Category Archives: Computation

Computing residues per turn in an alpha helix

Last month I wrote a blog on my Biochemistry Blog about computing the number of residues within an alpha helix. This was in relation to a project concerning predicting a “coiled-coil” structure. It was more complicated than I thought. The link to the original article is here: Computing residues per turn in an alpha helix… Read More »

Download Google Drive Files using wget

Cross-posting from post:  Download Google Drive Files using wget The problem: transfer file between clouds Files on Google drive can be shared between users, but the default access to the file is via we web browser graphical interface. However, sometimes it may be useful, or even necessary, to access and download a file from a command line,… Read More »

Default preference reversal in R 4.0.x

I just wrote an entry on my Biochem blog which I think would fit on this site: 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 though in retrospect… Read More »

in2csv: the Excel killer is part of csvkit the command-line spreadsheet

Summary csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats. (csvkit can convert XLSX files to CSV.) A good docker container for csvkit: thomasleplus/csv Inspiration: stack overflow article: convert-xlsx-file-to-csv-using-batch Note: I wrote a different version of this on this post elsewhere: csvkit command-line spreadsheet can convert and… Read More »

A great Unix tutorial suitable for beginners

More than once I have written my own tutorials for learning how to use the command line within the bash shell in the context of a Unix or Unix-like computer. Recently I found a very well done tutorial that, while titled “Unix for Neuroimagers”  provides a wonderfully well done, easy to understand set of small… Read More »

PCA as Metro-Maps & Hierarchical Clustering on Principal Components

The iris dataset is perhaps one of the most famous datasets used to learn and teach statistics and now machine learning. Being curious about this dataset lead me last time to the TableConvert.com  web site that I discussed in my previous post here (and there.) “Metro Maps” Today while revisiting the Wikipedia link for this dataset (Iris_flower_data_set) my… Read More »

TableConvert.com – free tabular data formats converter

This is a repost of my post on the Biochemistry department: tableconvert-com-free-tabular-data-formats-converter Tabular formats When I first came to Madison in 1986 as a postdoc with Biochemistry professor Paul Kaesberg to learn cloning and sequencing, I was surprised when he said that the most important program to work with sequences was the (now defunct GCG) program… Read More »