Category Archives: Computation

Bioinformatics Training Materials

The Bioinformatics Core at the UC Davis Genome Center has all the Documentation for the workshops and courses, past and current, available on the bioinformatics training program GitHub page. The Genome Center Event Registration offers the same material in a different listing order based on the date. Most of the material is available as Github… Read More »

Python Data Science with Jupyter on Docker

Inspired by article “How to set up and run Python Data Science Development Environment with Jupyter on Docker” [Archived] Data Scientists coders must work with a variety of Data Science development tools, including the  Anaconda (or Miniconda) Python distribution platform, the Python programming language, the R programming language, Matplotlib library, Pandas Library, the Jupyter application, and many others. The article describes how to… Read More »

1985 computing in action

This YouTube video from the BBC Archive channel gives a glimpse of computing in 1995 when the DIGITAL VT100 terminal was king! Description based on info on YouTube: At the Boston software company Infocom, Fred Harris gets behind the scenes. The developer has had considerable success with its series of text-based adventure games, including The… Read More »

File not found. The vanishing concept of File

The complete title from this article is “File not found A generation that grew up with Google is forcing professors to rethink their lesson plans” (Archived version.) Here is a short summary: It’s the idea that a modern computer doesn’t just save a file in an infinite expanse; it saves it in the “Downloads” folder,… Read More »

Do yourself a favor: learn Markdown. BibTex for PubMed

In the series Do yourself a favor: learn Markdown I added a very useful web site for bibliography in R/Rstudio. The original post is here: Episode 5. BibTeX interface for PubMed Summary: A web site to create BibTex entries for bibliography in R Markdown. The most useful tool I found is from www.bioinformatics.org titled: TeXMed… Read More »

PyMOD 3: Structural Bioinformatics within PyMOL

Web page: http://schubert.bio.uniroma1.it/pymod/GitHub: https://github.com/pymodproject/pymod Reference Giacomo Janson, Alessandro Paiardini, PyMod 3: a complete suite for structural bioinformatics in PyMOL, Bioinformatics, Volume 37, Issue 10, 15 May 2021, Pages 1471–1472, https://doi.org/10.1093/bioinformatics/btaa849 Abstract The PyMod project is designed to act as a fully integrated interface between the popular molecular graphics viewer PyMOL, and some of the most… Read More »

Big Book of R

www.bigbookofr.com by Oscar Baruffa This online book is a compendium list of ~300 books using R for data analysis. Fro example, one useful example contained within is Computational Genomics with R by Altuna Akalin (2020-09-30.) The big book is available on GitHub as BigBookofR. If you take time to check the site and file 020-book_list.Rmd… Read More »

DataChat: Guided English Language© Ai and ML data analysis

A new spin-off company from the University of Wisconsin-Madison proposes a new interface for data analysis based on Guided English Language© (GEL) to command Artificial Intelligence and Machine Learning methods via “utterances” i.e. English-like phrases easier to write than code whether R, python, SQL, or other traditional tools. The web site is at datachat.ai The… Read More »