Summary Part 1: A general overview of the dplyr package for data exploration and manipulation to summarize or extract information. Part 2: Next post will provide worked examples. 1 Motivation The Biochemistry R Club is following …
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Foundational concepts to understand AI: free online curricula
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 …
Faster image creation in PyMOL: Shortcuts and Docker
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 …
Install Local Docker Desktop on macOS without Admin
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. …
Interactive bioinformatics tutorials
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 …
AlphaFold2 with full databases and multimer option
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 …
No GUI PyMOL for high throughput images and optional Docker
Summary Computing a PNG image for each of 1,000 PDB file 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 …
Using Docker containers on Biochemistry Linux Cluster
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 …
Five ways to run AlphaFold
What is AlphaFold AlphaFold can accurately predict 3D models of protein structures by providing an amino acid sequence. (Ref: Deep Mind.) The AlphaFold network directly predicts the 3D coordinates of all heavy atoms for a …
Centralizing R & Python Data Projects: Posit Cloud Essentials Event
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 …