Summary Workshop Series available on Campus on R and Python: R and Python at Biochem R and Python “Clubs” were established in late 2022. The Python Club is currently closed but may be restarted in a new format. Minutes and scripts from the sessions are available online: beginners, intermediate_advanced, communication. The R-Club is continuously meeting …
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 Apple Silicon. The installation will require about 8Gb of space. Installing AlphaFold2 AlphaFold2 is a trained Machine Learning set of …
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 the web browser “Safari” and does not require any plug-in or specialized software, only that portable electronics (iPhone, iPad) have …
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 page. However, the system kept stalling, but I was given access to the “raw” script. To my surprise the format …
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 more importantly a special “Bioinformatics” journal issue has been compiled from the proceedings of this conference: Most articles link to …
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 below is inspired by post number-of-occurences-of-letters-in-a-word. I found the process useful, and in addition applicable to nucleic acids as well. …
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 or properties), and the code is in the form of procedures (often known as methods).(Wikipedia) Summary of OOP concepts I …
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 local chapter of Software Carpentry at the UW–Madison Data Science Hub, March 13th – 17th , 9am-1pm: This course aims …
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 a version of Markdown that I could use to update a software documentation. Pandoc can convert many documents types into …
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 analysis on their next-generation sequence data in comparison to an annotated reference sequence. – Materials: Analyzing & Visualizing NextGen Reads …