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 A short example on running software within a Docker container on a Linux cluster. Since the software is installed within the container no installation is necessary. The computation can be scaled to accommodate large sample files. Docker on Biochemistry Compute Cluster The HTCondor scheduler software on the Biochemistry Compute Cluster (BCC) can run Docker …
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. …
NCBI Magic-BLAST Workshop The intermediate level workshop Analyzing & Visualizing NextGen Reads with Magic-BLAST – [Archived] is designed for biologists who are comfortable working with the command-line (bash) and who are interested in performing some early analysis on their next-generation sequence data in comparison to an annotated reference sequence. – Materials: Analyzing & Visualizing NextGen Reads …
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 …
Summary Useful ramblings about the difficulties to understand Python installation on macOS. In this Tutorial-like post we’ll see: – Where is Python installed, and which version – Upgrading to a new Python.org version, without replacement of previous version – Adding an alternate Python: Anaconda – Could Docker help? Python mess? The problem with Python is …
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 …