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 …
What is AlphaFold How to access AlphaFold There are multiple options to access AlphaFold. Here are four options using the limited databases. One options for the full databases. Using limited Databases: 1.) Casual users can use “Google Colab” with a web browser. Familiarity with Jupyter Notebook for running Python is helpful. The service is free …
Cloud event Users of RStudio may be interested in this monthly event presented by “Posit” which is the new name of the company that produces RStudio, as the software can be used with many more languages beyond R, including Python. This event will occur monthly online on the last Tuesday of every month. Next occurrence …
Summary Workshop Series available on Campus on R and Python: R and Python at Biochem R and Python “Clubs” were established in late 2022. The Python Club is currently closed but may be restarted in a new format. Minutes and scripts from the sessions are available online: beginners, intermediate_advanced, communication. The R-Club is continuously meeting …
Summary This post is a summary of installation of AlphaFold2 onto a Macintosh with an M1 style (arm64) computer chip (i.e. not an Intel/AMD Chip.) This post started with the blog post Installing Alphafold2 on Apple Silicon. The installation will require about 8Gb of space. Installing AlphaFold2 AlphaFold2 is a trained Machine Learning set of …