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 …
Blog
Why every PhD should be on LinkedIn
UWMadison affiliations The social media landscape is vast and it is easy to miss important connections. For example, I just found out that UW-Madison is a member of “Beyond the Professoriate” (requires NetID login.) with 31 …
Wastewater surveillance for SARS-CoV-2 in Wisconsin
Café des sciences webinar This first collaborative Café des sciences webinar is organized by the Office for Science and Technology of the Consulate General of France in Chicago in collaboration with UW-Madison, the Wisconsin State …
Google Docs Tutorials
Google Docs is a free, web-based document creator system to create and collaborate on online documents in real-time and from any device. The type of documents that can be created can be text, notes, spreadsheet, …
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.