Summary We run a script to compute the distance between 2 atoms in a series of PDB files with identical molecules in different conformations and save the distance results into a plain text file. No …
shell
Install Local Docker Desktop on macOS without Admin
NOT FOR USE AT UW SYSTEMS Important note (oct 07, 2024): changes in the licensing of Docker Desktop has changed. It is no longer recommended to UW personnel to download Docker Desktop to install Docker. …
Interactive bioinformatics tutorials
Summary sandbox.bio provides interactive tutorials for exploring bioinformatics command-line tools within a web browser. Bioinformatics When people ask “what is bioinformatics” I have to pause. When I named a computer “bioinformatics” at the dawn of …
AlphaFold2 with full databases and multimer option
Summary This article describes running AlphaFold2 with full databases at the UW-Madison Center for High Throughput Computing (CHTC) and is part of an article series titled Five ways to run AlphaFold. CHTC cluster, HTCondor, Containerization …
Fast Sequence Composition
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 …
PATH: the overlooked crucial variable
What is PATH There are many technical definitions that can be found, but in simple terms, PATH is a list of directories.The listed directories will contain the software that run on the computer, including the …
Accessing BOX on macOS with command line
UW personnel has access to Box, a cloud drive to store documents. While the older “Box Sync” application kept a copy of every file and folder on the local computer, the newer “box drive” …