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 …
python
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 …
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 …
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 …
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 …
Python wins popularity of programming languages
Summary Python ranks #1 in popularity of programming languages on the TIOBE Index TIOBE Index The popularity of programming languages is reflected in the TIOBE Programming Community index which is updated once a month. The …
Understanding Python installation mess
Summary Useful ramblings about the difficulties to understand Python installation on macOS. In this Tutorial-like post we’ll see: – Where is Python installed, and which version – Upgrading to a new Python.org version, without replacement …
Python for the Life Sciences – A Gentle Introduction
Summary This book will be used to learn Python in workshop settings. For Biologists, Life Scientists There are many books, even free books, with the objective to teach Python or other programming languages. I previously …
New classroom, computers, workshops
New classroom, computers, workshops New Apple Macintosh M1 computers are ready for hosting new workshops in person again. Apple M1 Macintosh The classroom is now equipped with Macintosh mac-mini computers with the new M1 chip. …