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 …
bioinformatics
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 …
Jupytext 2-way reformat of Jupyter notebooks
Jupytext can save and reformat Jupyter notebooks I was trying to test a Jupyter notebook from NCBI titled “Getting Started with NCBI Data in Python” (March 2, 2022) that is now on a “Binder” web …
PyCharm IDE installation without Admin
PyCharm IDE Installation Having “Admin privileges” on an educational or business computer is becoming a rarity, as security reasons are increasingly important. However, there are often way to install a software for “just one user” …
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.) …
Fast Sequence Composition
Sequence Composition: fast shell method Motivation This post was inspired to “verify” a Python Script meant to compute the sequence composition of amino acids, as suggested by ChatGPT. (See ChatGPT_Protein_Composition.ipynb, or viewer ChatGPT_Protein_Composition.ipynb.) The code …