Summary Simpson’s paradox is a fascinating statistical phenomenon where the observed relationship between two variables can be reversed when the data is divided into subgroups. For biologists and biochemists, this means that the correlation between …
Computing
ChatMOL: PyMOL ChatGPT Plugin with Free chatlite version
Summary ChatMol is a ChatGPT plugin that offers a Free chatlite version that does not require an API key. ChatMol ChatMol is a PyMOL plugin based on large language models, that provide a conversational interface …
Nobel-Winning AlphaFold2 and RosettaFold: Cracking the Protein Folding Mystery
Summary “Explore how David Baker, Demis Hassabis, and John Jumper won the 2024 Nobel Prize in Chemistry for their advances in computer-assisted protein design.” Video: How AI Cracked the Protein Folding Code and Won a …
AlphaFold2 with ColabFold in Container
Summary Run the ColabFold version of AlphaFold2 on your laptop (slow without GPU) or on a large Linux cluster. The full tutorial with scripts is located at ColabFold with HTCondor What is AlphaFold2 Excerpt from …
R and Python workshops on Campus – Fall 2024
Summary Workshop Series available on Campus on R and Python. (For more details see further below.) – Biochem – Social Science Computing Cooperative (SSCC) – UW Libraries – SSteenbock Library Workshops – Computational Biology, Ecology, …
No GUI PyMOL – computing distances for thousands of PDB files from Rosetta
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 …
Python NumPy 2.0 incompatibilities
Summary The new Numpy 2.0 is not compatible with many other packages, as I discovered after many lost hours. The final Docker images can be downloaded from alleleanalyzer. NumPy in a Docker I was interested …
Environmental Health Tabular data analysis with R and Tidyverse
R and Tidyverse Tabular Data Analysis I have updated the Tabular data analysis with R and Tidyverse course that analyze environmental health data from National Health and Nutrition Examination Survey (NHANES) a survey research program …
Webinar Data visualisation principles for enhancing effective scientific communication
“Data visualisation principles for enhancing effective scientific communication” Webinar Announcement: “Live Training” This webinar will provide an introduction to data visualisation principles. It includes a review of basic concepts and showcases tools to improve your …
PyMOL and Biological Units from REMARK 350
Summary Compute biological assembly from coordinates with a python script. Symmetry X-ray crystallography solved the mathematical problem to provide 3D (cartesian) coordinates but the resulting “asymmetric unit cell” does not necessarily represent the biological structure. …