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Python

AlphaFold2 on Macintosh M1

Posted on April 27, 2023

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 …

Posted in Announcements, biochemistry, bioinformatics, Computing, Molecular Graphics, Protein Structure, PyMOL, Python, Scientific Communication

Jupytext 2-way reformat of Jupyter notebooks

Posted on March 29, 2023

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 …

Posted in bioinformatics, Computing, Markdown, PythonTagged bioinformatics, Jupiter, jupyter lab, jupyter notebook, markdown, python, Rmarkdown

PyCharm IDE installation without Admin

Posted on March 14, 2023

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” …

Posted in bioinformatics, Programming, Python

Intelligent Systems for Molecular Biology – 2022 proceedings

Posted on March 14, 2023

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 …

Posted in bioinformatics, Books, Computing, Programming, Protein Structure, Python, Scientific Communication

Python Concepts of Object-Oriented Programming

Posted on February 16, 2023

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 …

Posted in bioinformatics, Computing, Programming, PythonTagged Object Oriented Programming, OOP, python

Intermediate Research Software Development in Python

Posted on February 5, 2023

  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 …

Posted in Announcements, bioinformatics, Computing, PythonTagged bioinformatics, python, Software Carpentry, software developmement

Python and Object Programming AhAh moment

Posted on December 2, 2022

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 …

Posted in Computing, Programming, PythonTagged dot notation, Object Oriented, Object Oriented Programming, python

Using Python within RStudio

Posted on December 1, 2022

Summary Finding and implementing settings in RStudio to use Pyhon. RStudio and Python RStudio can handle a large number of languages (> 50) in addition to its basic support of R. (This month the RStudio …

Posted in bioinformatics, Computing, Programming, Python, RStudio

Python wins popularity of programming languages

Posted on December 1, 2022

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 …

Posted in Computing, Programming, PythonTagged index, language, popuylarity, programming, python, TIOBE index

Python Data Science with Jupyter on Docker

Posted on November 30, 2022

Inspired by article “How to set up and run Python Data Science Development Environment with Jupyter on Docker” [Archived] Data Scientists that write or use code must work with a variety of Data Science development …

Posted in bioinformatics, Computing, Docker, Python
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