Summary 1. How to easily convert a string of character to appear one character per line> Either of: echo “abcdefg” | fold -w1 echo “abcdefg” | grep -o . 2. How to convert amino acid …
bioinformatics
Guide to Submitting HTCondor jobs
High Throughput Computing (HTC) First a note: HTC is meant for a large number of small to medium size jobs. HTC is different than HPC (High Performance Computing) that would run large size jobs that …
Reformat every other line with paste
Sometimes a very simple command can accomplish amazing tasks. Recently I had a list with alternating entries on every other line with about 200 lines, and lots of uneven text. But I wanted to …
AlphaFold – How to interpret structures
3D Protein structure prediction (4) This YouTube video from the European Bioinformatics Institute – EMBL-EBI webinar was recorded on 08 September 2021 This webinar will introduce AlphaFold system for prediction and interpretation of protein structures. …
AlphaFold – run from ChimeraX
The new ChimeraX menu “Tools > Structure Prediction > AlphaFold” provides a simple interface to run AlphaFold2 Colab that does not require the user to know how to use a Jupyter Notebook.
AlphaFold code
DeepMind and Google have created a method to access the code on GitHub. All the details to install AlphaFold locally are on the “readme” page, visible on the lower portion of the GitHub page ColabFold (See my Blog: Google colab is a free cloud notebook environment).
AlphaFold background
Predicting protein three-dimensional (3D) structures given a linear sequence of amino acids. The AlphaFold2 breakthrough.
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 …
Data Analysis Workshops Winter 2021
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,” “R: introduction / visualization / reports” (Software Carpentry through UW-Madison Data Science (fees apply).)
Default preference reversal in R
Default preferences I enjoy using R and RStudio, but I am always weary of upgrading R because that usually leads to some issue(s). The most recent was a bit long for me to diagnose, even …