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 …
Computing
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 …
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 …
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 …
Intermediate Research Software Development in Python
Intermediate Research Software Development in Python Greetings everyone and Club members, (apologies i you receive duplicates) This may be more of interest to intermediate/advanced Python users: A Spring Break mini course offered by the …
Learn Markdown – Episode 6. Convert Word to Markdown with pandoc
Summary Pandoc is a document converter for multiple type of files. Converting example Format conversion is a chore that often takes a lot of time. I recently wanted to convert a long MSWord document into …
Magic-BLAST analysis of NextGen Reads
NCBI Magic-BLAST Workshop The intermediate level workshop Analyzing & Visualizing NextGen Reads with Magic-BLAST – [Archived] is designed for biologists who are comfortable working with the command-line (bash) and who are interested in performing some early …
Python and Object Programming AhAh moment
Summary Clarifying Python code containing the mysterious “dot notation” of object-oriented languages. An object is a combination of data stored within a specific class. A class is a blue-print (or framework) that defines attributes (containing …