mike Hallock10:00-10:30 jLM: Next Generation Python Interface to LM (jupyter notebook), Tyler Earnest
10:30-11:00 Coffee Break
11:00-12:00 EXP-2-LM: Using Real Experimental Data to Build Cell Scale Models, Tyler Earnest
12:00-12:30 Q & A
12:30-14:00 Lunch Break
14:00-14:30 Overview of Lattice Microbes Tutorials, Tyler Earnest
14:30-18:00 Lattice Microbes Tutorials
Friday, July 20:
09:00-10:00 Quantitative Microscopy Pipeline for Building a Model of the Human Cell, Winfried Wiegraebe10:00-11:00 Building Simulation Geometry from Scratch (jupyter notebook1, notebook2), Tyler Earnest
11:00-11:30 Coffee Break
11:30-12:30 Building Simulation Geometry from Data, Tyler Earnest
12:30-14:00 Lunch Break
14:00-14:30 Visualization of Cell Simulations with VMD, David Bianchi
14:30-16:30 Advanced Tutorials
16:30-17:00 LM Installation
17:00-18:00 Try Your Own Tutorials