Summary P-value hacking is the process of manipulating or analyzing data in a way that increases the likelihood of obtaining statistically significant results. I used 4 different AI chatbots to obtain an explanation with examples. …
Year: 2023
Do yourself a favor: learn Markdown – Episode 7: BibTeX for online articles
Summary A tool to create a BibTeX entry for online articles or blogs. Generate BibTeX from URL This is a follow-up on 6 “Episode”” in previous posts titled “Do yourself a favor: learn Markdown…” In …
Data exploration in R with Tidyverse dplyr – part 2 – 10 examples
Summary Part 1 (Sgro (2023)) : was a general overview of the dplyr package for data exploration and manipulation to summarize or extract information from tabular data. Part 2: (This post) provides worked examples while …
Data exploration in R with Tidyverse dplyr – part 1 – overview
Summary Part 1: A general overview of the dplyr package for data exploration and manipulation to summarize or extract information. Part 2: Next post will provide worked examples. 1 Motivation The Biochemistry R Club is following …
Foundational concepts to understand AI: free online curricula
Summary Alignment Course is an online curriculum that provides materials in a useful order to learn fundamentals. The Governance Course offers similar material at the beginning, but then moves towards governance (regulations etc.). Within the first …
Faster image creation in PyMOL: Shortcuts and Docker
Summary PyMOL command scripts are available natively and within Docker images. PyMOL Scripts PyMOL offers a very easy-to-use graphical user interface (GUI) to manipulate loaded molecule, and alter the appearance and coloring options. However, while …
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 …
No GUI PyMOL for high throughput images and optional Docker
Summary Computing a PNG image for each of 1,000 PDB file as a cartoon, color-coded by B factor. PyMOL without GUI PyMOL is routinely used by Biologists to illustrate molecules, using the graphical user interface …