Summary A short example on running software within a Docker container on a Linux cluster. Since the software is installed within the container no installation is necessary. The computation can be scaled to accommodate large …
Docker
Five ways to run AlphaFold
What is AlphaFold AlphaFold can accurately predict 3D models of protein structures by providing an amino acid sequence. (Ref: Deep Mind.) The AlphaFold network directly predicts the 3D coordinates of all heavy atoms for a …
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 …
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 …
Python Data Science with Jupyter on Docker
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 …
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 …
R and Python workshops – Fall 2022
Summary Check the Calendar listing for data analysis workshops links and registration forms. Below are workshop dates for SSCC, Madison chapter of Software Carpentry, and Steenbock Library series. Social Science Computing Cooperative (SSCC) The table …
Computing residues per turn in an alpha helix
Single mutation to be modeled I recently had an interesting challenge, that of creating a molecular model of a protein expressed from a gene with a newly identified single amino acid mutation. I (wrongly) assumed …
csvkit command-line spreadsheet can convert and compute multiple Excel files
(Last edit: April 11, 2023) Summary csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats. (csvkitis written in python.) csvkit Documentation: csvkit.rtfd.org csvkit Repository: …
Data Analysis Workshops Fall 2020
SUMMARY: Check calendar for Free “R” and “Python” workshops (Steenbock Library.) “Introduction to R with RStudio,” “Data Wrangling in R” (SSCC – Social Science Computing Cooperative.) “Automating Tasks with the Unix Shell,” “Data Management with SQL,” “Introduction to Docker” (Software Carpentry through UW-Madison Data Science (fees apply).)