For this session we will use the KEGG relational database and UCSF Chimera to examine how drugs interact with target proteins in the signaling pathways of cells. Bring a laptop with UCSF Chimera installed [download here] and I will demonstrate how to interact with the Protein Data Bank to find structures, analyze electron density and electrostatic surface charge, and run homology modeling, molecular docking and dynamic simulations.

In this talk, I’ll discuss how to implement a simple numerical hydrodynamics code, and discuss various pitfalls one can encounter along the way. I’ll discuss both of the leading options, grid-based Eulerian hydrodynamics and particle-based Lagrangian dynamics, noting which kinds of approach work better for which problems. Time permitting, pretty pictures and movies will be shown.

I will give an overview of CuPy, an open-source Python library that serves as a high-level interface to the proprietary NVIDIA CUDA language. It makes writing lightning-fast GPU accelerated code almost as easy as using Python’s standard NumPy library, as it re-implements much of NumPy’s API. Due to the ubiquitous nature of NumPy in scientific Python applications, CuPy will likely make porting your existing CPU code to a GPU as painless as possible.

Unixes — especially Linux — are close to ubiquitous in scientific computing. At least in astronomy! However, as an operating system Linux is entirely unlike Windows and quite dissimilar to a Mac. In this talk I will cover not so much how to use your new OS — that comes from time and practice — but how to configure things, what all the jargon means, and most importantly what to do with things go wrong.

First meeting of the Fall 2018 semester. This will serve as an introduction for new members, including a quick recap of what the group has done in the past. Then we will talk about what people would like to see done this semester, such as subjects they’d like to learn or speak about, and what we can do to make our meetings even better.