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 …
Scientific Communication
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 …
No GUI PyMOL for high troughput 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 …
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 …
R and Python workshops on Campus – Fall 2023
Summary Workshop Series available on Campus on R and Python: Biochem SSCC UW Libraries R and Python at Biochem R and Python “Clubs” were established in late 2022. The Python Club is currently closed but …
AlphaFold2 on Macintosh M1
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 …
Augmented Reality of Molecules – episode 1
What is Augmented Reality? Augmented Reality (AR) is an exciting technology that overlays virtual elements on top of the real world, allowing for a unique and immersive user experience. The Apple AR platform only uses …
Intelligent Systems for Molecular Biology – 2022 proceedings
Intelligent Systems for Molecular Biology – in Madison The International Society for Computational Biology (ISMB) Conference held the Intelligent Systems for Molecular Biology (ISMB) in Madison in July 2022. Conference details are still available online, but …
3D Molecular Structures Analysis with NCBI iCn3D
NCBI tutorial: iCn3D hands-on workshop “I see in 3D” (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode […] – (Longer description.) …