Summary Workshop Series available on Campus on R and Python. (For more details see further below.) – UW Libraries – Steenbock Library Workshops – UW Data Science Hub / Software Carpentry – Social Science Computing Cooperative (SSCC) Steenbock Library Workshops See details on announcement page: Learn how to use Python and/or R programming languages for …
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 GUI PyMOL In previous posts I explained how we can use PyMOL as a command-line tool from a Terminal when …
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. Changes will take effect on November 14th, 2024. The before Nov 14th and after Nov 14th pricing would seem to …
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 the Internet Age (1994) it made sense to me base on the French language: “informatique” is a French word for …
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 The UW-Madison Center for High Throughput Computing (CHTC) offers free computing accounts for all UW-Madison personnel and offer the full …
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 below is inspired by post number-of-occurences-of-letters-in-a-word. I found the process useful, and in addition applicable to nucleic acids as well. …
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 command-line programs. PATH is a variable, and thus this list is flexible and new directories can be added. When the …
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” software keeps only chosen folders or files on the local machine, everything else stays in the “cloud.” The location of …