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 …
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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.) …
PyMOL Stereo viewing
PyMOL Stereo viewing PyMOL can display stereo in many ways. Unless special equipment is available, the method is to split the PyMOL 3D view area in two with the command stereo on (and stereo …
Free New York Times through UW-Madison
Registering for The New York Times through UW-Madison All necessary information can be found at: https://www.library.wisc.edu/help/research-tips-tricks/registering-for-the-new-york-times-through-uw-madison/ duplicated below: UW-Madison students, faculty, and staff have free access to The New York Times Digital (NYTImes.com) through the UW-Madison …
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 …
Python Concepts of Object-Oriented Programming
Python and Object-oriented programming Object-oriented programming (OOP) is a programming paradigm based on the concept of “objects“, which can contain data and code. The data is in the form of fields (often known as attributes …