Summary Alignment Course is an online curriculum that provides materials in a useful order to learn fundamentals. The Governance Course offers similar material at the beginning, but then moves towards governance (regulations etc.). Within the first “SESSION” both offer a video insight titled: How ChatGPT Works Technically. Wisconsin AI Safety Initiative Founded in Spring 2023, the …
Summary PyMOL command scripts are available natively and within Docker images. PyMOL Scripts PyMOL offers a very easy-to-use graphical user interface (GUI) to manipulate loaded molecule, and alter the appearance and coloring options. However, while this is easy, it is not the “best way” to use PyMOL if one wants to be able to reproduce …
NOT FOR USE AT UW SYSTEMS Important note (oct 07, 2024): changes in the licensing of Docker Desktop has changed. It is no longer recommended to UW personnel to download Docker Desktop to install Docker. Changes will take effect on November 14th, 2024. The before Nov 14th and after Nov 14th pricing would seem to …
Summary sandbox.bio provides interactive tutorials for exploring bioinformatics command-line tools within a web browser. Bioinformatics When people ask “what is bioinformatics” I have to pause. When I named a computer “bioinformatics” at the dawn of the Internet Age (1994) it made sense to me base on the French language: “informatique” is a French word for …
Summary This article describes running AlphaFold2 with full databases at the UW-Madison Center for High Throughput Computing (CHTC) and is part of an article series titled Five ways to run AlphaFold. CHTC cluster, HTCondor, Containerization The UW-Madison Center for High Throughput Computing (CHTC) offers free computing accounts for all UW-Madison personnel and offer the full …
Summary Computing a PNG image for each of 1,000 PDB files as a cartoon, color-coded by B factor. PyMOL without GUI PyMOL is routinely used by Biologists to illustrate molecules, using the graphical user interface (GUI.) However, there are situations where it may be beneficial to run PyMOL without using the mouse. I recently computed …
Summary A short example on running software within a Docker container on a Linux cluster. Since the software is installed within the container no installation is necessary. The computation can be scaled to accommodate large sample files. Docker on Biochemistry Compute Cluster The HTCondor scheduler software on the Biochemistry Compute Cluster (BCC) can run Docker …